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Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism
How pluripotency transcription factors regulate the cellular architecture and energetics has remained largely unknown. Here the authors identify Lima1 as a key effector that mediates the pluripotency control of membrane dynamics and cellular metabolism.
- Binyamin Duethorn
- , Fabian Groll
- & Ivan Bedzhov
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| Open Access
Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids
3D brain organoids have been used to investigate human brain development and pathology. Here the authors establish human ventral midbrain organoids coupled with single cell sequencing to study developing and mature dopamine neurons and use silk scaffolding to generate bioengineered brain organoids
- Alessandro Fiorenzano
- , Edoardo Sozzi
- & Malin Parmar
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| Open Access
Epithelial phenotype restoring drugs suppress macular degeneration phenotypes in an iPSC model
Age-related macular degeneration is characterized by lipid-rich drusen deposits underneath the retinal pigment epithelium (RPE). Here the authors report an in vitro iPSC-RPE model for AMD that recapitulates drusen and RPE atrophy, and identify two drugs that reduce drusen deposits and restore RPE epithelial phenotype.
- Ruchi Sharma
- , Aman George
- & Kapil Bharti
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Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors
Enhancers for endodermal organs are primed at the chromatin level prior to lineage induction by FOXA pioneer transcription factors; how pervasive this is, is not well known. Here the authors show that only a small subset of organ-specific enhancers are bound and primed by FOXA prior to lineage induction, whereas the majority do not undergo chromatin priming and engage FOXA upon lineage induction.
- Ryan J. Geusz
- , Allen Wang
- & Maike Sander
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A tissue-bioengineering strategy for modeling rare human kidney diseases in vivo
The lack of animal models for some human diseases precludes our understanding of disease mechanisms and our ability to test new therapies in vivo. Here the authors present a tissue bioengineering strategy for the study of a rare kidney tumor called angiomyolipoma, in vitro and in vivo, using patient-derived hiPSCs.
- J. O. R. Hernandez
- , X. Wang
- & D. R. Lemos
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Plexin-B2 orchestrates collective stem cell dynamics via actomyosin contractility, cytoskeletal tension and adhesion
Biomechanical mechanisms orchestrating stem cell dynamics in development remain unclear. Here the authors show that guidance receptor Plexin-B2 organizes actomyosin contractility, cytoskeletal tension and adhesion during multicellular development of human embryonic stem cells and neuroprogenitor cells.
- Chrystian Junqueira Alves
- , Rafael Dariolli
- & Roland H. Friedel
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| Open Access
Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder
Mutations in CNTNAP2 have been associated with a syndromic form of Autism Spectrum Disorder. Here the authors show that forebrain organoids generated from induced pluripotent stem cells of patients with a syndromic form of ASD with a homozygous truncating mutation in CNTNAP2 displayed an increase in volume and total cell number, which is driven by abnormal cellular proliferation and neurogenesis.
- Job O. de Jong
- , Ceyda Llapashtica
- & Sander Markx
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| Open Access
DL4-μbeads induce T cell lineage differentiation from stem cells in a stromal cell-free system
T cells derived from stem cells can be harnessed for regenerative medicine and cancer immunotherapy, but current technologies limit production and translation. Here, the authors present a serum-free, stromal-cell free DLL4-coated microbead method for the scalable production of T-lineage cells from multiple sources of stem cells.
- Ashton C. Trotman-Grant
- , Mahmood Mohtashami
- & Juan Carlos Zúñiga-Pflücker
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Grafting of iPS cell-derived tenocytes promotes motor function recovery after Achilles tendon rupture
Tendon self-renewal occurs rarely and reconstructive surgery comes with significant limitations. Here the authors present an induced pluripotent stem cell-based method to generate tenocytes, analyze their developmental trajectory using scRNA-seq, and demonstrate their contribution to motor function recovery after Achilles tendon injury via engraftment and paracrine effects.
- Taiki Nakajima
- , Akihiro Nakahata
- & Makoto Ikeya
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| Open Access
Human iPS-derived pre-epicardial cells direct cardiomyocyte aggregation expansion and organization in vitro
The authors form pre-epicardial cells (PECs) from hiPSC-derived lateral plate mesoderm on treating with BMP4, RA and VEGF, and co-culture these PECs with cardiomyocytes, inducing cardiomyocyte aggregation, proliferation and network formation with more mature structures and improved beating/contractility.
- Jun Jie Tan
- , Jacques P. Guyette
- & Harald C. Ott
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Article
| Open Access
Human sensorimotor organoids derived from healthy and amyotrophic lateral sclerosis stem cells form neuromuscular junctions
Organoids have improved disease modeling. Here, the authors generate human sensorimotor organoids derived from hiPSCs of individuals with ALS. These organoids contain skeletal muscle, sensory and motor neurons as well as astrocytes, microglia, and vasculature and form neuromuscular junctions.
- João D. Pereira
- , Daniel M. DuBreuil
- & Brian J. Wainger
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| Open Access
Retinoblastoma from human stem cell-derived retinal organoids
Retinoblastoma is a heritable pediatric cancer driven by mutations in RB1. Here, the authors demonstrate the first patient derived model of retinoblastoma using iPSCs from patients with germline mutations in RB1.
- Jackie L. Norrie
- , Anjana Nityanandam
- & Michael A. Dyer
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Development of a quantitative prediction algorithm for target organ-specific similarity of human pluripotent stem cell-derived organoids and cells
Quantitative methods to assess the quality of hPSC-derived organoids have not been developed. Here they present a prediction algorithm to assess the transcriptomic similarity between hPSC-derived organoids and the corresponding human target organs and perform validation on lung bud organoids, antral gastric organoids, and cardiomyocytes.
- Mi-Ok Lee
- , Su-gi Lee
- & Hyun-Soo Cho
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SS18 regulates pluripotent-somatic transition through phase separation
Emerging evidence suggests that exit from pluripotency is a regulated, rather than passive process. Here the authors identify a requirement for SS18-mediated Brg/Brahma-associated factors (BAF) chromatin remodeling complex assembly during exit from pluripotency, and that SS18 promotes BAF assembly through liquidliquid phase separation.
- Junqi Kuang
- , Ziwei Zhai
- & Duanqing Pei
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Article
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ERRγ enhances cardiac maturation with T-tubule formation in human iPSC-derived cardiomyocytes
Cardiomyocytes (CMs) derived from human induced pluripotent stem cells (hiPSCs) suffer from limited maturation. Here the authors identify ERRγ agonist as a factor that enhances cardiac morphological, metabolic, contractile and electrical maturation of hiPSC-derived CMs with T-tubule formation.
- Kenji Miki
- , Kohei Deguchi
- & Yoshinori Yoshida
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Chemical combinations potentiate human pluripotent stem cell-derived 3D pancreatic progenitor clusters toward functional β cells
Human pluripotent stem cell (hPSC) derived pancreatic beta cells are a promising and potentially limitless source for cell replacement therapy. Here the authors perform stage-wise chemical screening to develop an improved protocol for hPSC differentiation to functional pancreatic beta cells at high efficiency.
- Haisong Liu
- , Ronghui Li
- & Juan Carlos Izpisua Belmonte
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Generation of mature compact ventricular cardiomyocytes from human pluripotent stem cells
Cardiomyocytes of heart ventricles consist of subpopulations of trabecular and compact subtypes. Here the authors describe the generation of structurally, metabolically and functionally mature compact ventricular cardiomyocytes as well as mature atrial cardiomyocytes from human pluripotent stem cells.
- Shunsuke Funakoshi
- , Ian Fernandes
- & Gordon Keller
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Decreased GLUT2 and glucose uptake contribute to insulin secretion defects in MODY3/HNF1A hiPSC-derived mutant β cells
Heterozygous HNF1A mutations can give rise to maturity onset diabetes of the young 3 (MODY3), characterized by insulin secretion defects. Here the authors show that MODY3-related HNF1A mutation in patient hiPSCderived pancreatic cells decreases glucose transporter GLUT2 expression due to compromised DNA binding.
- Blaise Su Jun Low
- , Chang Siang Lim
- & Adrian Kee Keong Teo
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Co-development of central and peripheral neurons with trunk mesendoderm in human elongating multi-lineage organized gastruloids
The authors generate EMLOs (elongating multi-lineage organized gastruloids): organoids that self-organize to form compartments with characteristics of the central nervous system, peripheral nervous system, mesenchyme, and gut tube.
- Zachary T. Olmsted
- & Janet L. Paluh
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PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus
Phc1 is a subunit of the polycomb repressive complex 1 (PRC1), which represses gene expression during development. Here the authors show that Phc1 acts independently from PRC1 to activate Nanog transcription by stabilizing genome-wide chromatin interactions of the Nanog locus, and in turn stabilize pluripotency.
- Li Chen
- , Qiaoqiao Tong
- & Junfeng Ji
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Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states
The role of transcriptional enhancers and 3D chromatin organisation in coordinating the transition from naive to primed pluripotency remains poorly understood. Here the authors generate a high-resolution atlas of gene regulatory interactions, chromatin profiles and transcription factor occupancy in naive and primed human pluripotent stem cells to provide insights into these developmental processes.
- Peter Chovanec
- , Amanda J. Collier
- & Peter J. Rugg-Gunn
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Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome
Leigh syndrome (LS) is a severe neurometabolic disorder which lacks effective models. Here, the authors developed human neuronal models of LS carrying mutations in SURF1 which show impaired neuronal morphogenesis due to metabolic deficiencies.
- Gizem Inak
- , Agnieszka Rybak-Wolf
- & Alessandro Prigione
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Pharmacological rescue in patient iPSC and mouse models with a rare DISC1 mutation
Previous work has shown in iPSC derived neurons that synaptic impairments are associated with a 4bp DISC1 deletion. Here the authors demonstrate a role for the PDE4 signalling pathway in these synaptic impairments.
- Nam-Shik Kim
- , Zhexing Wen
- & Guo-li Ming
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Article
| Open Access
Blastocyst complementation using Prdm14-deficient rats enables efficient germline transmission and generation of functional mouse spermatids in rats
The uptake of donor pluripotent stem cells (PSCs) in hosts of different species and subsequent germline transmission is very inefficient. Here, the authors show, using Prdm14 gene depleted rat host blastocysts to remove functional sperm, that germline transmission from donor rat or mouse PSCs is possible.
- Toshihiro Kobayashi
- , Teppei Goto
- & Masumi Hirabayashi
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| Open Access
Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells
Brain myelinating oligodendrocytes are rare and difficult to isolate, which has limited data on their development. Here the authors develop a reporter for scalable purification of human pluripotent stem cell derived oligodendrocyte lineage cells, and use this to map differentiation using single cell RNA-sequencing,
- Xitiz Chamling
- , Alyssa Kallman
- & Donald J. Zack
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| Open Access
Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesis
Application of human induced pluripotent stem cells (hiPSCs) for tissue regeneration is hindered by off-target cell differentiation. Here, the authors use bulk and single cell RNA-sequencing to identify WNT and MITF as off-target hubs during chondrogenic differentiation; inhibiting these pathways enhanced homogeneity and yield.
- Chia-Lung Wu
- , Amanda Dicks
- & Farshid Guilak
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| Open Access
BrainPhys neuronal medium optimized for imaging and optogenetics in vitro
Current media for neuronal cell and organoid cultures are suboptimal for functional imaging and optogenetics experiments, owing to phototoxicity and unphysiological performance. Here the authors formulate an optimised neuronal medium to support live cell imaging and electrophysiological activity.
- Michael Zabolocki
- , Kasandra McCormack
- & Cedric Bardy
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| Open Access
Generation and trapping of a mesoderm biased state of human pluripotency
Application of pluripotent cells in regenerative medicine requires an understanding of how they exit pluripotency. Here the authors demonstrate support for the idea that pluripotency exit involves pluripotent intermediates that exhibit lineage bias by identifying and trapping a mesoderm biased sub-state in culture.
- Dylan Stavish
- , Charlotta Böiers
- & Tariq Enver
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Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation
TET mediated RNA-hydroxymethylation (5hmC) has been detected in mammals, but its physiological role remains unclear. Here the authors map 5hmC during embryonic stem cell (ESC) differentiation and find that Tet-mediated RNA hydroxymethylation reduces the stability of crucial pluripotency related transcripts.
- Jie Lan
- , Nicholas Rajan
- & François Fuks
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| Open Access
Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level
Current methods of neuronal network imaging cannot be used for continuous, long-term functional recordings. Here, the authors present a dual-mode high-density microelectrode array, which can simultaneously record in full-frame and high-signal-to-noise modes for label-free electrophysiological measurements.
- Xinyue Yuan
- , Manuel Schröter
- & Urs Frey
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Article
| Open Access
Frataxin gene editing rescues Friedreich’s ataxia pathology in dorsal root ganglia organoid-derived sensory neurons
Friedreich’s ataxia (FRDA) is an autosomal-recessive disorder. Here the authors describe a DRG organoid from patient derived-neurons and co-culture with muscle cells to mimic the disorder in vitro and demonstrate potential correction of the phenotype by CRISPR based editing.
- Pietro Giuseppe Mazzara
- , Sharon Muggeo
- & Vania Broccoli
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| Open Access
Targeting QKI-7 in vivo restores endothelial cell function in diabetes
Vascular endothelial cell (EC) dysfunction contributes to the occurrence of diabetic complications. Here the authors report that in diabetic conditions, upregulation of the RNA binding protein QKI-7 in ECs due to the imbalance of RNA splicing factors CUG-BP and hnRNPM contributes to EC dysfunction, and that in vivo QKI-7 silencing improves blood flow recovery in diabetic mice with limb ischemia.
- Chunbo Yang
- , Magdalini Eleftheriadou
- & Andriana Margariti
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| Open Access
Pre-clinical study of induced pluripotent stem cell-derived dopaminergic progenitor cells for Parkinson’s disease
Induced pluripotent stem cell (iPSC) derived dopaminergic neurons are a promising source for cell-based Parkinson’s disease (PD) therapy. Here the authors report a comprehensive pre-clinical evaluation of the safety and efficacy of dopaminergic progenitors derived from a clinical-grade human iPSC line.
- Daisuke Doi
- , Hiroaki Magotani
- & Jun Takahashi
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| Open Access
Characterization of a pluripotent stem cell-derived matrix with powerful osteoregenerative capabilities
Production of a safe and manufacturable material to mimic anabolic bone for tissue engineering has been hard to achieve to date. Here the authors use a mesenchymal stem cell line generated from induced pluripotent stem cells to produce osteogenic cell-matrix, displaying significant healing properties in mice.
- Eoin P. McNeill
- , Suzanne Zeitouni
- & Carl A. Gregory
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| Open Access
Synergistic gene editing in human iPS cells via cell cycle and DNA repair modulation
Precision editing with CRISPR-Cas9 often suffers from poor efficiency. Here the authors identify culture conditions and small molecules that synergize to promote homology-directed repair (HDR) in induced pluripotent stem (iPS) cells.
- Thomas L. Maurissen
- & Knut Woltjen
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| Open Access
Improving the safety of human pluripotent stem cell therapies using genome-edited orthogonal safeguards
Human pluripotent stem cell derived therapies can have serious safety risks. Here the authors design two drug inducible genetic safeguards to deplete undifferentiated hPSCs and hPSC-derived cell types.
- Renata M. Martin
- , Jonas L. Fowler
- & Kyle M. Loh
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| Open Access
The mutational impact of culturing human pluripotent and adult stem cells
Genetic changes acquired during in vitro culture pose a challenge to application of stem cells. Here the authors use whole genome sequencing to show that cultured human adult and pluripotent stem cells have a high mutational load caused by oxidative stress and reduced oxygen tension in culture lowers mutation rates.
- Ewart Kuijk
- , Myrthe Jager
- & Edwin Cuppen
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| Open Access
Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson’s disease
What happens to cells on engrafting into the brain in animal models to treat Parkinson’s disease is unclear. Here, the authors use scRNA-seq to examine ventral midbrain (VM)-patterned human embryonic stem cells after functional maturation in a pre-clinical rat model for Parkinson’s disease and identify perivascular-like cells.
- Katarína Tiklová
- , Sara Nolbrant
- & Malin Parmar
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Article
| Open Access
Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal
Human pluripotent cells (hPSCs) in standard culture are similar to mouse epiblast cells, but heterogeneity within hPSC cultures complicates comparisons. Here the authors show that a subpopulation of hPSCs enriched for self-renewal capacity have distinct cell cycle, metabolic, DNA methylation, and ATAC-seq profiles.
- Kevin X. Lau
- , Elizabeth A. Mason
- & Martin F. Pera
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Article
| Open Access
Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric mouse brain
Human microglia present unique features; therefore, chimeric mouse models can enhance modelling of human microglia response in health and disease. Here, the authors show that hiPSC-derived mature microglia developed in the mouse brain, retain their identity and respond to demyelination.
- Ranjie Xu
- , Xiaoxi Li
- & Peng Jiang
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Article
| Open Access
Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions
Mutations in human pluripotent stem cells (PSC) and whether any form during culture prior to use in a human clinical context are a concern. Here, the authors use hPSCs derived to cGMP standards and show they have low mutation rates after culture, noting this decreases on culturing in low (5%) oxygen conditions.
- Oliver Thompson
- , Ferdinand von Meyenn
- & Peter W. Andrews
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| Open Access
A critical role of PRDM14 in human primordial germ cell fate revealed by inducible degrons
PRDM14 is a critical transcription factor for mouse primordial germ cell specification, but its role in human remains unclear. Here, PRDM14 protein depletion using auxin-inducible degron uncovers a critical role for human germ cell specification, but regulation of a different set of target genes than in mouse.
- Anastasiya Sybirna
- , Walfred W. C. Tang
- & M. Azim Surani
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| Open Access
Vascular progenitors generated from tankyrase inhibitor-regulated naïve diabetic human iPSC potentiate efficient revascularization of ischemic retina
hPSCs in culture acquire a more naïve pluripotent state upon tankyrase inhibition. Here, the authors show that tankyrase inhibitor-regulated naïve hiPSCs from diabetic donors generate more vascular progenitors and more efficient engraftment into mouse retina than conventional PSCs.
- Tea Soon Park
- , Ludovic Zimmerlin
- & Elias T. Zambidis
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| Open Access
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Studying the genetic effects on early stages of human development is challenging due to a scarcity of biological material. Here, the authors utilise induced pluripotent stem cells from 125 donors to track gene expression changes and expression quantitative trait loci at single cell resolution during in vitro endoderm differentiation.
- Anna S. E. Cuomo
- , Daniel D. Seaton
- & Oliver Stegle
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| Open Access
The in vivo genetic program of murine primordial lung epithelial progenitors
The identity of the earliest murine in vivo lung epithelial progenitors (marked by NKX2-1 expression) is unclear. Here, the authors use single-cell RNA sequencing to define the genetic program of these lung primordial progenitors, which will improve in vitro lung specification of pluripotent stem cells.
- Laertis Ikonomou
- , Michael J. Herriges
- & Darrell N. Kotton
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| Open Access
Generation of mesenchyme free intestinal organoids from human induced pluripotent stem cells
Human induced pluripotent stem cell-derived intestinal organoids (HIOs) are powerful tools to study development and diseases of the gastrointestinal tract. Here, the authors develop a directed differentiation protocol to generate mesenchyme-free HIOs that can be patterned towards proximal small intestine or colonic epithelium, and demonstrated their utility in modeling CFTR function.
- Aditya Mithal
- , Amalia Capilla
- & Gustavo Mostoslavsky
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| Open Access
Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency
Point mutations have been found in induced pluripotent stem cells (iPSCs) but when they arise is unclear. Here, the authors show that a G1/S cell cycle checkpoint deficiency transiently occurs early in genome reprogramming, suggesting a common developmental pathway between iPSC and tumorigenesis, and generate genetic burden-free human iPSCs.
- Ryoko Araki
- , Yuko Hoki
- & Masumi Abe
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Article
| Open Access
Generating ring-shaped engineered heart tissues from ventricular and atrial human pluripotent stem cell-derived cardiomyocytes
The cellular composition of previous engineered heart tissue is often heterogeneous. Here, the authors create chamber-specific human pluripotent stem cell-derived cardiomyocytes to form both ventricular and atrial cells before embedding in collagen-based matrix to form ring-shaped engineered heart tissue.
- Idit Goldfracht
- , Stephanie Protze
- & Lior Gepstein
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| Open Access
Superresolution architecture of cornerstone focal adhesions in human pluripotent stem cells
Pluripotent stem cell colonies are encircled by large cornerstone focal adhesions (FAs). Here, using super-resolution imaging, the authors describe features in the nanoscale makeup of these stable FAs such as inverted vinculin, lateral talin segregation and distinct kank protein distributions.
- Aki Stubb
- , Camilo Guzmán
- & Johanna Ivaska
Transcription Factor 4 loss-of-function is associated with deficits in progenitor proliferation and cortical neuron content