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PubMed2001

Atrioventricular pacemaker. Incidence and causes of reprogramming in long-term follow-up.

OBJECTIVE: To assess the incidence of problems requiring reprogramming of atrioventricular pacemakers in a long-term follow-up, and also the causes for this procedure. METHODS: During the period from May '98 to December '99, 657 patients were retrospectively studied, An actuarial curve for the event reprogramming of the stimulation mode was drawn. RESULTS: The follow-up period ranged from 12 to 178 months (mean = 81 months). Eighty-two (12.4%) patients underwent reprogramming of the stimulation mode as follows: 63 (9.5%) changed to VVI,(R/C); 10 (1.5%) changed to DVI,C; 6 (0.9%) changed to VDD,C; and 3 (0.5%) changed to DOO. The causes for the reprogramming were as follows: arrhythmia conducted by the pacemaker in 39 (37.6%) patients; loss of atrial sensitivity or capture, or both, in 39 (38.6%) patients; and microfracture of atrial electrode in 5 (4.9%) patients. The stimulation mode reprogramming free probability after 15 years was 58%. CONCLUSION: In a long-term follow-up, the atrioventricular pacemaker provided a low incidence of complications, a high probability of permanence in the DDD,C mode, and the most common cause of reprogramming was arrhythmia conducted by the pacemaker.

Actuarial Analysis↗
PubMed2025

Identification and analysis of metabolic reprogramming-related genes in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is notorious for its rapid progression, tendency to metastasize, high recurrence rates, dismal outcomes, and limited treatment options, underscoring the urgent need to uncover new biomarkers and molecular pathways to enhance diagnosis, prognosis, and therapeutic strategies. Metabolic reprogramming continues to play a role throughout the life cycle of cancer, evolving and adapting. In this study, we aimed to identify specific genes associated with metabolic reprogramming in TNBC, which can potentially become unique biomarkers of this cancer. TNBC datasets retrieved from the Gene Expression Omnibus were employed to pinpoint genes exhibiting altered expression linked to tumor metabolic reprogramming. Key genes were accurately screened through machine learning algorithms, and then externally verified using the TBNC dataset based on the Cancer Genome Atlas database. Finally, immunohistochemical methods were used to clinically confirm the differential expression and trends of these key genes. Our analysis accurately identified four genes-CLEC7A, IRS1, RSPO3, and ALB-that are closely correlated with the metabolic reprogramming characteristics of cancer, and could be regarded as innovative biomarkers for TNBC. This opens a new avenue for further investigation into the mechanisms of metabolic reprogramming in TNBC and new treatment strategies.

Humans↗
PubMed2026

Harnessing Endogenous Plasticity Rather than Reprogramming of Mature Cells Will Advance Regenerative Medicine, Cancer Treatment and Rejuvenation.

The successful culture of human embryonic stem (hES) cells from inner cell mass cells of blastocyst stage 'spare' embryos in 1998, followed by induced pluripotent stem (iPS) cells in 2006, which allowed somatic cells to be reprogrammed to pluripotency using the Yamanaka factors, transformed regenerative biology and inspired extensive global efforts towards developing pluripotent stem cell-based applications. However, hES and iPS cells, as well as organoids generated from them, largely retain fetal-like characteristics, which limits their relevance for clinical translation. Concurrently, the prevailing assumption published in leading journals that adult tissues lack endogenous stem cells has led to the belief that mature cells dedifferentiate and reprogram during in vivo regeneration upon chronic injury, and that the appearance of embryonic/fetal markers in diabetes, heart failure, cancer, and many other chronic disease states reflects dedifferentiation of mature cells. We suggest that the prevailing concepts of dedifferentiation and reprogramming, both in vitro and in vivo, require careful re-evaluation. Adult somatic cells possibly do not truly dedifferentiate, neither in vitro nor in vivo. Instead, tissue-resident, pluripotent, very small embryonic-like stem cells (VSELs) in multiple organs account for the observed biology. In vitro "reprogramming" responses to Yamanaka factors likely reflect selective activation and expansion of VSELs/early progenitors rather than the dedifferentiation/ reprogramming of mature adult somatic cells. Likewise, the embryonic/fetal-like signatures reported in multiple disease states including cancer reflect expansion of immature tissue-specific progenitors that arise from VSELs but fail to differentiate normally due to a damaged microenvironment in vivo. Therapeutic strategies involving transplantation of MSCs, MUSE cells, or their secreted exosomes improve disease outcomes, possibly by restoring the damaged niche that supports functional tissue repair by VSELs. Although direct evidence to support this is lacking at present, recognising the central role of VSELs/progenitors and their niche in maintaining tissue homeostasis in vivo could resolve existing roadblocks and guide more effective endogenous regenerative therapies for diseased tissues and age-related dysfunctions.

Humans↗
PubMed2024

DNA methylation reprogramming in teleosts.

Early embryonic development is crucially important but also remarkably diverse among animal taxa. Axis formation and cell lineage specification occur due to both spatial and temporal control of gene expression. This complex system involves various signaling pathways and developmental genes such as transcription factors as well as other molecular interactants that maintain cellular states, including several types of epigenetic marks. 5mC DNA methylation, the chemical modification of cytosines in eukaryotes, represents one such mark. By influencing the compaction of chromatin (a high-order DNA structure), DNA methylation can either repress or induce transcriptional activity. Mammals exhibit a reprogramming of DNA methylation from the parental genomes in the zygote following fertilization, and later in primordial germ cells (PGCs). Whether these periods of methylation reprogramming are evolutionarily conserved, or an innovation in mammals, is an emerging question. Looking into these processes in other vertebrate lineages is thus important, and teleost fish, with their extensive species richness, phenotypic diversity, and multiple rounds of whole genome duplication, provide the perfect research playground for answering such a question. This review aims to present a concise state of the art of DNA methylation reprogramming in early development in fish by summarizing findings from different research groups investigating methylation reprogramming patterns in teleosts, while keeping in mind the ramifications of the methodology used, then comparing those patterns to reprogramming patterns in mammals.

Animals↗
PubMed2006

Methylation dynamics in the early mammalian embryo: implications of genome reprogramming defects for development.

In mouse and most other mammalian species, the paternal and maternal genomes undergo parent-specific epigenetic reprogramming during preimplantation development. The paternal genome is actively demethylated within a few hours after fertilization in the mouse, rat, pig, bovine, and human zygote, whereas the maternal genome is passively demethylated by a replication-dependent mechanism after the two-cell embryo stage. These genome-wide demethylation waves may have a role in reprogramming of the genetically inactive sperm and egg chromatin for somatic development. Disturbances in this highly coordinated process may contribute to developmental failures and defects in mammals. The frequency and severity of abnormal phenotypes increase after interfering with or bypassing essential steps of gametogenesis, early embryogenesis, or both. Nevertheless, it is plausible that normal fertilization, assisted reproduction, and embryo cloning are all susceptible to similar dysregulation of epigenetic components. Although the mouse maybe an excellent model for early human development, species and strain differences in the molecular and cellular events shortly after fertilization may have important implications for the efficiency of epigenetic reprogramming and the incidence of reprogramming defects. Some species, i.e., rabbit and sheep, do not require drastic genome-wide demethylation for early development, most likely because the transition from maternal to embryonic control occurs relatively late during preimplantation development. A better understanding of key reprogramming factors--in particular the demethylase activity in the fertilized egg--is crucial for improving human infertility treatment and the efficiency of mammalian embryo cloning.

Animals↗
PubMed2004

Interpretation of reprogramming to predict the success of somatic cell cloning.

In the context of mammalian somatic cell cloning, the term reprogramming refers to the processes that enable a somatic cell nucleus to adopt the role of a zygotic nucleus. Gene re-expression is one measure of reprogramming if correlated with subsequent developmental potential. This paper describes several experiments utilizing pre-implantation gene expression to evaluate reprogramming and clone viability. We have established a direct correlation between Oct4 expression in mouse clones at the blastocyst stage and their potential to maintain pluripotent embryonic cells essential for post-implantation development. Furthermore, the quality of gene expression in clones dramatically improves when genetically identical clones are combined in clone-clone aggregate chimeras. Clone--clone aggregates exhibit a higher developmental potential than single clones both in vitro and in vivo. This could be mediated by complementation between blastomeres from epigenetically different clones within the aggregate rather than by the increase in cell number resulting from aggregation. We also discuss the use of tetraploid embryos as a model to evaluate reprogramming using gene expression and demonstrate that somatic cell nuclei can be reprogrammed by blastomeres to re-express embryonic specific genes but not to contribute to post-implantation development.

Animals↗
PubMed2003

Nuclei of adult mammalian somatic cells are directly reprogrammed to oct-4 stem cell gene expression by amphibian oocytes.

Nuclear reprogramming by the transplantation of somatic cell nuclei to eggs (in second meiotic metaphase) is always followed by a phase of chromosome replication and cell division before new gene expression is seen. To help understand the mechanism of nuclear reprogramming, we have asked whether the nuclei of normal, nontransformed, nondividing, and terminally differentiated mammalian cells can be directly reprogrammed, without DNA replication, by Xenopus oocytes. We find that nuclei of adult mouse thymocytes and of adult human blood lymphocytes, injected into Xenopus oocytes, are induced to extinguish a differentiation marker and to strongly express oct-4, the most diagnostic mammalian stem cell/pluripotency marker. In the course of 2 days at 18 degrees C, the mammalian oct-4 transcripts are spliced to mature mRNA. We conclude that normal mammalian nuclei can be directly reprogrammed by the nucleus (germinal vesicle) of amphibian oocytes to express oct-4 at a rate comparable to that of oct-4 in mouse ES cells. To our knowledge, this is the first demonstration of a stem cell marker being induced in a differentiated adult human cell nucleus. This is an early step toward the long-term aim of developing a procedure for reprogramming readily accessible human adult cells for cell replacement therapy.

Animals↗
PubMed2002

Reprogramming fibroblasts to express T-cell functions using cell extracts.

We demonstrate here the functional reprogramming of a somatic cell using a nuclear and cytoplasmic extract derived from another somatic cell type. Reprogramming of 293T fibroblasts in an extract from primary human T cells or from a transformed T-cell line is evidenced by nuclear uptake and assembly of transcription factors, induction of activity of a chromatin remodeling complex, histone acetylation, and activation of lymphoid cell specific genes. Reprogrammed cells express T cell specific receptors and assemble the interleukin-2 receptor in response to T cell receptor CD3 (TCR CD3) complex stimulation. Reprogrammed primary skin fibroblasts also express T cell specific antigens. After exposure to a neuronal precursor extract, 293T fibroblasts express a neurofilament protein and extend neurite-like outgrowths. In vitro reprogramming of differentiated somatic cells creates possibilities for producing isogenic replacement cells for therapeutic applications.

Biotechnology↗
PubMed2005

Early and delayed aspects of nuclear reprogramming during cloning.

The successful production of viable progeny following adult somatic cell nuclear transfer (cloning) provides exciting new opportunities for basic research for investigating early embryogenesis, for the propagation of valuable or endangered animals, for the production of genetically engineered animals, and possibly for developing therapeutically valuable stem cells. Successful cloning requires efficient reprogramming of gene expression to silence donor cell gene expression and activate an embryonic pattern of gene expression. Recent observations indicate that reprogramming may be initiated by early events that occur soon after nuclear transfer, but then continues as development progresses through cleavage and probably to gastrulation. Because reprogramming is slow and progressive, cloned embryos have dramatically altered characteristics in comparison with fertilized embryos. Events that occur early following nuclear transfer may be essential prerequisites for the later events. Additionally, the later reprogramming events may be inhibited by sub-optimum culture environments that exist because of the altered characteristics of cloned embryos. By addressing the unique requirements of cloned embryos, the entire process of reprogramming may be accelerated, thus increasing cloning efficiency.

Animals↗
PubMed2003

Reprogramming of bovine somatic cell nuclei is not directly regulated by maturation promoting factor or mitogen-activated protein kinase activity.

Cloned mammals with normal fertility have been produced by nuclear transfer. Thus, oocyte cytoplasm has the ability to convert differentiated somatic cell nuclei into a state that resembles the conditions that occur at fertilization (nuclear reprogramming). Despite the long-held assumption that reprogramming factors are present in mammalian oocytes, the molecular nature of these factors is not known. The present study demonstrates that the process of nuclear reprogramming is not directly regulated by maturation promoting factor or mitogen-activated protein kinase activity. The potential for nuclear-transferred oocytes to develop to the blastocyst stage was not different when somatic cells at the M phase were fused with oocytes activated with ionomycin and cycloheximide 1-5 h before (12%-22%) but was significantly decreased when oocytes were activated 6 h before (1%). Further molecular studies on the differences between oocytes with and without reprogramming potential are required and will be useful for the identification of reprogramming factors.

Animals↗
PubMed2003

Nuclear reprogramming in cell-free extracts.

Methods for directly turning a somatic cell type into another type (a process referred to as transdifferentiation) would be beneficial for producing replacement cells for therapeutic applications. Adult stem cells have been shown to display a broader differentiation potential than anticipated and may contribute to tissues other than those in which they reside. In addition, novel transdifferentiation strategies are being developed. I report recent results on the functional reprogramming of a somatic cell using a nuclear and cytoplasmic extract derived from another somatic cell type. The reprogramming of 293T fibroblasts in an extract from T cells is evidenced by nuclear uptake and the assembly of transcription factors, induction of activity of a chromatin remodelling complex, changes in chromatin composition and activation of lymphoid cell-specific genes. The reprogrammed cells express T-cell-specific surface molecules and a complex regulatory function. Reprogramming cells in cell-free extracts may create possibilities for producing replacement cells for therapeutic applications. The system may also constitute a powerful tool to examine the mechanisms of nuclear reprogramming, at least as they occur in vitro.

Adult↗
PubMed2005

Differential reprogramming of somatic cell nuclei after transfer into mouse cleavage stage blastomeres.

Mammalian somatic cell cloning requires factors specific to the oocyte for reprogramming to succeed. This does not exclude that reprogramming continues during the zygote and cleavage stages. The capacity or role of zygotic and cleavage stages to reprogram somatic cell nuclei is difficult to assess due to the limited development of somatic cell nuclei transplanted into cytoplasts of these stages. Alternatively, tetraploid embryos have been used to study reprogramming and can be assessed for their contribution to extra-embryonic lineages. When mouse cumulus cell nuclei transgenic for Oct4-green fluorescent protein (GFP) were injected into intact two- and four-cell stage blastomeres, manipulated embryos developed into blastocysts with expression of Oct4-GFP as observed in embryos produced by nuclear transfer into metaphase II oocytes. However, only the latter contributed to extra-embryonic tissues in day 10.5 conceptuses, with the exclusion of the somatic genome in cells originating from transfer into blastomeres already at 5.5 days post conception. Somatic nuclei transferred into cleavage stage blastomeres reinitiated expression of an embyronic-specific transgene, but lacked the extent of reprogramming required for contribution to postimplantation development, even when complemented by an embryonic genome.

Animals↗
PubMed2025

In vivo differentiation of embryonic cells devoid of key reprogramming factors.

Embryonic cell differentiation depends on reprogramming of the oocyte and sperm nucleus into a transient totipotent state. In zebrafish, this coincides with genome activation, which is regulated by the pioneer factors Nanog, Pou5f3, and Sox19b (NPS). Here, we investigate the role of NPS in developmental reprogramming and differentiation by analyzing the fate of NPS mutant cells in a wild-type embryo using single-cell RNA-seq. We find that many cells fail to activate transcription or undergo cell death, while others acquire gene expression profiles that resemble germ cells, neural progenitors, and motoneuron states. These cells achieve intermediate transcriptional states, revealing the essential role of NPS in coordinating nuclear and cytoplasmic reprogramming and preventing the premature activation of lineage-specific differentiation programs. These results demonstrate that most developmental programs require developmental reprogramming by NPS, yet some cells can bypass transient totipotency to achieve intermediate developmental states resembling wild-type states in vivo.

Animals↗
PubMed2026

Patient-specific modeling identifies metabolic interventions for reversing glucose use reprogramming in alcohol-associated hepatitis.

Alcoholic hepatitis (AH) is an acute form of alcohol-associated liver disease with very few treatment options. Recent studies highlighted liver metabolic reprogramming in AH as an indicator of severity. We aim at identifying new intervention points to reverse liver metabolic dysregulation across varying degrees of AH. We develop 89 personalized genome-scale metabolic models by integrating a generic human cellular metabolic model with liver transcriptomics data from AH patients with varying disease severity and healthy controls. We grade the AH patients based on the model-predicted level of glycolysis reprogramming and validate the results using published metabolomics data. We test in silico gene knockdown interventions to reverse the aberrant metabolic reprogramming in AH. Knockdown of two glycolytic genes, Hkdc1 and Pkm, significantly rebalance the metabolic fluxes toward a healthy liver metabolic phenotype. We use machine learning on the glycolysis fluxes to develop a quantitative glucose use reprogramming score, which correlates with AH severity and patient-specific responses to in silico gene knockdown interventions. The score was independently validated using a published AH liver transcriptomics dataset. We propose a cellular metabolism-based therapy targeting Hkdc1 and Pkm in the glycolysis pathway as a potential treatment for reversing the aberrant glucose metabolism in AH.

Humans↗
PubMed2026

IRAK4 constrains cellular plasticity during chemically-induced cell fate reprogramming into multiple lineages.

Chemical reprogramming holds transformative potential for regenerative medicine. However, the regulatory mechanisms governing cell fate transitions are not well understood. Here, we identify Interleukin-1 Receptor-Associated Kinase 4 (IRAK4) as a barrier to multi-lineage reprogramming. Pharmacological inhibition of IRAK4 enhances the reprogramming of mouse embryonic fibroblasts (MEFs) through a chemically activated multi-lineage priming (CaMP) state and extraembryonic endoderm (XEN)-like intermediates, increasing colony formation, and the expression of core XEN regulators (Sox17, Gata4, Sall4, and Foxa2). Genetic knockdown of Irak4 similarly accelerates reprogramming, whereas its overexpression blocks cell fate transitions. IRAK4 inhibition enhances chromatin accessibility and reshapes cell cycle dynamics, characterized by G0/G1 shortening and G2/M lengthening, potentially contributing to multi-lineage state establishment. Furthermore, IRAK4 suppression enhances the direct conversion of MEFs to neuron-like and hepatocyte-like cells, which exhibit enhanced functional maturity, including increased glycogen storage and improved detoxification capacity. Our findings establish IRAK4 as a regulator that constrains cellular plasticity potentially by coordinating chromatin accessibility and cell cycle dynamics.

Animals↗
PubMed2006

From nuclear transfer to nuclear reprogramming: the reversal of cell differentiation.

This is a personal historical account of events leading from the earliest success in vertebrate nuclear transfer to the current hope that nuclear reprogramming may facilitate cell replacement therapy. Early morphological evidence in Amphibia for the toti- or multipotentiality of some nuclei from differentiated cells first established the principle of the conservation of the genome during cell differentiation. Molecular markers show that many somatic cell nuclei are reprogrammed to an embryonic pattern of gene expression soon after nuclear transplantation to eggs. The germinal vesicles of oocytes in first meiotic prophase have a direct reprogramming activity on mammalian as well as amphibian nuclei and offer a route to identify nuclear reprogramming molecules. Amphibian eggs and oocytes have a truly remarkable ability to transcribe genes as DNA or nuclei, to translate mRNA, and to modify or localize proteins injected into them. The development of nuclear transplant embryos depends on the ability of cells to interpret small concentration changes of signal factors in the community effect and in morphogen gradients. Many difficulties in a career can be overcome by analyzing in increasing depth the same fundamentally interesting and important problem.

Animals↗
PubMed2026

Characterization of DNA methylation in PBMCs and donor-matched iPSCs shows age-related methylation is reset during stem cell reprogramming.

DNA methylation is an important epigenetic mechanism that helps define and maintain cellular functions. It is influenced by many factors, including environmental exposures, genotype, cell type, sex, and aging. Since age is the primary risk factor for developing neurodegenerative diseases, it is important to determine if age-related DNA methylation is retained when cells are reprogrammed to an induced Pluripotent Stem Cell (iPSC) state. Here, we selected peripheral blood mononuclear cells (PBMCs; n = 99) from a cohort of diverse and healthy individuals enrolled in the Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing (GESTALT) study to reprogram to iPSCs. After reprogramming, the resulting iPSCs were evaluated for DNA methylation signatures to determine if they reflect the confounding factors of aging and environmental effects. Data from genome-wide DNA methylation arrays in both cell types showed that age-related methylation measured by epigenetic clocks is largely reset to an early methylation age after reprogramming of PBMCs to iPSCs. We further examined the epigenetic age of each cell type using an Epigenome-wide Association Study (EWAS) and identified a set of methylation Quantitative Trait Loci in each cell type. Our results show that age-related DNA methylation is largely reset in iPSCs, and each cell type has a unique set of methylation sites that are modified by population-level genetic variation.

DNA Methylation↗
PubMed1993

Lipopolysaccharide structure-function relationship in activation versus reprogramming of mouse peritoneal macrophages.

Lipopolysaccharide (LPS) is one of the most potent stimuli for macrophages. The activities of LPS have been attributed to the lipid A region of the molecule. We have previously shown that pretreatment of macrophages with very low doses of LPS can selectively "reprogram" these cells to respond differentially to subsequent activation, as assessed by tumor necrosis factor-alpha and nitric oxide (NO) production. Here we demonstrate that the relative capacity of various LPS preparations for induction of down-regulation of subsequent LPS-activated NO production correlates well with their relative potency for initiation of NO formation. Although LPS-dependent activation can be regulated by pertussis toxin (PT)-sensitive factor, the LPS pretreatment-induced reprogramming is shown here to be refractory to regulation by PT. These results suggest that, although the structural components of LPS dictating the relative activities of the molecule for activation versus reprogramming are similar, there may exist different pathways in initiation of LPS-induced activation versus reprogramming.

Animals↗