• cellular reprogramming
• induced pluripotent stem cells
• microRNAs
• stem cells

• MicroRNAs/genetics
• MicroRNAs/metabolism
• Induced Pluripotent Stem Cells/cytology
• Induced Pluripotent Stem Cells/metabolism
• Animals
• Kruppel-Like Factor 4
• Fibroblasts/cytology
• Fibroblasts/metabolism
• Cellular Reprogramming/genetics
• Mice
• Humans
• Cell Differentiation

• F32 HD070572 NICHD NIH HHS
• UCSF Discovery Fellows
• R01 GM101180 NIH HHS
• National Institutes of Health

• energy
• induced pluripotent stem cells
• mesenchymal stem cells
• metabolism
• mitochondria
• mitochondrial DNA
• mitochondrial diseases
• stem cells

• Optic Atrophy, Hereditary, Leber/therapy
• Optic Atrophy, Hereditary, Leber/genetics
• Optic Atrophy, Hereditary, Leber/metabolism
• DNA, Mitochondrial/genetics
• DNA, Mitochondrial/metabolism
• Humans
• Induced Pluripotent Stem Cells/metabolism
• Induced Pluripotent Stem Cells/cytology
• Neural Stem Cells/metabolism
• Neural Stem Cells/cytology
• Mesenchymal Stem Cells/metabolism
• Mesenchymal Stem Cells/cytology
• Mitochondria/metabolism
• Cell Differentiation
• Mutation
• Coculture Techniques
• Neurons/metabolism
• Cells, Cultured

• developmental biology
• computational biology and bioinformatics

• Humans
• RNA, Small Untranslated/genetics
• RNA, Small Untranslated/metabolism
• Embryonic Development/genetics
• Blastocyst/metabolism
• Gene Expression Regulation, Developmental
• MicroRNAs/genetics
• MicroRNAs/metabolism
• RNA, Transfer/genetics
• RNA, Transfer/metabolism
• Female
• RNA, Small Interfering/metabolism
• RNA, Small Interfering/genetics
• Chromosomes, Human, Pair 19/genetics
• RNA, Small Nucleolar/genetics
• RNA, Small Nucleolar/metabolism

• 2016-01919 Vetenskapsrådet (Swedish Research Council)
• S16-0039 Svenska Sällskapet för Medicinsk Forskning (Swedish Society for Medical Research)
• PJT-178082 Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)
• 950-233204 Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)
• CReATe Fertility Centre

• Stem cells
• cellular reprogramming
• induced pluripotent stem cells
• microRNAs

• F32 HD070572 NICHD NIH HHS
• R01 GM101180 NIGMS NIH HHS
• T32 HD007263 NICHD NIH HHS
• T32 HD007470 NICHD NIH HHS
• F30 HD084120 NICHD NIH HHS

• stem cells
• reprogramming
• chromatin remodelling

• Animals
• Mice
• Transcription Factors/metabolism
• Transcription Factors/genetics
• Nanog Homeobox Protein/metabolism
• Nanog Homeobox Protein/genetics
• Cellular Reprogramming/genetics
• Chromatin/metabolism
• Chromatin/genetics
• DNA Helicases/metabolism
• DNA Helicases/genetics
• Cell Differentiation
• Cell Engineering/methods
• Nuclear Proteins/metabolism
• Nuclear Proteins/genetics

• National Natural Science Foundation of China (31830060, 92068201, 3200050044) and Yangtze River Delta Sci-Tech Innovation Community Joint Research Project (2022CSJGG1000)

• Advocacy
• Biomedicine
• EMT
• Epithelial
• Mesenchymal

• Animals
• Humans
• Cell Differentiation
• Epithelial-Mesenchymal Transition
• Epithelial Cells
• Fibrosis
• Organogenesis

• GZLAB
• 18H02452 Japan Society for the Promotion of Science
• JPMJSC19E5 Japan Science and Technology Agency
• Takeda Science Foundation
• Revive & Restore
• GIBHBRP23-02 Chinese Academy of Sciences

• MicroRNA (miR)
• cancer biomarker
• epigenetics
• esophageal cancer
• gastrointestinal malignancy
• miR-182
• miR-183
• miR-96

• HES7
• Notch signaling
• cellular reprogramming
• developmental allochrony
• segmentation clock
• species-specific developmental timing
• transgene-free porcine iPSC

• Humans
• Animals
• Mice
• Swine
• Induced Pluripotent Stem Cells
• Cellular Reprogramming
• Cell Differentiation
• Transgenes
• Pluripotent Stem Cells
• Mammals

• CYLD
• ECM organization
• EMT
• MET
• TGF-beta
• dedifferentiation
• pluripotency
• somatic cell reprogramming

• ΟΠΣ 5000432 State Scholarships Foundation
• Cooperative Grants Synergasia I #969 Greek General Secretariat for Research and Technology (GSRT)
• EL0084 European Economic Area
• MIS 5002802 The Greek Research Infrastructure for Personalised Medicine (pMED-GR)
• MIS 93225 Bodossaki Foundation

• cell cycle regulators
• embryonic development
• embryonic stem cells
• microRNA clusters

• RRF-2.3.1-21-2022-00007 National Research, Development and Innovation Office
• 2019-2.1.11-TÉT-2019-00036 National Research, Development and Innovation Office

• RNA alternative processing
• RNA degradation
• cell fate decision
• post-transcriptional regulation
• stem cell

• canine tumors
• epithelial-to-mesenchymal transition (EMT)
• mesenchymal-to-epithelial transition (MET)
• translational medicine

• human corneal endothelial cells
• interferon-γ
• miR-302a
• senescence

• CRISPR/Cas
• induced pluripotent stem cells
• retinal disorders

• Humans
• Gene Editing
• Induced Pluripotent Stem Cells
• CRISPR-Cas Systems/genetics
• Retinal Degeneration/genetics
• Retinal Degeneration/therapy
• Genetic Therapy

• MR/P02582X/1 Medical Research Council
• 5129/5130 Fight for Sight

• Human urine cells
• Intermediate mesoderm progenitor like cells
• Kidney organoids
• Mitochondria
• Partial reprogramming

Cardiac muscle damage-induced loss of cardiomyocytes (CMs) and dysfunction of the remaining ones leads to heart failure, which nowadays is the number one killer worldwide. Therapies fostering effective cardiac regeneration are the holy grail of cardiovascular research to stop the heart failure epidemic. The main goal of most myocardial regeneration protocols is the generation of new functional CMs through the differentiation of endogenous or exogenous cardiomyogenic cells. Understanding the cellular and molecular basis of cardiomyocyte commitment, specification, differentiation and maturation is needed to devise innovative approaches to replace the CMs lost after injury in the adult heart. The transcriptional regulation of CM differentiation is a highly conserved process that require sequential activation and/or repression of different genetic programs. Therefore, CM differentiation and specification have been depicted as a step-wise specific chemical and mechanical stimuli inducing complete myogenic commitment and cell-cycle exit. Yet, the demonstration that some microRNAs are sufficient to direct ESC differentiation into CMs and that four specific miRNAs reprogram fibroblasts into CMs show that CM differentiation must also involve negative regulatory instructions. Here, we review the mechanisms of CM differentiation during development and from regenerative stem cells with a focus on the involvement of microRNAs in the process, putting in perspective their negative gene regulation as a main modifier of effective CM regeneration in the adult heart.

• cardiac stem cells
• microRNA
• myogenesis
• regeneration

The mammalian target of rapamycin (mTOR) plays a critical role in controlling cellular homeostasis, and its dysregulation has been implicated in Alzheimer’s disease (AD). Presenilin-1 (PS1) mutations account for the most common causes of familial Alzheimer’s disease (FAD); however, whether PS1 mutation causes mTOR dysregulation in human neurons remains a key unresolved issue.

We generated heterozygotes and homozygotes of PS1 F105C knock-in mutation in human induced pluripotent stem cells (iPSCs) via CRISPR/Cas9/piggyback-based gene editing and differentiated them into human neurons. Secreted Aβ and tau accumulation were determined by ELISA assay, immunofluorescence staining, and western blotting analysis. mTOR signaling was evaluated by western blotting analysis, immunofluorescence staining, and co-immunoprecipitation. Autophagy/lysosome activities were determined by LC3-based assay, LysoTracker Red staining, and DQ-Red BSA staining.

Through comparison among these isogenic neurons, PS1 F105C mutant neurons exhibited elevated Aβ and tau accumulation. In addition, we found that the response of mTORC1 to starvation decreases in PS1 F105C mutant neurons. The Akt/mTORC1/p70S6K signaling pathway remained active upon EBSS starvation, leading to the co-localization of the vast majority of mTOR with lysosomes. Consistently, PS1 F105C neurons displayed a significant decline in starvation-induced autophagy. Notably, Torin1, a mTOR inhibitor, could efficiently reduce prominent tau pathology that occurred in PS1 F105C neurons.

We demonstrate that Chinese PS1 F105C mutation causes dysregulation of mTORC1 signaling, contributing to tau accumulation in human neurons. This study on inherited FAD PS1 mutation provides unprecedented insights into our understanding of the molecular mechanisms of AD. It supports that pharmaceutical blocking of mTOR is a promising therapeutic strategy for the treatment of AD.

The online version contains supplementary material available at 10.1186/s13578-022-00874-8.

• EMT
• aspirin
• breast cancer
• miR-302/367
• reprogramming

• RNA
• aging
• epigenetics
• iPSC
• reprogramming
• senescence
• stem cells

Non-genetically modified somatic cells can only be inefficiently and stochastically reprogrammed to pluripotency by exogenous expression of reprogramming factors. Low competence of natural reprogramming factors may prevent the majority of cells to successfully and synchronously reprogram. Here we screened DNA-interacting amino acid residues in the zinc-finger domain of KLF4 for enhanced reprogramming efficiency using alanine-substitution scanning methods. Identified KLF4 L507A mutant accelerated and stabilized reprogramming to pluripotency in both mouse and human somatic cells. By testing all the variants of L507 position, variants with smaller amino acid residues in the KLF4 L507 position showed higher reprogramming efficiency. L507A bound more to promoters or enhancers of pluripotency genes, such as KLF5, and drove gene expression of these genes during reprogramming. Molecular dynamics simulations predicted that L507A formed additional interactions with DNA. Our study demonstrates how modifications in amino acid residues of DNA-binding domains enable next-generation reprogramming technology with engineered reprogramming factors.

•

KLF4 L507A variant accelerates and stabilizes reprogramming to pluripotency

• Molecular biology
• Stem cell plasticity

• haemoglobin F
• hemopoietic
• miRNA
• regulation
• sickle cell
• stem cells

• Anemia, Sickle Cell/drug therapy
• Anemia, Sickle Cell/genetics
• Child
• Fetal Hemoglobin/genetics
• Fetal Hemoglobin/metabolism
• Hematopoietic Stem Cells/metabolism
• Hemoglobinopathies/genetics
• Hemoglobinopathies/therapy
• Humans
• MicroRNAs/genetics
• MicroRNAs/therapeutic use

• U01 HL156942 NHLBI NIH HHS

The breakthrough in human induced pluripotent stem cells (hiPSCs) has revolutionized the field of biomedical and pharmaceutical research and opened up vast opportunities for drug discovery and regenerative medicine, especially when combined with gene-editing technology. Numerous healthy and patient-derived hiPSCs for human disease modeling have been established, enabling mechanistic studies of pathogenesis, platforms for preclinical drug screening, and the development of novel therapeutic targets/approaches. Additionally, hiPSCs hold great promise for cell-based therapy, serving as an attractive cell source for generating stem/progenitor cells or functional differentiated cells for degenerative diseases, due to their unlimited proliferative capacity, pluripotency, and ethical acceptability. In this review, we provide an overview of hiPSCs and their utility in the study of hematologic disorders through hematopoietic differentiation. We highlight recent hereditary and acquired genetic hematologic disease modeling with patient-specific iPSCs, and discuss their applications as instrumental drug screening tools. The clinical applications of hiPSCs in cell-based therapy, including the next-generation cancer immunotherapy, are provided. Lastly, we discuss the current challenges that need to be addressed to fulfill the validity of hiPSC-based disease modeling and future perspectives of hiPSCs in the field of hematology.

• blood disorders
• cell-based therapy
• disease modeling
• genetic disorders
• induced pluripotent stem cells

Sheep-induced pluripotent stem cells (siPSCs) have low reprogramming efficiency, thereby hampering their use in biotechnology and agriculture. Several studies have shown that some microRNAs play an important role in promoting somatic reprogramming in mouse and human. In this study, we investigated the effect of miR-200c-141 on somatic reprogramming in sheep and explored the mechanism of promoting the reprogramming.

The lentivirus system driven by tetracycline (TET)-on carrying Oct4, Sox2, c-Myc, Klf4, Nanog, Lin28, hTERT, and SV40LT (OSKMNLST) could reprogram sheep kidney cells into pluripotent cells. Overexpression of miR-200c-141 in combination with OSKMNLST could significantly improve the efficiency of sheep iPSC generation (p<0.01). Sheep iPSCs derived from miR-200c-141 showed embryonic stem cell (ESC)-like pluripotent properties, were positive for alkaline phosphatase and some pluripotent markers by quantitative real-time PCR (qRT-PCR) and immunofluorescence, and were able to differentiate into three germ layers in vitro. Oar-miR-200c was transfected into HEK293FT cells and was able to target the zinc finger E-box-binding homeobox 1 (ZEB1) 3’UTR using dual luciferase reporting analysis. Overexpression of oar-miR-200c in SKCs significantly reduced the expression of ZEB1, but increased the expression of E-cadherin by qRT-PCR and western blotting analysis.

These results suggest that miR-200c-141 can promote the reprogramming of sheep somatic cells to iPSCs, and oar-miR-200c targeted ZEB1 3’UTR, significantly decreased expression of ZEB1, and increased expression of E-cadherin. Oar-miR-200c may improve the MET process by affecting the TGF-β signaling pathway, thus improving the efficiency of somatic cell reprogramming in sheep.

• E-cadherin
• Sheep
• ZEB1
• iPSC
• miR-200c

• Induced pluripotent stem cell
• Myocardial differentiation
• Reprogramming
• TEAD2
• TEAD4
• Transcription factor
• Urine cells
• ZIC3

• MicroRNAs
• Regulatory
• Stem cells
• Viruses

• Cell Differentiation
• Female
• Histones/metabolism
• Humans
• Placenta
• Pluripotent Stem Cells
• Pregnancy
• Trophoblasts

• National Natural Science Foundation of China
• China Postdoctoral Science Foundation
• Guangzhou Municipal Science and Technology Project
• Natural Science Foundation of Guangdong Province
• Presidential Foundation of Nanfang Hospital
• CHIR
• the State Key Development Program for Basic Research of China

• Clinical translation
• EPC
• Reprogramming
• Self-replicating mRNA
• iPSC

• developmental biology
• mesenchymal-to-epithelial transition
• metastasis
• microRNA

• ESCs
• NPCs
• Type I Collagen
• iPSCs
• neural differentiation

Local Chinese local pig breeds have thinner muscle fiber and higher intramuscular-fat (IMF) content. But its regulation mechanism has not been discussed in-depth. Studies indicated that long non coding RNAs (lncRNAs) play important role in muscle and fat development.

The lncRNAs expressional differences in the longissimus dorsi (LD) muscle were identified between Huainan pigs (local Chinese pigs, fat-type, HN) and Large White pigs (lean-type, LW) at 38, 58, and 78 days post conception (dpc). In total, 2131 novel lncRNAs were identified in 18 samples, and 291, 305, and 683 differentially expressed lncRNAs (DELs) were found between these two breeds at three stages, respectively. The mRNAs that co-expressed with these DELs were used for GO and KEGG analysis, and the results showed that muscle development and energy metabolism were more active at 58 dpc in HN, but at 78 dpc in LW pigs. Muscle cell differentiation and myofibril assembly might associated with earlier myogenesis and primary-muscle-fiber assembly in HN, and cell proliferation, insulin, and the MAPK pathway might be contribute to longer proliferation and elevated energy metabolism in LW pigs at 78 dpc. The PI3K/Akt and cAMP pathways were associated with higher IMF deposition in HN. Intramuscular fat deposition-associated long noncoding RNA 1 (IMFlnc1) was selected for functional verification, and results indicated that it regulated the expressional level of caveolin-1 (CAV-1) by acting as competing endogenous RNA (ceRNA) to sponge miR-199a-5p.

Our data contributed to understanding the role of lncRNAs in porcine-muscle development and IMF deposition, and provided valuable information for improving pig-meat quality.

The online version contains supplementary material available at 10.1186/s12860-020-00324-8.

• CAV-1
• Intramuscular adipocyte adipogenesis
• ceRNA
• lncRNA
• miR-199a-5p

• Cell reprogramming
• Epigenetics
• Reprogramming barriers/roadblocks
• Transcription factors
• induced Pluripotent Stem Cells

• EMT
• OXPHOS
• cancer
• energy metabolism
• glycolysis
• reprogramming

• Cell reprogramming
• Clinical-grade
• Induced pluripotent stem cells
• Non-integrative approaches
• Reprogramming factors
• Transgene-free

The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions. This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome. Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long non-coding RNAs (lncRNAs), a type of traditionally neglected RNA species that are increasingly viewed as critical regulators of cellular function. Deeper understanding of lncRNAs in reprogramming may not only help to improve this process but also have implications for studying cell plasticity in other contexts, such as development, aging, and cancer. In this review, we summarize the current progress made in profiling and analyzing the role of lncRNAs in various phases of somatic cell reprogramming, with emphasis on the re-establishment of the pluripotency gene network and X chromosome reactivation.

• Apoptosis
• Mesenchymal-to-epithelial transition
• Proliferation
• X chromosome reactivation

• Animals
• Cellular Reprogramming/genetics
• Humans
• Induced Pluripotent Stem Cells/cytology
• Induced Pluripotent Stem Cells/metabolism
• Induced Pluripotent Stem Cells/physiology
• RNA, Long Noncoding/genetics
• RNA, Long Noncoding/physiology
• Transcriptome
• X Chromosome

• Cell Differentiation
• Cellular Reprogramming
• Humans
• Induced Pluripotent Stem Cells

• R21 NS082618 NINDS NIH HHS

Identifying new mechanisms that underlie the complex process of metastasis is vital to combat this fatal step in prostate cancer (PCa) progression. Small non-coding RNAs are emerging as important regulators of tumor cell biology. Here we take an integrative approach to elucidate the contribution of microRNAs to metastatic progression, combining transcriptomic analysis with functional screens for migration and morphology. We developed high-content microscopy, high-throughput functional screens for migration and morphology in PCa cells using a microRNA library. RNA-Seq analysis of paired epithelial and mesenchymal PCa cells identified differential expression of 200 microRNAs. Data integration identified two microRNAs that inhibited migration, induced an epithelial-like morphology and were increased in epithelial PCa cells. An overrepresentation of the AAGUGC seed sequence was detected in all three datasets. Analysis of published datasets of patients with PCa identified microRNAs of clinical relevance. The integration of high-throughput functional and expression analyses identifies microRNAs with clinical significance that modulate metastatic behavior in PCa.

• EMT - epithelial to mesenchymal transition
• microRNA
• migration screening
• morphological analysis
• prostate cancer
• screening

• differentiation
• reprogramming

• Biomarkers/metabolism
• Cell Differentiation/genetics
• Cell Hypoxia/genetics
• Cellular Reprogramming/genetics
• Chromosomes, Human, Pair 19/genetics
• Epithelial-Mesenchymal Transition/genetics
• Female
• Gene Expression Regulation
• HEK293 Cells
• Humans
• Induced Pluripotent Stem Cells/cytology
• Induced Pluripotent Stem Cells/metabolism
• MicroRNAs/genetics
• MicroRNAs/metabolism
• Multigene Family
• Placenta/metabolism
• Pregnancy
• Transcriptional Activation/genetics
• Trophoblasts/metabolism

• K99 HL109133 NHLBI NIH HHS
• R00 HL109133 NHLBI NIH HHS
• R01 HL128411 NHLBI NIH HHS
• R01 HL145397 NHLBI NIH HHS

• Epithelial-to-mesenchymal transition
• Prostate cancer
• Slug
• Vimentin
• Zeb1
• hsa-miR-200c

• RNA virus vector
• Sendai virus
• artificial miRNA
• cell reprogramming
• iPSCs
• miRNA delivery

Induced pluripotent stem cells (iPSCs)-derived dopaminergic neurons might be reset back to the fetal state due to reprogramming. Thus, it is a compelling challenge to reliably and efficiently induce disease phenotypes of iPSCs-derived dopaminergic neurons to model late-onset Parkinson’s disease (PD). Here, we applied a small molecule, hydroxyurea (HU), to promote the manifestation of disease relevant phenotypes in iPSCs-based modeling of PD. We established two iPS cell lines derived from two sporadic PD patients. Both patients-iPSCs-derived dopaminergic neurons did not display PD relevant phenotypes after 6 weeks culture. HU treatment remarkably induced ER stress on patients-iPSCs-derived dopaminergic neurons. Moreover, HU treatment significantly reduced neurite outgrowth, decreased the expression of p-AKT and its downstream targets (p-4EBP1 and p-ULK1), and increased the expression level of cleaved-Caspase 3 in patients-iPSCs-derived dopaminergic neurons. The findings of the present study suggest that HU administration could be a convenient and reliable approach to induce disease relevant phenotypes in PD-iPSCs-based models, facilitating to study disease mechanisms and test drug effects.

• ER stress
• Parkinson’s disease
• disease phenotypes
• hydroxyurea
• induced pluripotent stem cells

• EMT–MET
• microRNA
• pig iPSCs
• reprogramming

Epigenetic alterations of the malignantly transformed cells have increasingly been regarded as an important event in the carcinogenic development. Induction of some miRNAs such as miR-302/367 cluster has been shown to induce reprogramming of breast cancer cells and exert a tumor suppressive role by induction of mesenchymal to epithelial transition, apoptosis and a lower proliferation rate. Here, we aimed to investigate the impact of miR-302/367 overexpression on transforming growth factor-beta (TGF-β) signaling and how this may contribute to tumor suppressive effects of miR-302/367 cluster.

In this experimental study, MDA-MB-231 and SK-BR-3 breast cancer cells were cultured and transfected with miR-302/367 expressing lentivector. The impact of miR-302/367 overexpression on several mediators of TGF-β signaling and cell cycle was assessed by quantitative real-time polymerase chain reaction (qPCR) and flow cytometry.

Ectopic expression of miR-302/367 cluster downregulated expression of some downstream elements of TGF-β pathway in MDA-MB-231 and SK-BR-3 breast cancer cell lines. Overexpression of miR-302/367 cluster inhibited proliferation of the breast cancer cells by suppressing the S-phase of cell cycle which was in accordance with inhibition of TGF-β pathway.

TGF-β signaling is one of the key pathways in tumor progression and a general suppression of TGF-β mediators by the pleiotropically acting miR-302/367 cluster may be one of the important reasons for its anti-tumor effects in breast cancer cells.

• Breast Cancer
• Reprogramming
• Transforming Growth Factor-Beta
• miR-302/367