1
|
Lo Conte M, Lucchino V, Scalise S, Zannino C, Valente D, Rossignoli G, Murfuni MS, Cicconetti C, Scaramuzzino L, Matassa DS, Procopio A, Martello G, Cuda G, Parrotta EI. Unraveling the impact of ZZZ3 on the mTOR/ribosome pathway in human embryonic stem cells homeostasis. Stem Cell Reports 2024; 19:729-743. [PMID: 38701777 DOI: 10.1016/j.stemcr.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Embryonic stem cells (ESCs) are defined as stem cells with self-renewing and differentiation capabilities. These unique properties are tightly regulated and controlled by complex genetic and molecular mechanisms, whose understanding is essential for both basic and translational research. A large number of studies have mostly focused on understanding the molecular mechanisms governing pluripotency and differentiation of ESCs, while the regulation of proliferation has received comparably less attention. Here, we investigate the role of ZZZ3 (zinc finger ZZ-type containing 3) in human ESCs homeostasis. We found that knockdown of ZZZ3 negatively impacts ribosome biogenesis, translation, and mTOR signaling, leading to a significant reduction in cell proliferation. This process occurs without affecting pluripotency, suggesting that ZZZ3-depleted ESCs enter a "dormant-like" state and that proliferation and pluripotency can be uncoupled also in human ESCs.
Collapse
Affiliation(s)
- Michela Lo Conte
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | - Valeria Lucchino
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | - Stefania Scalise
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | - Clara Zannino
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | - Desirèe Valente
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | - Giada Rossignoli
- Department of Biology (DiBio), University of Padua, Padua, Italy
| | - Maria Stella Murfuni
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | - Chiara Cicconetti
- Department of Life Sciences and Systems Biology, University of Turin, Via Nizza 52, 10126 Torino, Italy; Italian Institute for Genomic Medicine (IIGM), 10060 Candiolo Torino, Italy
| | - Luana Scaramuzzino
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | - Danilo Swann Matassa
- Department of Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Anna Procopio
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy
| | | | - Giovanni Cuda
- Department of Experimental and Clinical Medicine, University Magna Graecia, 88100 Catanzaro, Italy.
| | | |
Collapse
|
2
|
Frasson I, Diamante L, Zangrossi M, Carbognin E, Dalla Pietà A, Penna A, Rosato A, Verin R, Torrigiani F, Salata C, Dizanzo MP, Vaccaro L, Cacchiarelli D, Richter SN, Montagner M, Martello G. Identification of druggable host dependency factors shared by multiple SARS-CoV-2 variants of concern. J Mol Cell Biol 2024:mjae004. [PMID: 38305139 DOI: 10.1093/jmcb/mjae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
The high mutation rate of SARS-CoV-2 leads to the emergence of multiple variants, some of which are resistant to vaccines and drugs targeting viral elements. Targeting host dependency factors, e.g. cellular proteins required for viral replication, would help prevent resistance. However, it remains unclear whether different SARS-CoV-2 variants induce conserved cellular responses and exploit the same core host factors. To this end, we compared three variants of concern and found that the host transcriptional response was conserved, differing only in kinetics and magnitude. Through CRISPR screening, we identified host genes required for infection by each variant. Most of the genes were shared by multiple variants. We validated our hits with small molecules and repurposed Food and Drug Administration-approved drugs. All the drugs were highly active against all the variants tested, including new variants that emerged during the study (Delta and Omicron). Mechanistically, we identified reactive oxygen species production as a key step in early virus replication. Antioxidants such as N-acetyl cysteine (NAC) were effective against all the variants in both human lung cells and a humanised mouse model. Our study supports the use of available antioxidant drugs, such as NAC, as a general and effective anti-COVID-19 approach.
Collapse
Affiliation(s)
- Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Linda Diamante
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
- Department of Biology, Armenise/Harvard Pluripotent Stem Cell Biology Laboratory, University of Padua, Padua 35131, Italy
| | - Manuela Zangrossi
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Elena Carbognin
- Department of Biology, Armenise/Harvard Pluripotent Stem Cell Biology Laboratory, University of Padua, Padua 35131, Italy
| | - Anna Dalla Pietà
- Department. of Surgery, Oncology and Gastroenterology, University of Padua, Padua 35128, Italy
| | - Alessandro Penna
- Department. of Surgery, Oncology and Gastroenterology, University of Padua, Padua 35128, Italy
| | - Antonio Rosato
- Department. of Surgery, Oncology and Gastroenterology, University of Padua, Padua 35128, Italy
- Veneto Institute of Oncology IOV-IRCCS, Padua 35128, Italy
| | - Ranieri Verin
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua 35020, Italy
| | - Filippo Torrigiani
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua 35020, Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | | | - Lorenzo Vaccaro
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli 80078, Italy
- Department of Translational Medicine, Federico II University, Naples 80138, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli 80078, Italy
- Department of Translational Medicine, Federico II University, Naples 80138, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples "Federico II", Naples 80138, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
- Microbiology and Virology Unit, Padua University Hospital, Padua 35128, Italy
| | - Marco Montagner
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Graziano Martello
- Department of Biology, Armenise/Harvard Pluripotent Stem Cell Biology Laboratory, University of Padua, Padua 35131, Italy
| |
Collapse
|
3
|
Martello G. The rules of the totipotency treasure hunt. Nat Cell Biol 2024; 26:19-21. [PMID: 38228827 DOI: 10.1038/s41556-023-01282-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
|
4
|
Monteleone E, Corrieri P, Provero P, Viavattene D, Pulvirenti L, Raggi L, Carbognin E, Bianchi ME, Martello G, Oliviero S, Pandolfi PP, Poli V. STAT3-dependent long non-coding RNA Lncenc1 contributes to mouse ES cells pluripotency via stabilizing K mRNA. Brief Funct Genomics 2023:elad045. [PMID: 37801430 DOI: 10.1093/bfgp/elad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/28/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023] Open
Abstract
Embryonic stem cells (ESCs) preserve the unique ability to differentiate into any somatic cell lineage while maintaining their self-renewal potential, relying on a complex interplay of extracellular signals regulating the expression/activity of pluripotency transcription factors and their targets. Leukemia inhibitory factor (LIF)-activated STAT3 drives ESCs' stemness by a number of mechanisms, including the transcriptional induction of pluripotency factors such as Klf4 and the maintenance of a stem-like epigenetic landscape. However, it is unknown if STAT3 directly controls stem-cell specific non-coding RNAs, crucial to balance pluripotency and differentiation. Applying a bioinformatic pipeline, here we identify Lncenc1 in mouse ESCs as an STAT3-dependent long non-coding RNA that supports pluripotency. Lncenc1 acts in the cytoplasm as a positive feedback regulator of the LIF-STAT3 axis by competing for the binding of microRNA-128 to the 3'UTR of the Klf4 core pluripotency factor mRNA, enhancing its expression. Our results unveil a novel non-coding RNA-based mechanism for LIF-STAT3-mediated pluripotency.
Collapse
Affiliation(s)
- Emanuele Monteleone
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Paola Corrieri
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy
| | - Daniele Viavattene
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy
| | - Lorenzo Pulvirenti
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy
| | - Laura Raggi
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy
- San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET), Milan, Italy
| | | | | | | | | | - Pier Paolo Pandolfi
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy
- William N. Pennington Cancer Institute, Nevada System of Higher Education, Reno, Nevada
| | - Valeria Poli
- Department of Molecular Biotechnology and Health Science, University of Torino, Via Nizza 52, 10126 Torino, Italy
| |
Collapse
|
5
|
Dinarello A, Betto RM, Diamante L, Tesoriere A, Ghirardo R, Cioccarelli C, Meneghetti G, Peron M, Laquatra C, Tiso N, Martello G, Argenton F. STAT3 and HIF1α cooperatively mediate the transcriptional and physiological responses to hypoxia. Cell Death Discov 2023; 9:226. [PMID: 37407568 DOI: 10.1038/s41420-023-01507-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/04/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
STAT3 and HIF1α are two fundamental transcription factors involved in many merging processes, like angiogenesis, metabolism, and cell differentiation. Notably, under pathological conditions, the two factors have been shown to interact genetically, but both the molecular mechanisms underlying such interactions and their relevance under physiological conditions remain unclear. In mouse embryonic stem cells (ESCs) we manage to determine the specific subset of hypoxia-induced genes that need STAT3 to be properly transcribed and, among them, fundamental genes like Vegfa, Hk1, Hk2, Pfkp and Hilpda are worth mentioning. Unexpectedly, we also demonstrated that the absence of STAT3 does not affect the expression of Hif1α mRNA nor the stabilization of HIF1α protein, but the STAT3-driven regulation of the hypoxia-dependent subset of gene could rely on the physical interaction between STAT3 and HIF1α. To further elucidate the physiological roles of this STAT3 non-canonical nuclear activity, we used a CRISPR/Cas9 zebrafish stat3 knock-out line. Notably, hypoxia-related fluorescence of the hypoxia zebrafish reporter line (HRE:mCherry) cannot be induced when Stat3 is not active and, while Stat3 Y705 phosphorylation seems to have a pivotal role in this process, S727 does not affect the Stat3-dependent hypoxia response. Hypoxia is fundamental for vascularization, angiogenesis and immune cells mobilization; all processes that, surprisingly, cannot be induced by low oxygen levels when Stat3 is genetically ablated. All in all, here we report the specific STAT3/HIF1α-dependent subset of genes in vitro and, for the first time with an in vivo model, we determined some of the physiological roles of STAT3-hypoxia crosstalk.
Collapse
Affiliation(s)
| | | | - Linda Diamante
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | | | | | | | - Claudio Laquatra
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Padova, Italy
| | | | | |
Collapse
|
6
|
Ferlazzo GM, Gambetta AM, Amato S, Cannizzaro N, Angiolillo S, Arboit M, Diamante L, Carbognin E, Romani P, La Torre F, Galimberti E, Pflug F, Luoni M, Giannelli S, Pepe G, Capocci L, Di Pardo A, Vanzani P, Zennaro L, Broccoli V, Leeb M, Moro E, Maglione V, Martello G. Genome-wide screening in pluripotent cells identifies Mtf1 as a suppressor of mutant huntingtin toxicity. Nat Commun 2023; 14:3962. [PMID: 37407555 DOI: 10.1038/s41467-023-39552-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by CAG-repeat expansions in the huntingtin (HTT) gene. The resulting mutant HTT (mHTT) protein induces toxicity and cell death via multiple mechanisms and no effective therapy is available. Here, we employ a genome-wide screening in pluripotent mouse embryonic stem cells (ESCs) to identify suppressors of mHTT toxicity. Among the identified suppressors, linked to HD-associated processes, we focus on Metal response element binding transcription factor 1 (Mtf1). Forced expression of Mtf1 counteracts cell death and oxidative stress caused by mHTT in mouse ESCs and in human neuronal precursor cells. In zebrafish, Mtf1 reduces malformations and apoptosis induced by mHTT. In R6/2 mice, Mtf1 ablates motor defects and reduces mHTT aggregates and oxidative stress. Our screening strategy enables a quick in vitro identification of promising suppressor genes and their validation in vivo, and it can be applied to other monogenic diseases.
Collapse
Affiliation(s)
- Giorgia Maria Ferlazzo
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
- Aptuit (Verona) S.r.l., an Evotec Company, Campus Levi-Montalcini, 37135, Verona, Italy
| | - Anna Maria Gambetta
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Sonia Amato
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
- Department of Neuroscience, University of Padova, Via Belzoni, 160, 35131, Padua, Italy
| | - Noemi Cannizzaro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Silvia Angiolillo
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Linda Diamante
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Elena Carbognin
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Patrizia Romani
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Federico La Torre
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy
| | - Elena Galimberti
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Florian Pflug
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Mirko Luoni
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Serena Giannelli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | | | | | | | - Paola Vanzani
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Lucio Zennaro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | - Vania Broccoli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20854, Vedrano al Lambro, Italy
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Dr Bohr Gasse 9, 1030, Vienna, Austria
| | - Enrico Moro
- Department of Molecular Medicine, Medical School, University of Padua, 35131, Padua, Italy
| | | | - Graziano Martello
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131, Padua, Italy.
| |
Collapse
|
7
|
Carbognin E, Carlini V, Panariello F, Chieregato M, Guerzoni E, Benvegnù D, Perrera V, Malucelli C, Cesana M, Grimaldi A, Mutarelli M, Carissimo A, Tannenbaum E, Kugler H, Hackett JA, Cacchiarelli D, Martello G. Esrrb guides naive pluripotent cells through the formative transcriptional programme. Nat Cell Biol 2023; 25:643-657. [PMID: 37106060 PMCID: PMC7614557 DOI: 10.1038/s41556-023-01131-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2023] [Indexed: 04/29/2023]
Abstract
During embryonic development, naive pluripotent epiblast cells transit to a formative state. The formative epiblast cells form a polarized epithelium, exhibit distinct transcriptional and epigenetic profiles and acquire competence to differentiate into all somatic and germline lineages. However, we have limited understanding of how the transition to a formative state is molecularly controlled. Here we used murine embryonic stem cell models to show that ESRRB is both required and sufficient to activate formative genes. Genetic inactivation of Esrrb leads to illegitimate expression of mesendoderm and extra-embryonic markers, impaired formative expression and failure to self-organize in 3D. Functionally, this results in impaired ability to generate formative stem cells and primordial germ cells in the absence of Esrrb. Computational modelling and genomic analyses revealed that ESRRB occupies key formative genes in naive cells and throughout the formative state. In so doing, ESRRB kickstarts the formative transition, leading to timely and unbiased capacity for multi-lineage differentiation.
Collapse
Affiliation(s)
- Elena Carbognin
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Valentina Carlini
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | | | - Elena Guerzoni
- Department of Biology, University of Padua, Padua, Italy
| | | | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Cristina Malucelli
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples 'Federico II', Naples, Italy
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Margherita Mutarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto di Scienze Applicate e Sistemi Intelligenti 'Eduardo Caianiello', Consiglio Nazionale delle Ricerche, Pozzuoli, Italy
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto per le Applicazioni del Calcolo 'Mauro Picone,' Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Eitan Tannenbaum
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Hillel Kugler
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Jamie A Hackett
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Translational Medicine, University of Naples 'Federico II', Naples, Italy.
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples 'Federico II', Naples, Italy.
| | | |
Collapse
|
8
|
Zorzan I, Betto RM, Rossignoli G, Arboit M, Drusin A, Corridori C, Martini P, Martello G. Chemical conversion of human conventional PSCs to TSCs following transient naive gene activation. EMBO Rep 2023; 24:e55235. [PMID: 36847616 PMCID: PMC10074076 DOI: 10.15252/embr.202255235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
In human embryos, naive pluripotent cells of the inner cell mass (ICM) generate epiblast, primitive endoderm and trophectoderm (TE) lineages, whence trophoblast cells derive. In vitro, naive pluripotent stem cells (PSCs) retain this potential and efficiently generate trophoblast stem cells (TSCs), while conventional PSCs form TSCs at low efficiency. Transient histone deacetylase and MEK inhibition combined with LIF stimulation is used to chemically reset conventional to naive PSCs. Here, we report that chemical resetting induces the expression of both naive and TSC markers and of placental imprinted genes. A modified chemical resetting protocol allows for the fast and efficient conversion of conventional PSCs into TSCs, entailing shutdown of pluripotency genes and full activation of the trophoblast master regulators, without induction of amnion markers. Chemical resetting generates a plastic intermediate state, characterised by co-expression of naive and TSC markers, after which cells steer towards one of the two fates in response to the signalling environment. The efficiency and rapidity of our system will be useful to study cell fate transitions and to generate models of placental disorders.
Collapse
Affiliation(s)
- Irene Zorzan
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | | | | | - Mattia Arboit
- Department of Biology, University of Padua, Padua, Italy
| | - Andrea Drusin
- Department of Biology, University of Padua, Padua, Italy
| | | | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | |
Collapse
|
9
|
Kraunsoe S, Azami T, Pei Y, Martello G, Jones K, Boroviak T, Nichols J. Requirement for STAT3 and its target, TFCP2L1, in self-renewal of naïve pluripotent stem cells in vivo and in vitro. Biol Open 2023; 12:bio059650. [PMID: 36504370 PMCID: PMC9884119 DOI: 10.1242/bio.059650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
We previously demonstrated gradual loss of epiblast during diapause in embryos lacking components of the LIF/IL6 receptor. Here, we explore the requirement for the downstream signalling transducer andactivator of transcription STAT3 and its target, TFCP2L1, in maintenance of naïve pluripotency. Unlike conventional markers, such as NANOG, which remains high in epiblast until implantation, both STAT3 and TFCP2L1 proteins decline during blastocyst expansion, but intensify in the embryonic region after induction of diapause, as observed visually and confirmed using our image-analysis pipeline, consistent with our previous transcriptional expression data. Embryos lacking STAT3 or TFCP2L1 underwent catastrophic loss of most of the inner cell mass during the first few days of diapause, indicating involvement of signals in addition to LIF/IL6 for sustaining naïve pluripotency in vivo. By blocking MEK/ERK signalling from the morula stage, we could derive embryonic stem cells with high efficiency from STAT3 null embryos, but not those lacking TFCP2L1, suggesting a hitherto unknown additional role for this essential STAT3 target in transition from embryo to embryonic stem cells in vitro. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Sophie Kraunsoe
- Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
- Department of Biology, University of Padua, Padova 35121, Italy
| | - Takuya Azami
- Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Yihan Pei
- Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
| | | | - Kenneth Jones
- Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Thorsten Boroviak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| |
Collapse
|
10
|
Cesare E, Urciuolo A, Stuart HT, Torchio E, Gesualdo A, Laterza C, Gagliano O, Martewicz S, Cui M, Manfredi A, Di Filippo L, Sabatelli P, Squarzoni S, Zorzan I, Betto RM, Martello G, Cacchiarelli D, Luni C, Elvassore N. 3D ECM-rich environment sustains the identity of naive human iPSCs. Cell Stem Cell 2022; 29:1703-1717.e7. [PMID: 36459970 DOI: 10.1016/j.stem.2022.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/07/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022]
Abstract
The establishment of in vitro naive human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signaling pathways have been characterized during maintenance of human naive pluripotency. However, little is known about the role exerted by the extracellular matrix (ECM) and its three-dimensional (3D) organization. Here, using an unbiased and integrated approach combining microfluidic cultures with transcriptional, proteomic, and secretome analyses, we found that naive, but not primed, hiPSC colonies are characterized by a self-organized ECM-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naive hiPSCs and also allows direct and timely developmental morphogenesis simply by modulating the signaling environment. Our study opens new perspectives for future applications of naive hiPSCs to study critical stages of human development in 3D starting from a single cell.
Collapse
Affiliation(s)
- Elisa Cesare
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy
| | - Anna Urciuolo
- University College London Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; Institute of Pediatric Research IRP, Corso Stati Uniti, Padova 35127, Italy; Department of Molecular Medicine, University of Padova, Via G. Colombo 3, 35131 Padova, Italy
| | - Hannah T Stuart
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Erika Torchio
- Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy
| | - Alessia Gesualdo
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy
| | - Cecilia Laterza
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy
| | - Onelia Gagliano
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy
| | - Sebastian Martewicz
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Meihua Cui
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Lucio Di Filippo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Next Generation Diagnostic srl, Pozzuoli, Italy
| | - Patrizia Sabatelli
- CNR - Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" - Unit of Bologna, Bologna, Italy; IRCCS-Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Stefano Squarzoni
- CNR - Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" - Unit of Bologna, Bologna, Italy; IRCCS-Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Irene Zorzan
- Epigenetics Programme, Babraham Institute, CB22 3AT Cambridge, UK
| | - Riccardo M Betto
- Department of Molecular Medicine, University of Padova, Via G. Colombo 3, 35131 Padova, Italy
| | - Graziano Martello
- Department of Biology, University of Padova, Via G. Colombo 3, Padova 35131, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Department of Translational Medicine, University of Naples "Federico II", Naples, Italy; School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples "Federico II", Naples, Italy
| | - Camilla Luni
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China; Department of Civil, Chemical, Environmental, and Materials Engineering (DICAM), University of Bologna, Via Terracini 28, Bologna 40131, Italy
| | - Nicola Elvassore
- Department of Industrial Engineering, University of Padova, 6/a Via Gradenigo, Padova 35131, Italy; Veneto Institute of Molecular Medicine, 2 Via Orus, Padova 35131, Italy; University College London Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK.
| |
Collapse
|
11
|
Diamante L, Martello G. Metabolic regulation in pluripotent stem cells. Curr Opin Genet Dev 2022; 75:101923. [PMID: 35691147 DOI: 10.1016/j.gde.2022.101923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
Pluripotent stem cells (PSCs) have the capacity to give rise to all cell types of the adult body and to expand rapidly while retaining genome integrity, representing a perfect tool for regenerative medicine. PSCs are obtained from preimplantation embryos as embryonic stem cells (ESCs), or by reprogramming of somatic cells as induced pluripotent stem cells (iPSCs). Understanding the metabolic requirements of PSCs is instrumental for their efficient generation, expansion and differentiation. PSCs reshape their metabolic profile during developmental progression. Fatty acid oxidation is strictly required for energy production in naive PSCs, but becomes dispensable in more advanced, or primed, PSCs. Other metabolites directly affect proliferation, differentiation or the epigenetic profile of PSCs, showing how metabolism plays an instructive role on PSC behaviour. Developmental progression of pluripotent cells can be paused, both in vitro and in vivo, in response to hormonal and metabolic alterations. Such reversible pausing has been recently linked to mammalian target of rapamycin activity, lipid metabolism and mitochondrial activity. Finally, metabolism is not simply regulated by exogenous stimuli or nutrient availability in PSCs, as key pluripotency regulators, such as Oct4, Stat3 and Tfcp2l1, actively shape the metabolic profile of PSCs.
Collapse
Affiliation(s)
- Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | | |
Collapse
|
12
|
Romani P, Nirchio N, Arboit M, Barbieri V, Tosi A, Michielin F, Shibuya S, Benoist T, Wu D, Hindmarch CCT, Giomo M, Urciuolo A, Giamogante F, Roveri A, Chakravarty P, Montagner M, Calì T, Elvassore N, Archer SL, De Coppi P, Rosato A, Martello G, Dupont S. Mitochondrial fission links ECM mechanotransduction to metabolic redox homeostasis and metastatic chemotherapy resistance. Nat Cell Biol 2022; 24:168-180. [PMID: 35165418 PMCID: PMC7615745 DOI: 10.1038/s41556-022-00843-w] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 01/06/2022] [Indexed: 01/07/2023]
Abstract
Metastatic breast cancer cells disseminate to organs with a soft microenvironment. Whether and how the mechanical properties of the local tissue influence their response to treatment remains unclear. Here we found that a soft extracellular matrix empowers redox homeostasis. Cells cultured on a soft extracellular matrix display increased peri-mitochondrial F-actin, promoted by Spire1C and Arp2/3 nucleation factors, and increased DRP1- and MIEF1/2-dependent mitochondrial fission. Changes in mitochondrial dynamics lead to increased production of mitochondrial reactive oxygen species and activate the NRF2 antioxidant transcriptional response, including increased cystine uptake and glutathione metabolism. This retrograde response endows cells with resistance to oxidative stress and reactive oxygen species-dependent chemotherapy drugs. This is relevant in a mouse model of metastatic breast cancer cells dormant in the lung soft tissue, where inhibition of DRP1 and NRF2 restored cisplatin sensitivity and prevented disseminated cancer-cell awakening. We propose that targeting this mitochondrial dynamics- and redox-based mechanotransduction pathway could open avenues to prevent metastatic relapse.
Collapse
Affiliation(s)
- Patrizia Romani
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy
| | - Nunzia Nirchio
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy
| | - Mattia Arboit
- Department of Biology (DiBio), University of Padua, Padua, Italy
| | - Vito Barbieri
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Padua, Italy
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Anna Tosi
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Federica Michielin
- Institute of Child Health, NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health, UCL, London, UK
| | - Soichi Shibuya
- Institute of Child Health, NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health, UCL, London, UK
| | - Thomas Benoist
- Institute of Child Health, NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health, UCL, London, UK
| | - Danchen Wu
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | | | - Monica Giomo
- Department of Industrial Engineering (DII), University of Padua, Padua, Italy
- Venetian Institute of Molecular Medicine (VIMM), Padua, Italy
| | - Anna Urciuolo
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padua, Italy
| | - Flavia Giamogante
- Department of Biomedical Sciences (DSB), University of Padua, Padua, Italy
| | - Antonella Roveri
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy
| | | | - Marco Montagner
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy
| | - Tito Calì
- Department of Biomedical Sciences (DSB), University of Padua, Padua, Italy
| | - Nicola Elvassore
- Institute of Child Health, NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health, UCL, London, UK
- Department of Industrial Engineering (DII), University of Padua, Padua, Italy
- Venetian Institute of Molecular Medicine (VIMM), Padua, Italy
| | - Stephen L Archer
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Paolo De Coppi
- Institute of Child Health, NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health, UCL, London, UK
| | - Antonio Rosato
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Padua, Italy
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Sirio Dupont
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy.
| |
Collapse
|
13
|
Abstract
Human induced pluripotent stem cells (iPSCs) are generated from somatic cells by the expression of a cocktail of transcription factors, and iPSCs have the capacity to generate in vitro all cell types of the human body. In addition to primed (conventional) iPSCs, several groups recently reported the generation of human naïve iPSCs, which are in a more primitive developmental state and have a broader developmental potential, as shown by their ability to form cells of the placenta. Human iPSCs have broad medical potential but their generation is often time-consuming, not scalable and requires viral vectors or stable genetic manipulations. To overcome such limitations, we developed protocols for high-efficiency generation of either conventional or naïve iPSCs by delivery of messenger RNAs (mRNAs) using a microfluidic system. In this protocol we describe how to produce microfluidic devices, and how to reprogram human somatic cells into naïve and primed iPSCs using these devices. We also describe how to transfer the iPSC colonies from the microfluidic devices over to standard multiwell plates for subsequent expansion of the cultures. Our approach does not require stable genetic modifications, is reproducible and cost-effective, allowing to produce patient-specific iPSCs for cell therapy, disease modeling, and in vitro developmental studies.
Collapse
Affiliation(s)
- Irene Zorzan
- Department of Biology, University of Padua, Padua, Italy
| | - Onelia Gagliano
- Department of Industrial Engineering, University of Padua, Padua, Italy
- Venetian Institute of Molecular Medicine, Padua, Italy
| | - Nicola Elvassore
- Department of Industrial Engineering, University of Padua, Padua, Italy
- Venetian Institute of Molecular Medicine, Padua, Italy
- Stem Cell and Regenerative Medicine Department, DBC Program, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China
| | | |
Collapse
|
14
|
Borella M, Martello G, Risso D, Romualdi C. PsiNorm: a scalable normalization for single-cell RNA-seq data. Bioinformatics 2021; 38:164-172. [PMID: 34499096 PMCID: PMC8696108 DOI: 10.1093/bioinformatics/btab641] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) enables transcriptome-wide gene expression measurements at single-cell resolution providing a comprehensive view of the compositions and dynamics of tissue and organism development. The evolution of scRNA-seq protocols has led to a dramatic increase of cells throughput, exacerbating many of the computational and statistical issues that previously arose for bulk sequencing. In particular, with scRNA-seq data all the analyses steps, including normalization, have become computationally intensive, both in terms of memory usage and computational time. In this perspective, new accurate methods able to scale efficiently are desirable. RESULTS Here, we propose PsiNorm, a between-sample normalization method based on the power-law Pareto distribution parameter estimate. Here, we show that the Pareto distribution well resembles scRNA-seq data, especially those coming from platforms that use unique molecular identifiers. Motivated by this result, we implement PsiNorm, a simple and highly scalable normalization method. We benchmark PsiNorm against seven other methods in terms of cluster identification, concordance and computational resources required. We demonstrate that PsiNorm is among the top performing methods showing a good trade-off between accuracy and scalability. Moreover, PsiNorm does not need a reference, a characteristic that makes it useful in supervised classification settings, in which new out-of-sample data need to be normalized. AVAILABILITY AND IMPLEMENTATION PsiNorm is implemented in the scone Bioconductor package and available at https://bioconductor.org/packages/scone/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Matteo Borella
- Department of Biology, University of Padova, Padua 35121, Italy
| | | | | | | |
Collapse
|
15
|
Peron M, Dinarello A, Meneghetti G, Martorano L, Betto RM, Facchinello N, Tesoriere A, Tiso N, Martello G, Argenton F. Y705 and S727 are required for the mitochondrial import and transcriptional activities of STAT3, and for regulation of stem cell proliferation. Development 2021; 148:272054. [PMID: 34473253 PMCID: PMC8451946 DOI: 10.1242/dev.199477] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022]
Abstract
The STAT3 transcription factor, acting both in the nucleus and mitochondria, maintains embryonic stem cell pluripotency and promotes their proliferation. In this work, using zebrafish, we determined in vivo that mitochondrial STAT3 regulates mtDNA transcription in embryonic and larval stem cell niches and that this activity affects their proliferation rates. As a result, we demonstrated that import of STAT3 inside mitochondria requires Y705 phosphorylation by Jak, whereas its mitochondrial transcriptional activity, as well as its effect on proliferation, depends on the MAPK target S727. These data were confirmed using mouse embryonic stem cells: although the Y705-mutated STAT3 cannot enter mitochondria, the S727 mutation does not affect import into the organelle and is responsible for STAT3-dependent mitochondrial transcription. Surprisingly, STAT3-dependent increase of mitochondrial transcription appears to be independent from STAT3 binding to STAT3-responsive elements. Finally, loss-of-function experiments, with chemical inhibition of the JAK/STAT3 pathway or genetic ablation of stat3 gene, demonstrated that STAT3 is also required for cell proliferation in the intestine of zebrafish. Summary: Mitochondrial import of STAT3 requires Y705 phosphorylation by Jak, whereas STAT3 mitochondrial transcriptional activity and its effect on proliferation depend on the MAPK target S727.
Collapse
Affiliation(s)
- Margherita Peron
- Department of Biology, University of Padova, 35121, Padova, Italy
| | | | | | - Laura Martorano
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Riccardo M Betto
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | | | | | - Natascia Tiso
- Department of Biology, University of Padova, 35121, Padova, Italy
| | | | | |
Collapse
|
16
|
Betto RM, Diamante L, Perrera V, Audano M, Rapelli S, Lauria A, Incarnato D, Arboit M, Pedretti S, Rigoni G, Guerineau V, Touboul D, Stirparo GG, Lohoff T, Boroviak T, Grumati P, Soriano ME, Nichols J, Mitro N, Oliviero S, Martello G. Metabolic control of DNA methylation in naive pluripotent cells. Nat Genet 2021; 53:215-229. [PMID: 33526924 PMCID: PMC7116828 DOI: 10.1038/s41588-020-00770-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/17/2020] [Indexed: 12/31/2022]
Abstract
Naive epiblast and embryonic stem cells (ESCs) give rise to all cells of adults. Such developmental plasticity is associated with genome hypomethylation. Here, we show that LIF-Stat3 signaling induces genomic hypomethylation via metabolic reconfiguration. Stat3-/- ESCs show decreased α-ketoglutarate production from glutamine, leading to increased Dnmt3a and Dnmt3b expression and DNA methylation. Notably, genome methylation is dynamically controlled through modulation of α-ketoglutarate availability or Stat3 activation in mitochondria. Alpha-ketoglutarate links metabolism to the epigenome by reducing the expression of Otx2 and its targets Dnmt3a and Dnmt3b. Genetic inactivation of Otx2 or Dnmt3a and Dnmt3b results in genomic hypomethylation even in the absence of active LIF-Stat3. Stat3-/- ESCs show increased methylation at imprinting control regions and altered expression of cognate transcripts. Single-cell analyses of Stat3-/- embryos confirmed the dysregulated expression of Otx2, Dnmt3a and Dnmt3b as well as imprinted genes. Several cancers display Stat3 overactivation and abnormal DNA methylation; therefore, the molecular module that we describe might be exploited under pathological conditions.
Collapse
Affiliation(s)
- Riccardo M Betto
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Neuroscience Sector, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Matteo Audano
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Stefania Rapelli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Andrea Lauria
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Danny Incarnato
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Silvia Pedretti
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Giovanni Rigoni
- Department of Biology, University of Padua, Padua, Italy
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Vincent Guerineau
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | | | - Tim Lohoff
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Thorsten Boroviak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy.
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.
| | - Graziano Martello
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy.
- Department of Biology, University of Padua, Padua, Italy.
| |
Collapse
|
17
|
Zorzan I, Pellegrini M, Arboit M, Incarnato D, Maldotti M, Forcato M, Tagliazucchi GM, Carbognin E, Montagner M, Oliviero S, Martello G. The transcriptional regulator ZNF398 mediates pluripotency and epithelial character downstream of TGF-beta in human PSCs. Nat Commun 2020; 11:2364. [PMID: 32398665 PMCID: PMC7217929 DOI: 10.1038/s41467-020-16205-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/17/2020] [Indexed: 12/16/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) have the capacity to give rise to all differentiated cells of the adult. TGF-beta is used routinely for expansion of conventional hPSCs as flat epithelial colonies expressing the transcription factors POU5F1/OCT4, NANOG, SOX2. Here we report a global analysis of the transcriptional programme controlled by TGF-beta followed by an unbiased gain-of-function screening in multiple hPSC lines to identify factors mediating TGF-beta activity. We identify a quartet of transcriptional regulators promoting hPSC self-renewal including ZNF398, a human-specific mediator of pluripotency and epithelial character in hPSCs. Mechanistically, ZNF398 binds active promoters and enhancers together with SMAD3 and the histone acetyltransferase EP300, enabling transcription of TGF-beta targets. In the context of somatic cell reprogramming, inhibition of ZNF398 abolishes activation of pluripotency and epithelial genes and colony formation. Our findings have clear implications for the generation of bona fide hPSCs for regenerative medicine.
Collapse
Affiliation(s)
- Irene Zorzan
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy
| | - Marco Pellegrini
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy.,UCL Great Ormond Street Institute of Child Health, Developmental Biology and Cancer, Stem Cells and Regenerative Medicine, 30 Guilford Street, WC1N 1EH, London, UK
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy
| | - Danny Incarnato
- Department of Life Sciences and Systems Biology and Molecular Biotechnology Center (MCB), University of Turin, 10126, Turin, Italy.,Italian Institute for Genomic Medicine (IIGM), 10060, Candiolo (TO), Italy.,Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Mara Maldotti
- Department of Life Sciences and Systems Biology and Molecular Biotechnology Center (MCB), University of Turin, 10126, Turin, Italy.,Italian Institute for Genomic Medicine (IIGM), 10060, Candiolo (TO), Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Guidantonio Malagoli Tagliazucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy.,UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, WC1E 6BT, London, UK
| | - Elena Carbognin
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy
| | - Marco Montagner
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology and Molecular Biotechnology Center (MCB), University of Turin, 10126, Turin, Italy. .,Italian Institute for Genomic Medicine (IIGM), 10060, Candiolo (TO), Italy.
| | - Graziano Martello
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy.
| |
Collapse
|
18
|
Abstract
Human induced Pluripotent Stem Cells (hiPSCs) have the capacity to generate a wide range of somatic cells, thus representing an ideal tool for regenerative medicine. Patient-derived hiPSCs are also used for in vitro disease modeling and drug screenings. Several studies focused on the identification of DNA mutations generated, or selected, during the derivation of hiPSCs, some of which are known to drive cancer formation. Avoiding such stable genomic aberrations is paramount for successful use of hiPSCs, but it is equally important to ensure that their epigenetic information is correct, given the critical role of epigenetics in transcriptional regulation and its involvement in a plethora of pathologic conditions. In this review we will focus on genomic imprinting, a prototypical epigenetic mechanism whereby a gene is expressed in a parent-of-origin specific manner, thanks to the differential methylation of specific DNA sequences. Conventional hiPSCs are thought to be in a pluripotent state primed for differentiation. They display a hypermethylated genome with an unexpected loss of DNA methylation at imprinted loci. Several groups recently reported the generation of hiPSCs in a more primitive developmental stage, called naïve pluripotency. Naïve hiPSCs share several features with early human embryos, such as a global genome hypomethylation, which is also accompanied by a widespread loss of DNA methylation at imprinted loci. Given that loss of imprinting has been observed in genetic developmental disorders as well as in a wide range of cancers, it is fundamental to make sure that hiPSCs do not show such epigenetic aberrations. We will discuss what specific imprinted genes, associated with human pathologies, have been found commonly misregulated in hiPSCs and suggest strategies to effectively detect and avoid such undesirable epigenetic abnormalities.
Collapse
Affiliation(s)
- Valentina Perrera
- Department of Molecular Medicine, School of Medicine and Surgery, University of Padova, Padua, Italy
| | - Graziano Martello
- Department of Molecular Medicine, School of Medicine and Surgery, University of Padova, Padua, Italy
| |
Collapse
|
19
|
Dunn SJ, Li MA, Carbognin E, Smith A, Martello G. A common molecular logic determines embryonic stem cell self-renewal and reprogramming. EMBO J 2018; 38:embj.2018100003. [PMID: 30482756 PMCID: PMC6316172 DOI: 10.15252/embj.2018100003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/03/2018] [Accepted: 10/04/2018] [Indexed: 11/18/2022] Open
Abstract
During differentiation and reprogramming, new cell identities are generated by reconfiguration of gene regulatory networks. Here, we combined automated formal reasoning with experimentation to expose the logic of network activation during induction of naïve pluripotency. We find that a Boolean network architecture defined for maintenance of naïve state embryonic stem cells (ESC) also explains transcription factor behaviour and potency during resetting from primed pluripotency. Computationally identified gene activation trajectories were experimentally substantiated at single‐cell resolution by RT–qPCR. Contingency of factor availability explains the counterintuitive observation that Klf2, which is dispensable for ESC maintenance, is required during resetting. We tested 124 predictions formulated by the dynamic network, finding a predictive accuracy of 77.4%. Finally, we show that this network explains and predicts experimental observations of somatic cell reprogramming. We conclude that a common deterministic program of gene regulation is sufficient to govern maintenance and induction of naïve pluripotency. The tools exemplified here could be broadly applied to delineate dynamic networks underlying cell fate transitions.
Collapse
Affiliation(s)
- Sara-Jane Dunn
- Microsoft Research, Cambridge, UK.,Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Meng Amy Li
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Elena Carbognin
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK .,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | |
Collapse
|
20
|
Abstract
Predictive biology is elusive because rigorous, data-constrained, mechanistic models of complex biological systems are difficult to derive and validate. Current approaches tend to construct and examine static interaction network models, which are descriptively rich, but often lack explanatory and predictive power, or dynamic models that can be simulated to reproduce known behavior. However, in such approaches implicit assumptions are introduced as typically only one mechanism is considered, and exhaustively investigating all scenarios is impractical using simulation. To address these limitations, we present a methodology based on automated formal reasoning, which permits the synthesis and analysis of the complete set of logical models consistent with experimental observations. We test hypotheses against all candidate models, and remove the need for simulation by characterizing and simultaneously analyzing all mechanistic explanations of observed behavior. Our methodology transforms knowledge of complex biological processes from sets of possible interactions and experimental observations to precise, predictive biological programs governing cell function.
Collapse
Affiliation(s)
- Boyan Yordanov
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Sara-Jane Dunn
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Hillel Kugler
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.,Faculty of Engineering, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Austin Smith
- Wellcome Trust Medical Research Council Cambridge Stem Cell Institute, University of Cambridge CB2 1QR, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Graziano Martello
- Dept. of Molecular Medicine, Complesso Vallisneri - 3 Piano Nord, University of Padua, Viale G. Colombo 3, 35131 Padua, Italy
| | - Stephen Emmott
- Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK.,Faculty of Engineering Science, University College London, Torrington Place, London WC1E 7JE, UK
| |
Collapse
|
21
|
Carbognin E, Betto RM, Soriano ME, Smith AG, Martello G. Stat3 promotes mitochondrial transcription and oxidative respiration during maintenance and induction of naive pluripotency. EMBO J 2016; 35:618-34. [PMID: 26903601 PMCID: PMC4801951 DOI: 10.15252/embj.201592629] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/15/2016] [Indexed: 02/02/2023] Open
Abstract
Transcription factor Stat3 directs self-renewal of pluripotent mouse embryonic stem (ES) cells downstream of the cytokine leukemia inhibitory factor (LIF). Stat3 upregulates pivotal transcription factors in the ES cell gene regulatory network to sustain naïve identity. Stat3 also contributes to the rapid proliferation of ES cells. Here, we show that Stat3 increases the expression of mitochondrial-encoded transcripts and enhances oxidative metabolism. Chromatin immunoprecipitation reveals that Stat3 binds to the mitochondrial genome, consistent with direct transcriptional regulation. An engineered form of Stat3 that localizes predominantly to mitochondria is sufficient to support enhanced proliferation of ES cells, but not to maintain their undifferentiated phenotype. Furthermore, during reprogramming from primed to naïve states of pluripotency, Stat3 similarly upregulates mitochondrial transcripts and facilitates metabolic resetting. These findings suggest that the potent stimulation of naïve pluripotency by LIF/Stat3 is attributable to parallel and synergistic induction of both mitochondrial respiration and nuclear transcription factors.
Collapse
Affiliation(s)
- Elena Carbognin
- Department of Molecular MedicineUniversity of PaduaPaduaItaly
| | | | | | - Austin G Smith
- Wellcome Trust – Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK,Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | |
Collapse
|
22
|
Abstract
The embryo of the African clawed frog Xenopus laevis plays a central role in the field of cell and developmental biology. One of the strengths of Xenopus as model system lies in the high degree of conservation between amphibians and mammals in the molecular mechanisms controlling tissue patterning and differentiation. As such, many signaling cascades were first investigated in frog embryos and then confirmed in mouse and/or human cells. The TGF-β signaling cascade greatly benefited from this model system. Here we review the overall logic and experimental planning for studying Smad activity in vivo in the context of Xenopus embryonic development, and provide a guide for the interpretation of the results.
Collapse
Affiliation(s)
- Marco Montagner
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35131, Padua, Italy
| | - Graziano Martello
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35131, Padua, Italy
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35131, Padua, Italy.
| |
Collapse
|
23
|
Abstract
Mouse embryonic stem (ES) cells perpetuate in vitro the broad developmental potential of naïve founder cells in the preimplantation embryo. ES cells self-renew relentlessly in culture but can reenter embryonic development seamlessly, differentiating on schedule to form all elements of the fetus. Here we review the properties of these remarkable cells. Arising from the stability, homogeneity, and equipotency of ES cells, we consider the concept of a pluripotent ground state. We evaluate the authenticity of ES cells in relation to cells in the embryo and examine their utility for dissecting mechanisms that confer pluripotency and that execute fate choice. We summarize current knowledge of the transcription factor circuitry that governs the ES cell state and discuss the opportunity to expose molecular logic further through iterative computational modeling and experimentation. Finally, we present a perspective on unresolved questions, including the challenge of deriving ground state pluripotent stem cells from non-rodent species.
Collapse
|
24
|
Abstract
The gene regulatory circuitry through which pluripotent embryonic stem (ES) cells choose between self-renewal and differentiation appears vast and has yet to be distilled into an executive molecular program. We developed a data-constrained, computational approach to reduce complexity and to derive a set of functionally validated components and interaction combinations sufficient to explain observed ES cell behavior. This minimal set, the simplest version of which comprises only 16 interactions, 12 components, and three inputs, satisfies all prior specifications for self-renewal and furthermore predicts unknown and nonintuitive responses to compound genetic perturbations with an overall accuracy of 70%. We propose that propagation of ES cell identity is not determined by a vast interactome but rather can be explained by a relatively simple process of molecular computation.
Collapse
Affiliation(s)
- S-J Dunn
- Computational Science Laboratory, Microsoft Research, Cambridge, CB1 2FB, UK
| | - G Martello
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - B Yordanov
- Computational Science Laboratory, Microsoft Research, Cambridge, CB1 2FB, UK
| | - S Emmott
- Computational Science Laboratory, Microsoft Research, Cambridge, CB1 2FB, UK
| | - AG Smith
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
25
|
Stuart HT, van Oosten AL, Radzisheuskaya A, Martello G, Miller A, Dietmann S, Nichols J, Silva JCR. NANOG amplifies STAT3 activation and they synergistically induce the naive pluripotent program. Curr Biol 2014; 24:340-6. [PMID: 24462001 PMCID: PMC3982126 DOI: 10.1016/j.cub.2013.12.040] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/05/2013] [Accepted: 12/13/2013] [Indexed: 01/17/2023]
Abstract
Reprogramming of a differentiated cell back to a naive pluripotent identity is thought to occur by several independent mechanisms. Two such mechanisms include NANOG and activated STAT3 (pSTAT3), known master regulators of naive pluripotency acquisition [1–5]. Here, we investigated the relationship between NANOG and pSTAT3 during the establishment and maintenance of naive pluripotency. Surprisingly, we found that NANOG enhances LIF signal transduction, resulting in elevated pSTAT3. This is mediated, at least in part, by suppression of the expression of the LIF/STAT3 negative regulator SOCS3. We also discovered NANOG to be limiting for the expression of KLF4, a canonical “Yamanaka” reprogramming factor [6] and key pSTAT3 target [2, 7, 8]. KLF4 expression resulted from the codependent and synergistic action of NANOG and pSTAT3 in embryonic stem cells and during initiation of reprogramming. Additionally, within 48 hr, the combined actions of NANOG and pSTAT3 in a reprogramming context resulted in reactivation of genes associated with naive pluripotency. Importantly, we show that NANOG can be bypassed during reprogramming by exogenous provision of its downstream effectors, namely pSTAT3 elevation and KLF4 expression. In conclusion, we propose that mechanisms of reprogramming are linked, rather than independent, and are centered on a small number of genes, including NANOG. NANOG amplifies STAT3 activation NANOG and STAT3 synergistically induce KLF4 expression NANOG and STAT3 rapidly induce naive gene expression in a reprogramming context Combined STAT3 and KLF4 bypass NANOG in reprogramming
Collapse
Affiliation(s)
- Hannah T Stuart
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Anouk L van Oosten
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Aliaksandra Radzisheuskaya
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Graziano Martello
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Anzy Miller
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Sabine Dietmann
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - José C R Silva
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
| |
Collapse
|
26
|
Affiliation(s)
- Graziano Martello
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| |
Collapse
|
27
|
Leitch H, Nichols J, Humphreys P, Mulas C, Martello G, Lee C, Jones K, Surani M, Smith A. Rebuilding pluripotency from primordial germ cells. Stem Cell Reports 2013; 1:66-78. [PMID: 24052943 PMCID: PMC3757743 DOI: 10.1016/j.stemcr.2013.03.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/22/2013] [Accepted: 03/23/2013] [Indexed: 02/02/2023] Open
Abstract
Mammalian primordial germ cells (PGCs) are unipotent progenitors of the gametes. Nonetheless, they can give rise directly to pluripotent stem cells in vitro or during teratocarcinogenesis. This conversion is inconsistent, however, and has been difficult to study. Here, we delineate requirements for efficient resetting of pluripotency in culture. We demonstrate that in defined conditions, routinely 20% of PGCs become EG cells. Conversion can occur from the earliest specified PGCs. The entire process can be tracked from single cells. It is driven by leukemia inhibitory factor (LIF) and the downstream transcription factor STAT3. In contrast, LIF signaling is not required during germ cell ontogeny. We surmise that ectopic LIF/STAT3 stimulation reconstructs latent pluripotency and self-renewal. Notably, STAT3 targets are significantly upregulated in germ cell tumors, suggesting that dysregulation of this pathway may underlie teratocarcinogenesis. These findings demonstrate that EG cell formation is a robust experimental system for exploring mechanisms involved in reprogramming and cancer. A defined system for generation of pluripotent EG cells at high efficiency 20% of single primordial germ cells become EG cells Stimulation with LIF but not FGF drives conversion to pluripotency LIF/STAT3 targets are upregulated in pluripotent germ cell tumors
Collapse
Affiliation(s)
- Harry G. Leitch
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Peter Humphreys
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Graziano Martello
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Caroline Lee
- Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Ken Jones
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - M. Azim Surani
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Corresponding author
| |
Collapse
|
28
|
Martello G, Sugimoto T, Diamanti E, Joshi A, Hannah R, Ohtsuka S, Göttgens B, Niwa H, Smith A. Esrrb Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal. Cell Stem Cell 2013. [PMCID: PMC3848011 DOI: 10.1016/j.stem.2013.04.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
29
|
Martello G, Sugimoto T, Diamanti E, Joshi A, Hannah R, Ohtsuka S, Göttgens B, Niwa H, Smith A. Esrrb is a pivotal target of the Gsk3/Tcf3 axis regulating embryonic stem cell self-renewal. Cell Stem Cell 2012; 11:491-504. [PMID: 23040478 PMCID: PMC3465555 DOI: 10.1016/j.stem.2012.06.008] [Citation(s) in RCA: 331] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 03/23/2012] [Accepted: 06/07/2012] [Indexed: 02/02/2023]
Abstract
Inhibition of glycogen synthase kinase-3 (Gsk3) supports mouse embryonic stem cells (ESCs) by modulating Tcf3, but the critical targets downstream of Tcf3 are unclear. We analyzed the intersection between genome localization and transcriptome data sets to identify genes repressed by Tcf3. Among these, manipulations of Esrrb gave distinctive phenotypes in functional assays. Knockdown and knockout eliminated response to Gsk3 inhibition, causing extinction of pluripotency markers and loss of colony forming capability. Conversely, forced expression phenocopied Gsk3 inhibition or Tcf3 deletion by suppressing differentiation and sustaining self-renewal. Thus the nuclear receptor Esrrb is necessary and sufficient to mediate self-renewal downstream of Gsk3 inhibition. Leukaemia inhibitory factor (LIF) regulates ESCs through Stat3, independently of Gsk3 inhibition. Consistent with parallel operation, ESCs in LIF accommodated Esrrb deletion and remained pluripotent. These findings highlight a key role for Esrrb in regulating the naive pluripotent state and illustrate compensation among the core pluripotency factors.
Collapse
Affiliation(s)
- Graziano Martello
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge UK,Department of Biochemistry, University of Cambridge, Cambridge UK
| | - Toshimi Sugimoto
- RIKEN Center for Developmental Biology, Kobe 650-0047, Japan,Laboratory for Development and Regenerative Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 6500017, Japan
| | - Evangelia Diamanti
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge UK,Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Cambridge UK
| | - Anagha Joshi
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge UK,Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Cambridge UK
| | - Rebecca Hannah
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge UK,Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Cambridge UK
| | - Satoshi Ohtsuka
- RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Berthold Göttgens
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge UK,Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Cambridge UK,Corresponding author
| | - Hitoshi Niwa
- RIKEN Center for Developmental Biology, Kobe 650-0047, Japan,Laboratory for Development and Regenerative Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 6500017, Japan,Corresponding author
| | - Austin Smith
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge UK,Department of Biochemistry, University of Cambridge, Cambridge UK,Corresponding author
| |
Collapse
|
30
|
Inui M, Manfrin A, Mamidi A, Martello G, Morsut L, Soligo S, Enzo E, Moro S, Polo S, Dupont S, Cordenonsi M, Piccolo S. USP15 is a deubiquitylating enzyme for receptor-activated SMADs. Nat Cell Biol 2011; 13:1368-75. [PMID: 21947082 DOI: 10.1038/ncb2346] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/17/2011] [Indexed: 12/12/2022]
Abstract
The TGFβ pathway is critical for embryonic development and adult tissue homeostasis. On ligand stimulation, TGFβ and BMP receptors phosphorylate receptor-activated SMADs (R-SMADs), which then associate with SMAD4 to form a transcriptional complex that regulates gene expression through specific DNA recognition. Several ubiquitin ligases serve as inhibitors of R-SMADs, yet no deubiquitylating enzyme (DUB) for these molecules has so far been identified. This has left unexplored the possibility that ubiquitylation of R-SMADs is reversible and engaged in regulating SMAD function, in addition to degradation. Here we identify USP15 as a DUB for R-SMADs. USP15 is required for TGFβ and BMP responses in mammalian cells and Xenopus embryos. At the biochemical level, USP15 primarily opposes R-SMAD monoubiquitylation, which targets the DNA-binding domains of R-SMADs and prevents promoter recognition. As such, USP15 is critical for the occupancy of endogenous target promoters by the SMAD complex. These data identify an additional layer of control by which the ubiquitin system regulates TGFβ biology.
Collapse
Affiliation(s)
- Masafumi Inui
- Department of Medical Biotechnologies, Section of Histology and Embryology, University of Padua, viale G. Colombo 3, 35100 Padua, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Martello G, Rosato A, Ferrari F, Manfrin A, Cordenonsi M, Dupont S, Enzo E, Guzzardo V, Rondina M, Spruce T, Parenti AR, Daidone MG, Bicciato S, Piccolo S. A MicroRNA targeting dicer for metastasis control. Cell 2010; 141:1195-207. [PMID: 20603000 DOI: 10.1016/j.cell.2010.05.017] [Citation(s) in RCA: 542] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 02/23/2010] [Accepted: 04/14/2010] [Indexed: 12/15/2022]
Abstract
Although specific microRNAs (miRNAs) can be upregulated in cancer, global miRNA downregulation is a common trait of human malignancies. The mechanisms of this phenomenon and the advantages it affords remain poorly understood. Here we identify a microRNA family, miR-103/107, that attenuates miRNA biosynthesis by targeting Dicer, a key component of the miRNA processing machinery. In human breast cancer, high levels of miR-103/107 are associated with metastasis and poor outcome. Functionally, miR-103/107 confer migratory capacities in vitro and empower metastatic dissemination of otherwise nonaggressive cells in vivo. Inhibition of miR-103/107 opposes migration and metastasis of malignant cells. At the cellular level, a key event fostered by miR-103/107 is induction of epithelial-to-mesenchymal transition (EMT), attained by downregulating miR-200 levels. These findings suggest a new pathway by which Dicer inhibition drifts epithelial cancer toward a less-differentiated, mesenchymal fate to foster metastasis.
Collapse
Affiliation(s)
- Graziano Martello
- Department of Histology, Microbiology and Medical Biotechnologies, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Dupont S, Mamidi A, Cordenonsi M, Montagner M, Zacchigna L, Adorno M, Martello G, Stinchfield MJ, Soligo S, Morsut L, Inui M, Moro S, Modena N, Argenton F, Newfeld SJ, Piccolo S. FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination. Cell 2009. [PMID: 19135894 DOI: 10.1016/j.cell.2008.10.051.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assembly of the Smad complex is critical for TGFbeta signaling, yet the mechanisms that inactivate or empower nuclear Smad complexes are less understood. By means of siRNA screen we identified FAM (USP9x), a deubiquitinase acting as essential and evolutionarily conserved component in TGFbeta and bone morphogenetic protein signaling. Smad4 is monoubiquitinated in lysine 519 in vivo, a modification that inhibits Smad4 by impeding association with phospho-Smad2. FAM reverts this negative modification, re-empowering Smad4 function. FAM opposes the activity of Ectodermin/Tif1gamma (Ecto), a nuclear factor for which we now clarify a prominent role as Smad4 monoubiquitin ligase. Our study points to Smad4 monoubiquitination and deubiquitination as a way for cells to set their TGFbeta responsiveness: loss of FAM disables Smad4-dependent responses in several model systems, with Ecto being epistatic to FAM. This defines a regulative ubiquitination step controlling Smads that is parallel to those impinging on R-Smad phosphorylation.
Collapse
Affiliation(s)
- Sirio Dupont
- Department of Histology, Microbiology, and Medical Biotechnologies, University of Padua School of Medicine, viale Colombo 3, 35131 Padua, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Dupont S, Mamidi A, Cordenonsi M, Montagner M, Zacchigna L, Adorno M, Martello G, Stinchfield MJ, Soligo S, Morsut L, Inui M, Moro S, Modena N, Argenton F, Newfeld SJ, Piccolo S. FAM/USP9x, a Deubiquitinating Enzyme Essential for TGFβ Signaling, Controls Smad4 Monoubiquitination. Cell 2009; 136:123-35. [PMID: 19135894 DOI: 10.1016/j.cell.2008.10.051] [Citation(s) in RCA: 389] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2008] [Revised: 09/29/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Affiliation(s)
- Sirio Dupont
- Department of Histology, Microbiology, and Medical Biotechnologies, University of Padua School of Medicine, viale Colombo 3, 35131 Padua, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Martello G, Zacchigna L, Inui M, Montagner M, Adorno M, Mamidi A, Morsut L, Soligo S, Tran U, Dupont S, Cordenonsi M, Wessely O, Piccolo S. MicroRNA control of Nodal signalling. Nature 2007; 449:183-8. [PMID: 17728715 DOI: 10.1038/nature06100] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 07/18/2007] [Indexed: 01/29/2023]
Abstract
MicroRNAs are crucial modulators of gene expression, yet their involvement as effectors of growth factor signalling is largely unknown. Ligands of the transforming growth factor-beta superfamily are essential for development and adult tissue homeostasis. In early Xenopus embryos, signalling by the transforming growth factor-beta ligand Nodal is crucial for the dorsal induction of the Spemann's organizer. Here we report that Xenopus laevis microRNAs miR-15 and miR-16 restrict the size of the organizer by targeting the Nodal type II receptor Acvr2a. Endogenous miR-15 and miR-16 are ventrally enriched as they are negatively regulated by the dorsal Wnt/beta-catenin pathway. These findings exemplify the relevance of microRNAs as regulators of early embryonic patterning acting at the crossroads of fundamental signalling cascades.
Collapse
Affiliation(s)
- Graziano Martello
- Department of Histology, Microbiology and Medical Biotechnologies, Section of Histology and Embryology, University of Padua, viale Colombo 3, 35126 Padua, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Cordenonsi M, Montagner M, Adorno M, Zacchigna L, Martello G, Mamidi A, Soligo S, Dupont S, Piccolo S. Integration of TGF-beta and Ras/MAPK signaling through p53 phosphorylation. Science 2007; 315:840-3. [PMID: 17234915 DOI: 10.1126/science.1135961] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
During development and tissue homeostasis, cells must integrate different signals. We investigated how cell behavior is controlled by the combined activity of transforming growth factor-beta (TGF-beta) and receptor tyrosine kinase (RTK) signaling, whose integration mechanism is unknown. We find that RTK/Ras/MAPK (mitogen-activated protein kinase) activity induces p53 N-terminal phosphorylation, enabling the interaction of p53 with the TGF-beta-activated Smads. This mechanism confines mesoderm specification in Xenopus embryos and promotes TGF-beta cytostasis in human cells. These data indicate a mechanism to allow extracellular cues to specify the TGF-beta gene-expression program.
Collapse
Affiliation(s)
- Michelangelo Cordenonsi
- Department of Medical Biotechnologies, Section of Histology and Embryology, University of Padua, Padua, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
A 65-year-old patient with a chief complaint of syncope had an ECG with ventricular preexcitation and intermittent second-degree atrioventricular (AV) block. AV conduction was maintained by the accessory pathway only, with no evidence of AV nodal conduction. Electrophysiological study demonstrated that the QRS duration and morphology did not increase with atrial pacing; however, A-H prolongation occurred with increased pacing rates.
Collapse
Affiliation(s)
- E Mossuti
- Divisione di Cardiologia, Ospedale Umberto I, Siracusa, Italy
| | | | | | | |
Collapse
|
37
|
Marconi G, Labate M, Pappalettera N, Martello G, Tamburrino G. [Chronobiologic resolution of disabling pathologies in shift workers]. Minerva Med 1985; 76:937-40. [PMID: 4000533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The annual sequence of sickness leaves was studied in 162 industrial workers with a high absenteeism level. An investigation of the swings in haemodynamic balance, and imbalances linked to alternations in vessel constriction and dilation throughout the biorhythmic cycle influenced by the alternation of night and day, hot and cold seasons, showed that each period of sick leave coincided with each period of haemodynamic balance caused by particular shifts. It was thus possible to identify groups of workers with syndromic sub groups whose performance was affected by night work and particular seasons. For optimal shift-worker deployment it is therefore suggested that workers should be assigned to shifts to which they are biologically suited.
Collapse
|
38
|
Negro R, Mossuti E, Sicuso G, Martello G, Elia F, Russo L. [Evaluation of subhisian conduction reserve]. Minerva Cardioangiol 1984; 32:355-60. [PMID: 6472633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
39
|
Mossuti E, Rapisarda A, Elia F, Martello G, Maltese B, Negro R. [Conduction disorder caused by conjunctival instillation of timolol. Description of a case]. G Ital Cardiol 1983; 13:125-7. [PMID: 6653957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report the case of a 46-year-old man, in whom A-V node electrophysiologic properties was worsened after therapeutic conjunctival instillation of timolol. We suggest that periodic, careful controls of the AV conduction are warranted in patients taking ocular hypertensive chronic timolol therapy.
Collapse
|
40
|
Trovato GM, Caruso G, Dammino ML, Martello G, Milone A, Vancheri FS, Cappuccio A. Juvenile hypertension epidemiology. Panminerva Med 1980; 22:219-21. [PMID: 7232021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
41
|
Caruso G, Martello G, Trovato GM, Vancheri FS. [Epidemiological, diagnostic and therapeutic aspects of hypertension in adolescence]. Recenti Prog Med 1979; 67:443-62. [PMID: 42954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
42
|
Martello G, Mattioli D, Balbo G. [On a case of probable Mediterranean eruptive fever]. G Mal Infett Parassit 1970; 22:383. [PMID: 5459590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|