scholarly journals Replacing reprogramming factors with antibodies selected from autocrine antibody libraries

2017 ◽  
Author(s):  
Joel W. Blanchard ◽  
Jia Xie ◽  
Nadja El-Mecharrafie ◽  
Simon Gross ◽  
Sohyon Lee ◽  
...  
Keyword(s):  
Cell Fate ◽  
Current Knowledge ◽  
Differentiated Cells ◽  
Extracellular Signaling ◽  
Nuclear Factors ◽  
Antibody Libraries ◽  
Membrane Bound ◽  
Reprogramming Factors ◽  
Induced Pluripotent ◽  
The Impact

SummarySignaling pathways initiated at the membrane establish and maintain cell fate during development and can be harnessed in the nucleus to generate induced pluripotent stem cells (iPSCs) from differentiated cells. Yet, the impact of extracellular signaling on reprogramming to pluripotency has not been systematically addressed. Here, we screen a lentiviral library encoding ˜100 million secreted and membrane-bound antibodies and identify multiple antibodies that can replace Sox2/c-Myc or Oct4 during reprogramming. We show that one Sox2-replacing antibody initiates reprogramming by antagonizing the membrane-associated protein Basp1, thereby inducing nuclear factors WT1 and Esrrb/Lin28 independent of Sox2. By successively manipulating this pathway we identify three new methods to generate iPSCs. This study expands current knowledge of reprogramming methods and mechanisms and establishes unbiased selection from autocrine antibody libraries as a powerful orthogonal platform to discover new biologics and pathways regulating pluripotency and cell fate.

scholarly journals Hypoxia Pathway Proteins in Normal and Malignant Hematopoiesis

Cells ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 155 ◽  
Author(s):  
Ben Wielockx ◽  
Tatyana Grinenko ◽  
Peter Mirtschink ◽  
Triantafyllos Chavakis
Keyword(s):  
Cell Fate ◽  
Current Knowledge ◽  
Hypoxia Inducible Factor ◽  
Adult Life ◽  
Low Oxygen ◽  
Hematopoietic Stem ◽  
Metabolism Regulation ◽  
Hsc Niche ◽  
Hif Pathway ◽  
The Impact

The regulation of oxygen (O2) levels is crucial in embryogenesis and adult life, as O2 controls a multitude of key cellular functions. Low oxygen levels (hypoxia) are relevant for tissue physiology as they are integral to adequate metabolism regulation and cell fate. Hence, the hypoxia response is of utmost importance for cell, organ and organism function and is dependent on the hypoxia-inducible factor (HIF) pathway. HIF pathway activity is strictly regulated by the family of oxygen-sensitive HIF prolyl hydroxylase domain (PHD) proteins. Physiologic hypoxia is a hallmark of the hematopoietic stem cell (HSC) niche in the bone marrow. This niche facilitates HSC quiescence and survival. The present review focuses on current knowledge and the many open questions regarding the impact of PHDs/HIFs and other proteins of the hypoxia pathway on the HSC niche and on normal and malignant hematopoiesis.

scholarly journals Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes

2020 ◽  
Vol 6 (47) ◽  
pp. eabc3851
Author(s):  
Laura S. Bisogno ◽  
Jun Yang ◽  
Brian D. Bennett ◽  
James M. Ward ◽  
Lantz C. Mackey ◽  
...  
Keyword(s):  
Cell Fate ◽  
Cancer Survival ◽  
Dermal Fibroblast ◽  
Biological Processes ◽  
White Americans ◽  
Differentiation Potential ◽  
Differentiated Cells ◽  
Reprogramming Efficiency ◽  
Induced Pluripotent ◽  
Independent Cohort

Induced pluripotent stem cells (iPSCs) can be derived from differentiated cells, enabling the generation of personalized disease models by differentiating patient-derived iPSCs into disease-relevant cell lines. While genetic variability between different iPSC lines affects differentiation potential, how this variability in somatic cells affects pluripotent potential is less understood. We generated and compared transcriptomic data from 72 dermal fibroblast–iPSC pairs with consistent variation in reprogramming efficiency. By considering equal numbers of samples from self-reported African Americans and White Americans, we identified both ancestry-dependent and ancestry-independent transcripts associated with reprogramming efficiency, suggesting that transcriptomic heterogeneity can substantially affect reprogramming. Moreover, reprogramming efficiency–associated genes are involved in diverse dynamic biological processes, including cancer and wound healing, and are predictive of 5-year breast cancer survival in an independent cohort. Candidate genes may provide insight into mechanisms of ancestry-dependent regulation of cell fate transitions and motivate additional studies for improvement of reprogramming.

scholarly journals Microglia Development and Maturation and Its Implications for Induction of Microglia-Like Cells from Human iPSCs

2021 ◽  
Vol 22 (6) ◽  
pp. 3088
Author(s):  
Johannes Wurm ◽  
Henna Konttinen ◽  
Christian Andressen ◽  
Tarja Malm ◽  
Björn Spittau
Keyword(s):  
Growth Factors ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Culture Conditions ◽  
Brain Parenchyma ◽  
Human Microglia ◽  
Differentiated Cells ◽  
Human Ipscs ◽  
Induced Pluripotent

Microglia are resident immune cells of the central nervous system and play critical roles during the development, homeostasis, and pathologies of the brain. Originated from yolk sac erythromyeloid progenitors, microglia immigrate into the embryonic brain parenchyma to undergo final postnatal differentiation and maturation driven by distinct chemokines, cytokines, and growth factors. Among them, TGFβ1 is an important regulator of microglial functions, mediating homeostasis, anti-inflammation, and triggering the expression of microglial homeostatic signature genes. Since microglia studies are mainly based on rodent cells and the isolation of homeostatic microglia from human tissue is challenging, human-induced pluripotent stem cells have been successfully differentiated into microglia-like cells recently. However, employed differentiation protocols strongly vary regarding used cytokines and growth factors, culture conditions, time span, and cell yield. Moreover, the incomplete differentiation of human microglia can hamper the similarity to primary human microglia and dramatically influence the outcome of follow-up studies with these differentiated cells. This review summarizes the current knowledge of the molecular mechanisms driving rodent microglia differentiation in vivo, further compares published differentiation protocols, and highlights the potential of TGFβ as an essential maturation factor.

scholarly journals iPSC Preparation and Epigenetic Memory: Does the Tissue Origin Matter?

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1470
Author(s):  
Giuseppe Scesa ◽  
Raffaella Adami ◽  
Daniele Bottai
Keyword(s):  
Stem Cells ◽  
Molecular Mechanisms ◽  
Embryonic Stem ◽  
Epigenetic Memory ◽  
Differentiated Cells ◽  
Ipsc Generation ◽  
Tissue Of Origin ◽  
Induced Pluripotent ◽  
The Impact

The production of induced pluripotent stem cells (iPSCs) represent a breakthrough in regenerative medicine, providing new opportunities for understanding basic molecular mechanisms of human development and molecular aspects of degenerative diseases. In contrast to human embryonic stem cells (ESCs), iPSCs do not raise any ethical concerns regarding the onset of human personhood. Still, they present some technical issues related to immune rejection after transplantation and potential tumorigenicity, indicating that more steps forward must be completed to use iPSCs as a viable tool for in vivo tissue regeneration. On the other hand, cell source origin may be pivotal to iPSC generation since residual epigenetic memory could influence the iPSC phenotype and transplantation outcome. In this paper, we first review the impact of reprogramming methods and the choice of the tissue of origin on the epigenetic memory of the iPSCs or their differentiated cells. Next, we describe the importance of induction methods to determine the reprogramming efficiency and avoid integration in the host genome that could alter gene expression. Finally, we compare the significance of the tissue of origin and the inter-individual genetic variation modification that has been lightly evaluated so far, but which significantly impacts reprogramming.

scholarly journals Role of Epigenetics in Cardiac Development and Congenital Diseases

2018 ◽  
Vol 98 (4) ◽  
pp. 2453-2475 ◽  
Author(s):  
Thomas Moore-Morris ◽  
Patrick Piet van Vliet ◽  
Gregor Andelfinger ◽  
Michel Puceat
Keyword(s):  
Cell Fate ◽  
Cardiac Development ◽  
Current Knowledge ◽  
Heart Diseases ◽  
Three Dimensional ◽  
Congenital Diseases ◽  
Heart Formation ◽  
Fate Decision ◽  
Essential Knowledge ◽  
The Impact

The heart is the first organ to be functional in the fetus. Heart formation is a complex morphogenetic process regulated by both genetic and epigenetic mechanisms. Congenital heart diseases (CHD) are the most prominent congenital diseases. Genetics is not sufficient to explain these diseases or the impact of them on patients. Epigenetics is more and more emerging as a basis for cardiac malformations. This review brings the essential knowledge on cardiac biology of development. It further provides a broad background on epigenetics with a focus on three-dimensional conformation of chromatin. Then, we summarize the current knowledge of the impact of epigenetics on cardiac cell fate decision. We further provide an update on the epigenetic anomalies in the genesis of CHD.

scholarly journals Metabolism Is a Key Regulator of Induced Pluripotent Stem Cell Reprogramming

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
James Spyrou ◽  
David K. Gardner ◽  
Alexandra J. Harvey
Keyword(s):  
Somatic Cell ◽  
Cell Fate ◽  
Nutrient Availability ◽  
Current Knowledge ◽  
Induced Pluripotent Stem Cell ◽  
Basic Research ◽  
Culture Conditions ◽  
Metabolic Memory ◽  
Memory Retention ◽  
Induced Pluripotent

Reprogramming to pluripotency involves drastic restructuring of both metabolism and the epigenome. However, induced pluripotent stem cells (iPSC) retain transcriptional memory, epigenetic memory, and metabolic memory from their somatic cells of origin and acquire aberrant characteristics distinct from either other pluripotent cells or parental cells, reflecting incomplete reprogramming. As a critical link between the microenvironment and regulation of the epigenome, nutrient availability likely plays a significant role in the retention of somatic cell memory by iPSC. Significantly, relative nutrient availability impacts iPSC reprogramming efficiency, epigenetic regulation and cell fate, and differentially alters their ability to respond to physiological stimuli. The significance of metabolites during the reprogramming process is central to further elucidating how iPSC retain somatic cell characteristics and optimising culture conditions to generate iPSC with physiological phenotypes to ensure their reliable use in basic research and clinical applications. This review serves to integrate studies on iPSC reprogramming, memory retention and metabolism, and identifies areas in which current knowledge is limited.

scholarly journals Metabolomics: A Tool to Understand the Impact of Genetic Mutations in Amyotrophic Lateral Sclerosis

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 537 ◽  
Author(s):  
Débora Lanznaster ◽  
Charlotte Veyrat-Durebex ◽  
Patrick Vourc’h ◽  
Christian R. Andres ◽  
Hélène Blasco ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Cell Metabolism ◽  
Disease Status ◽  
Genetic Mutations ◽  
Differentiated Cells ◽  
Sporadic Als ◽  
Induced Pluripotent ◽  
Als Patients ◽  
The Impact ◽  
Lateral Sclerosis

Metabolomics studies performed in patients with amyotrophic lateral sclerosis (ALS) reveal a set of distinct metabolites that can shed light on the pathological alterations taking place in each individual. Metabolites levels are influenced by disease status, and genetics play an important role both in familial and sporadic ALS cases. Metabolomics analysis helps to unravel the differential impact of the most common ALS-linked genetic mutations (as C9ORF72, SOD1, TARDBP, and FUS) in specific signaling pathways. Further, studies performed in genetic models of ALS reinforce the role of TDP-43 pathology in the vast majority of ALS cases. Studies performed in differentiated cells from ALS-iPSC (induced Pluripotent Stem Cells) reveal alterations in the cell metabolism that are also found in ALS models and ultimately in ALS patients. The development of metabolomics approaches in iPSC derived from ALS patients allow addressing and ultimately understanding the pathological mechanisms taking place in any patient. Lately, the creation of a “patient in a dish” will help to identify patients that may benefit from specific treatments and allow the implementation of personalized medicine.

scholarly journals Generation of Induced Pluripotent Stem (iPS) Cells by Nuclear Reprogramming

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Dilip Dey ◽  
Gregory R. D. Evans
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Adult Stem Cells ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Cell Types ◽  
Nuclear Reprogramming ◽  
Differentiated Cells ◽  
Reprogramming Factors ◽  
Induced Pluripotent

During embryonic development pluripotency is progressively lost irreversibly by cell division, differentiation, migration and organ formation. Terminally differentiated cells do not generate other kinds of cells. Pluripotent stem cells are a great source of varying cell types that are used for tissue regeneration or repair of damaged tissue. The pluripotent stem cells can be derived from inner cell mass of blastocyte but its application is limited due to ethical concerns. The recent discovery of iPS with defined reprogramming factors has initiated a flurry of works on stem cell in various laboratories. The pluripotent cells can be derived from various differentiated adult cells as well as from adult stem cells by nuclear reprogramming, somatic cell nuclear transfer etc. In this review article, different aspects of nuclear reprogramming are discussed.

scholarly journals Induced pluripotent stem cells: opportunities and challenges

2011 ◽  
Vol 366 (1575) ◽  
pp. 2198-2207 ◽  
Author(s):  
Keisuke Okita ◽  
Shinya Yamanaka
Keyword(s):  
Stem Cells ◽  
Transient Expression ◽  
Pluripotent Stem Cells ◽  
Current Knowledge ◽  
Epigenetic Modification ◽  
Somatic Cells ◽  
Ips Cells ◽  
Genomic Alteration ◽  
Reprogramming Factors ◽  
Induced Pluripotent

Somatic cells have been reprogrammed into pluripotent stem cells by introducing a combination of several transcription factors, such as Oct3/4 , Sox2 , Klf4 and c-Myc . Induced pluripotent stem (iPS) cells from a patient's somatic cells could be a useful source for drug discovery and cell transplantation therapies. However, most human iPS cells are made by viral vectors, such as retrovirus and lentivirus, which integrate the reprogramming factors into the host genomes and may increase the risk of tumour formation. Several non-integration methods have been reported to overcome the safety concern associated with the generation of iPS cells, such as transient expression of the reprogramming factors using adenovirus vectors or plasmids, and direct delivery of reprogramming proteins. Although these transient expression methods could avoid genomic alteration of iPS cells, they are inefficient. Several studies of gene expression, epigenetic modification and differentiation revealed the insufficient reprogramming of iPS cells, thus suggesting the need for improvement of the reprogramming procedure not only in quantity but also in quality. This report will summarize the current knowledge of iPS generation and discuss future reprogramming methods for medical application.

scholarly journals Epigenetic regulation in pluripotent stem cells: a key to breaking the epigenetic barrier

2013 ◽  
Vol 368 (1609) ◽  
pp. 20120292 ◽  
Author(s):  
Akira Watanabe ◽  
Yasuhiro Yamada ◽  
Shinya Yamanaka
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Classical Model ◽  
Population Declines ◽  
Developmental Potential ◽  
Temporal Regulation ◽  
Differentiated Cells ◽  
Reprogramming Factors ◽  
Spatio Temporal ◽  
Induced Pluripotent

The differentiation and reprogramming of cells are accompanied by drastic changes in the epigenetic profiles of cells. Waddington's classical model clearly describes how differentiating cells acquire their cell identity as the developmental potential of an individual cell population declines towards the terminally differentiated state. The recent discovery of induced pluripotent stem cells as well as of somatic cell nuclear transfer provided evidence that the process of differentiation can be reversed. The identity of somatic cells is strictly protected by an epigenetic barrier, and these cells acquire pluripotency by breaking the epigenetic barrier by reprogramming factors such as Oct3/4, Sox2, Klf4, Myc and LIN28. This review covers the current understanding of the spatio-temporal regulation of epigenetics in pluripotent and differentiated cells, and discusses how cells determine their identity and overcome the epigenetic barrier during the reprogramming process.

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