Publications by authors named "George Q Daley"

325 Publications

LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells.

Protein Cell 2021 Jul 31. Epub 2021 Jul 31.

Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.

LIN28 is an RNA binding protein with important roles in early embryo development, stem cell differentiation/reprogramming, tumorigenesis and metabolism. Previous studies have focused mainly on its role in the cytosol where it interacts with Let-7 microRNA precursors or mRNAs, and few have addressed LIN28's role within the nucleus. Here, we show that LIN28 displays dynamic temporal and spatial expression during murine embryo development. Maternal LIN28 expression drops upon exit from the 2-cell stage, and zygotic LIN28 protein is induced at the forming nucleolus during 4-cell to blastocyst stage development, to become dominantly expressed in the cytosol after implantation. In cultured pluripotent stem cells (PSCs), loss of LIN28 led to nucleolar stress and activation of a 2-cell/4-cell-like transcriptional program characterized by the expression of endogenous retrovirus genes. Mechanistically, LIN28 binds to small nucleolar RNAs and rRNA to maintain nucleolar integrity, and its loss leads to nucleolar phase separation defects, ribosomal stress and activation of P53 which in turn binds to and activates 2C transcription factor Dux. LIN28 also resides in a complex containing the nucleolar factor Nucleolin (NCL) and the transcriptional repressor TRIM28, and LIN28 loss leads to reduced occupancy of the NCL/TRIM28 complex on the Dux and rDNA loci, and thus de-repressed Dux and reduced rRNA expression. Lin28 knockout cells with nucleolar stress are more likely to assume a slowly cycling, translationally inert and anabolically inactive state, which is a part of previously unappreciated 2C-like transcriptional program. These findings elucidate novel roles for nucleolar LIN28 in PSCs, and a new mechanism linking 2C program and nucleolar functions in PSCs and early embryo development.
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http://dx.doi.org/10.1007/s13238-021-00864-5DOI Listing
July 2021

Lin28 paralogs regulate lung branching morphogenesis.

Cell Rep 2021 Jul;36(3):109408

Division of Pediatric Hematology/Oncology, Boston Children's Hospital Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

The molecular mechanisms that govern the choreographed timing of organ development remain poorly understood. Our investigation of the role of the Lin28a and Lin28b paralogs during the developmental process of branching morphogenesis establishes that dysregulation of Lin28a/b leads to abnormal branching morphogenesis in the lung and other tissues. Additionally, we find that the Lin28 paralogs, which regulate post-transcriptional processing of both mRNAs and microRNAs (miRNAs), predominantly control mRNAs during the initial phases of lung organogenesis. Target mRNAs include Sox2, Sox9, and Etv5, which coordinate lung development and differentiation. Moreover, we find that functional interactions between Lin28a and Sox9 are capable of bypassing branching defects in Lin28a/b mutant lungs. Here, we identify Lin28a and Lin28b as regulators of early embryonic lung development, highlighting the importance of the timing of post-transcriptional regulation of both miRNAs and mRNAs at distinct stages of organogenesis.
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http://dx.doi.org/10.1016/j.celrep.2021.109408DOI Listing
July 2021

Sequential regulation of hemogenic fate and hematopoietic stem and progenitor cell formation from arterial endothelium by Ezh1/2.

Stem Cell Reports 2021 Jul 17;16(7):1718-1734. Epub 2021 Jun 17.

Stem Cell Program, Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

Across species, hematopoietic stem and progenitor cells (HSPCs) arise during embryogenesis from a specialized arterial population, termed hemogenic endothelium. Here, we describe a mechanistic role for the epigenetic regulator, Enhancer of zeste homolog-1 (Ezh1), in vertebrate HSPC production via regulation of hemogenic commitment. Loss of ezh1 in zebrafish embryos favored acquisition of hemogenic (gata2b) and HSPC (runx1) fate at the expense of the arterial program (ephrinb2a, dll4). In contrast, ezh1 overexpression blocked hematopoietic progression via maintenance of arterial gene expression. The related Polycomb group subunit, Ezh2, functioned in a non-redundant, sequential manner, whereby inhibition had no impact on arterial identity, but was capable of blocking ezh1-knockdown-associated HSPC expansion. Single-cell RNA sequencing across ezh1 genotypes revealed a dropout of ezh1 cells among arterial endothelium associated with positive regulation of gene transcription. Exploitation of Ezh1/2 modulation has potential functional relevance for improving in vitro HSPC differentiation from induced pluripotent stem cell sources.
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http://dx.doi.org/10.1016/j.stemcr.2021.05.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8282472PMC
July 2021

ISSCR Guidelines for Stem Cell Research and Clinical Translation: The 2021 update.

Stem Cell Reports 2021 Jun 27;16(6):1398-1408. Epub 2021 May 27.

Histogen, San Diego, CA, USA.

The International Society for Stem Cell Research has updated its Guidelines for Stem Cell Research and Clinical Translation in order to address advances in stem cell science and other relevant fields, together with the associated ethical, social, and policy issues that have arisen since the last update in 2016. While growing to encompass the evolving science, clinical applications of stem cells, and the increasingly complex implications of stem cell research for society, the basic principles underlying the Guidelines remain unchanged, and they will continue to serve as the standard for the field and as a resource for scientists, regulators, funders, physicians, and members of the public, including patients. A summary of the key updates and issues is presented here.
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http://dx.doi.org/10.1016/j.stemcr.2021.05.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190668PMC
June 2021

Calmodulin inhibitors improve erythropoiesis in Diamond-Blackfan anemia.

Sci Transl Med 2020 10;12(566)

Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.

Diamond-Blackfan anemia (DBA) is a rare hematopoietic disease characterized by a block in red cell differentiation. Most DBA cases are caused by mutations in ribosomal proteins and characterized by higher than normal activity of the tumor suppressor p53. Higher p53 activity is thought to contribute to DBA phenotypes by inducing apoptosis during red blood cell differentiation. Currently, there are few therapies available for patients with DBA. We performed a chemical screen using zebrafish ribosomal small subunit protein 29 () mutant embryos that have a p53-dependent anemia and identified calmodulin inhibitors that rescued the phenotype. Our studies demonstrated that calmodulin inhibitors attenuated p53 protein amount and activity. Treatment with calmodulin inhibitors led to decreased p53 translation and accumulation but does not affect p53 stability. A U.S. Food and Drug Administration-approved calmodulin inhibitor, trifluoperazine, rescued hematopoietic phenotypes of DBA models in vivo in zebrafish and mouse models. In addition, trifluoperazine rescued these phenotypes in human CD34 hematopoietic stem and progenitor cells. Erythroid differentiation was also improved in CD34 cells isolated from a patient with DBA. This work uncovers a potential avenue of therapeutic development for patients with DBA.
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http://dx.doi.org/10.1126/scitranslmed.abb5831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709865PMC
October 2020

Mitochondrial and Redox Modifications in Huntington Disease Induced Pluripotent Stem Cells Rescued by CRISPR/Cas9 CAGs Targeting.

Front Cell Dev Biol 2020 22;8:576592. Epub 2020 Sep 22.

CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.

Mitochondrial deregulation has gained increasing support as a pathological mechanism in Huntington's disease (HD), a genetic-based neurodegenerative disorder caused by CAG expansion in the gene. In this study, we thoroughly investigated mitochondrial-based mechanisms in HD patient-derived iPSC (HD-iPSC) and differentiated neural stem cells (NSC) control cells, as well as in cells subjected to CRISPR/Cas9-CAG repeat deletion. We analyzed mitochondrial morphology, function and biogenesis, linked to exosomal release of mitochondrial components, glycolytic flux, ATP generation and cellular redox status. Mitochondria in HD cells exhibited round shape and fragmented morphology. Functionally, HD-iPSC and HD-NSC displayed lower mitochondrial respiration, exosomal release of cytochrome c, decreased ATP/ADP, reduced PGC-1α and complex III subunit expression and activity, and were highly dependent on glycolysis, supported by pyruvate dehydrogenase (PDH) inactivation. HD-iPSC and HD-NSC mitochondria showed ATP synthase reversal and increased calcium retention. Enhanced mitochondrial reactive oxygen species (ROS) were also observed in HD-iPSC and HD-NSC, along with decreased UCP2 mRNA levels. CRISPR/Cas9-CAG repeat deletion in HD-iPSC and derived HD-NSC ameliorated mitochondrial phenotypes. Data attests for intricate metabolic and mitochondrial dysfunction linked to transcriptional deregulation as early events in HD pathogenesis, which are alleviated following CAG deletion.
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http://dx.doi.org/10.3389/fcell.2020.576592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536317PMC
September 2020

An induced pluripotent stem cell model of Fanconi anemia reveals mechanisms of p53-driven progenitor cell differentiation.

Blood Adv 2020 10;4(19):4679-4692

Stem Cell Program, Boston Children's Hospital, Boston, MA.

Fanconi anemia (FA) is a disorder of DNA repair that manifests as bone marrow (BM) failure. The lack of accurate murine models of FA has refocused efforts toward differentiation of patient-derived induced pluripotent stem cells (IPSCs) to hematopoietic progenitor cells (HPCs). However, an intact FA DNA repair pathway is required for efficient IPSC derivation, hindering these efforts. To overcome this barrier, we used inducible complementation of FANCA-deficient IPSCs, which permitted robust maintenance of IPSCs. Modulation of FANCA during directed differentiation to HPCs enabled the production of FANCA-deficient human HPCs that recapitulated FA genotoxicity and hematopoietic phenotypes relative to isogenic FANCA-expressing HPCs. FANCA-deficient human HPCs underwent accelerated terminal differentiation driven by activation of p53/p21. We identified growth arrest specific 6 (GAS6) as a novel target of activated p53 in FANCA-deficient HPCs and modulate GAS6 signaling to rescue hematopoiesis in FANCA-deficient cells. This study validates our strategy to derive a sustainable, highly faithful human model of FA, uncovers a mechanism of HPC exhaustion in FA, and advances toward future cell therapy in FA.
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http://dx.doi.org/10.1182/bloodadvances.2020001593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7556119PMC
October 2020

COVID Highlights Another Crisis: Lack of Black Physicians and Scientists.

Med (N Y) 2021 Jan 24;2(1):2-3. Epub 2020 Jun 24.

Connecticut Convergence Institute for Translation in Regenerative Engineering, University of Connecticut Health Center, Farmington, CT 06030, USA.

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http://dx.doi.org/10.1016/j.medj.2020.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311898PMC
January 2021

Metabolic Regulation of Inflammasome Activity Controls Embryonic Hematopoietic Stem and Progenitor Cell Production.

Dev Cell 2020 10 17;55(2):133-149.e6. Epub 2020 Aug 17.

Stem Cell Program, Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA. Electronic address:

Embryonic hematopoietic stem and progenitor cells (HSPCs) robustly proliferate while maintaining multilineage potential in vivo; however, an incomplete understanding of spatiotemporal cues governing their generation has impeded robust production from human induced pluripotent stem cells (iPSCs) in vitro. Using the zebrafish model, we demonstrate that NLRP3 inflammasome-mediated interleukin-1-beta (IL1β) signaling drives HSPC production in response to metabolic activity. Genetic induction of active IL1β or pharmacologic inflammasome stimulation increased HSPC number as assessed by in situ hybridization for runx1/cmyb and flow cytometry. Loss of inflammasome components, including il1b, reduced CD41 HSPCs and prevented their expansion in response to metabolic cues. Cell ablation studies indicated that macrophages were essential for initial inflammasome stimulation of Il1rl1 HSPCs. Significantly, in human iPSC-derived hemogenic precursors, transient inflammasome stimulation increased multilineage hematopoietic colony-forming units and T cell progenitors. This work establishes the inflammasome as a conserved metabolic sensor that expands HSPC production in vivo and in vitro.
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http://dx.doi.org/10.1016/j.devcel.2020.07.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8008739PMC
October 2020

Pancreatic circulating tumor cell profiling identifies LIN28B as a metastasis driver and drug target.

Nat Commun 2020 07 3;11(1):3303. Epub 2020 Jul 3.

Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02114, USA.

Pancreatic ductal adenocarcinoma (PDAC) lethality is due to metastatic dissemination. Characterization of rare, heterogeneous circulating tumor cells (CTCs) can provide insight into metastasis and guide development of novel therapies. Using the CTC-iChip to purify CTCs from PDAC patients for RNA-seq characterization, we identify three major correlated gene sets, with stemness genes LIN28B/KLF4, WNT5A, and LGALS3 enriched in each correlated gene set; only LIN28B CTC expression was prognostic. CRISPR knockout of LIN28B-an oncofetal RNA-binding protein exerting diverse effects via negative regulation of let-7 miRNAs and other RNA targets-in cell and animal models confers a less aggressive/metastatic phenotype. This correlates with de-repression of let-7 miRNAs and is mimicked by silencing of downstream let-7 target HMGA2 or chemical inhibition of LIN28B/let-7 binding. Molecular characterization of CTCs provides a unique opportunity to correlated gene set metastatic profiles, identify drivers of dissemination, and develop therapies targeting the "seeds" of metastasis.
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http://dx.doi.org/10.1038/s41467-020-17150-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7335061PMC
July 2020

LIN28B regulates transcription and potentiates MYCN-induced neuroblastoma through binding to ZNF143 at target gene promotors.

Proc Natl Acad Sci U S A 2020 07 29;117(28):16516-16526. Epub 2020 Jun 29.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215;

LIN28B is highly expressed in neuroblastoma and promotes tumorigenesis, at least, in part, through inhibition of microRNA biogenesis. Here, we report that overexpression of either wild-type (WT) LIN28B or a LIN28B mutant that is unable to inhibit processing increases the penetrance of MYCN-induced neuroblastoma, potentiates the invasion and migration of transformed sympathetic neuroblasts, and drives distant metastases in vivo. Genome-wide chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) and coimmunoprecipitation experiments show that LIN28B binds active gene promoters in neuroblastoma cells through protein-protein interaction with the sequence-specific zinc-finger transcription factor ZNF143 and activates the expression of downstream targets, including transcription factors forming the adrenergic core regulatory circuitry that controls the malignant cell state in neuroblastoma as well as and that are involved in neuronal cell adhesion and migration. These findings reveal an unexpected -independent function of LIN28B in transcriptional regulation during neuroblastoma pathogenesis.
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http://dx.doi.org/10.1073/pnas.1922692117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368283PMC
July 2020

Oral health care in the 21st century: It is time for the integration of dental and medical education.

J Dent Educ 2020 Sep 20;84(9):999-1002. Epub 2020 May 20.

Faculty of Medicine, Harvard Medical School, Boston, Massachusetts, USA.

Major issues exist in the provision of oral health care in America, especially to underserved populations. Access to care, health disparities, an aging population with higher chronic disease burden, and rising healthcare costs continue to impact health outcomes for millions. The marginalization of oral health care, like that of behavioral health care, is a contributor. This perspective presents an idea whose time has come: putting the mouth back in the body. Several national reports stress the imperative to better integrate the practice of medicine and dentistry, including the first-ever Surgeon General's Report on Oral Health in 2000. A plan to lead a multifaceted integration of oral health into overall health is proposed. Leaders will come from new educational and practice models stressing teamwork, interprofessional education, innovative residency training programs and even dual degree options.
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http://dx.doi.org/10.1002/jdd.12191DOI Listing
September 2020

Transcriptome Dynamics of Hematopoietic Stem Cell Formation Revealed Using a Combinatorial Runx1 and Ly6a Reporter System.

Stem Cell Reports 2020 05 16;14(5):956-971. Epub 2020 Apr 16.

Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Stem Cell Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Boston, MA, USA. Electronic address:

Studies of hematopoietic stem cell (HSC) development from pre-HSC-producing hemogenic endothelial cells (HECs) are hampered by the rarity of these cells and the presence of other cell types with overlapping marker expression profiles. We generated a Tg(Runx1-mKO2; Ly6a-GFP) dual reporter mouse to visualize hematopoietic commitment and study pre-HSC emergence and maturation. Runx1-mKO2 marked all intra-arterial HECs and hematopoietic cluster cells (HCCs), including pre-HSCs, myeloid- and lymphoid progenitors, and HSCs themselves. However, HSC and lymphoid potential were almost exclusively found in reporter double-positive (DP) cells. Robust HSC activity was first detected in DP cells of the placenta, reflecting the importance of this niche for (pre-)HSC maturation and expansion before the fetal liver stage. A time course analysis by single-cell RNA sequencing revealed that as pre-HSCs mature into fetal liver stage HSCs, they show signs of interferon exposure, exhibit signatures of multi-lineage differentiation gene expression, and develop a prolonged cell cycle reminiscent of quiescent adult HSCs.
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http://dx.doi.org/10.1016/j.stemcr.2020.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7220988PMC
May 2020

The Toughest Triage - Allocating Ventilators in a Pandemic.

N Engl J Med 2020 May 23;382(21):1973-1975. Epub 2020 Mar 23.

From the Center for Bioethics (R.D.T., C.M.), the Department of Global Health and Social Medicine (R.D.T., C.M.), the Office of the Dean of the Faculty of Medicine (G.Q.D.), Harvard Medical School, and the Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children's Hospital (R.D.T.) - both in Boston.

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http://dx.doi.org/10.1056/NEJMp2005689DOI Listing
May 2020

Author Correction: Lin28 and let-7 regulate the timing of cessation of murine nephrogenesis.

Nat Commun 2020 Mar 9;11(1):1327. Epub 2020 Mar 9.

Division of Pediatric Hematology/Oncology, Children's Hospital Boston, Boston, MA, 02115, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41467-020-14944-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7062780PMC
March 2020

Introduction to the Special Issue on CRISPR.

Authors:
George Q Daley

Perspect Biol Med 2020 ;63(1):1-13

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http://dx.doi.org/10.1353/pbm.2020.0000DOI Listing
December 2020

A nanobody targeting the LIN28:let-7 interaction fragment of TUT4 blocks uridylation of let-7.

Proc Natl Acad Sci U S A 2020 03 14;117(9):4653-4663. Epub 2020 Feb 14.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;

The LIN28:pre-let-7:TUTase ternary complex regulates pluripotency and oncogenesis by controlling processing of the let-7 family of microRNAs. The complex oligouridylates the 3' ends of pre-let-7 molecules, leading to their degradation via the DIS3L2 exonuclease. Previous studies suggest that components of this complex are potential therapeutic targets in malignancies that aberrantly express LIN28. In this study we developed a functional epitope selection approach to identify nanobody inhibitors of the LIN28:pre-let-7:TUT4 complex. We demonstrate that one of the identified nanobodies, Nb-S2A4, targets the 106-residue LIN28:let-7 interaction (LLI) fragment of TUT4. Nb-S2A4 can effectively inhibit oligouridylation and monouridylation of pre-let-7g in vitro. Expressing Nb-S2A4 allows maturation of the let-7 species in cells expressing LIN28, highlighting the therapeutic potential of targeting the LLI fragment.
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http://dx.doi.org/10.1073/pnas.1919409117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060709PMC
March 2020

YAP Regulates Hematopoietic Stem Cell Formation in Response to the Biomechanical Forces of Blood Flow.

Dev Cell 2020 02 6;52(4):446-460.e5. Epub 2020 Feb 6.

Stem Cell Program, Division of Pediatric Hematology and Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

Hematopoietic stem and progenitor cells (HSPCs), first specified from hemogenic endothelium (HE) in the ventral dorsal aorta (VDA), support lifelong hematopoiesis. Their de novo production promises significant therapeutic value; however, current in vitro approaches cannot efficiently generate multipotent long-lived HSPCs. Presuming this reflects a lack of extrinsic cues normally impacting the VDA, we devised a human dorsal aorta-on-a-chip platform that identified Yes-activated protein (YAP) as a cyclic stretch-induced regulator of HSPC formation. In the zebrafish VDA, inducible Yap overexpression significantly increased runx1 expression in vivo and the number of CD41 HSPCs downstream of HE specification. Endogenous Yap activation by lats1/2 knockdown or Rho-GTPase stimulation mimicked Yap overexpression and induced HSPCs in embryos lacking blood flow. Notably, in static human induced pluripotent stem cell (iPSC)-derived HE culture, compound-mediated YAP activation enhanced RUNX1 levels and hematopoietic colony-forming potential. Together, our findings reveal a potent impact of hemodynamic Rho-YAP mechanotransduction on HE fate, relevant to de novo human HSPC production.
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http://dx.doi.org/10.1016/j.devcel.2020.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7398148PMC
February 2020

Author Correction: Epoxyeicosatrienoic acids enhance embryonic haematopoiesis and adult marrow engraftment.

Nature 2019 Sep;573(7772):E1

Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41586-019-1489-4DOI Listing
September 2019

Author Correction: A systems biology pipeline identifies regulatory networks for stem cell engineering.

Nat Biotechnol 2019 Aug;37(8):962

Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.

In the version of this article initially published, the second NIH grant "R24-DK49216" to author George Q. Daley contained an error. The grant number should have read U54DK110805. The error has been corrected in the HTML and PDF versions of the article.
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http://dx.doi.org/10.1038/s41587-019-0212-1DOI Listing
August 2019

A systems biology pipeline identifies regulatory networks for stem cell engineering.

Nat Biotechnol 2019 07 1;37(7):810-818. Epub 2019 Jul 1.

Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.

A major challenge for stem cell engineering is achieving a holistic understanding of the molecular networks and biological processes governing cell differentiation. To address this challenge, we describe a computational approach that combines gene expression analysis, previous knowledge from proteomic pathway informatics and cell signaling models to delineate key transitional states of differentiating cells at high resolution. Our network models connect sparse gene signatures with corresponding, yet disparate, biological processes to uncover molecular mechanisms governing cell fate transitions. This approach builds on our earlier CellNet and recent trajectory-defining algorithms, as illustrated by our analysis of hematopoietic specification along the erythroid lineage, which reveals a role for the EGF receptor family member, ErbB4, as an important mediator of blood development. We experimentally validate this prediction and perturb the pathway to improve erythroid maturation from human pluripotent stem cells. These results exploit an integrative systems perspective to identify new regulatory processes and nodes useful in cell engineering.
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http://dx.doi.org/10.1038/s41587-019-0159-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7235931PMC
July 2019

Stem Cells in the Treatment of Disease.

N Engl J Med 2019 05;380(18):1748-1760

From the Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA (H.M.B.); and the Department of Medicine, Harvard Medical School, Boston (G.Q.D.).

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http://dx.doi.org/10.1056/NEJMra1716145DOI Listing
May 2019

Induced pluripotent stem cells in disease modelling and drug discovery.

Nat Rev Genet 2019 07;20(7):377-388

Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.

The derivation of induced pluripotent stem cells (iPSCs) over a decade ago sparked widespread enthusiasm for the development of new models of human disease, enhanced platforms for drug discovery and more widespread use of autologous cell-based therapy. Early studies using directed differentiation of iPSCs frequently uncovered cell-level phenotypes in monogenic diseases, but translation to tissue-level and organ-level diseases has required development of more complex, 3D, multicellular systems. Organoids and human-rodent chimaeras more accurately mirror the diverse cellular ecosystems of complex tissues and are being applied to iPSC disease models to recapitulate the pathobiology of a broad spectrum of human maladies, including infectious diseases, genetic disorders and cancer.
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http://dx.doi.org/10.1038/s41576-019-0100-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584039PMC
July 2019

The developmental stage of the hematopoietic niche regulates lineage in rearranged leukemia.

J Exp Med 2019 03 6;216(3):527-538. Epub 2019 Feb 6.

Stem Cell Program, Boston Children's Hospital, Boston, MA

Leukemia phenotypes vary with age of onset. Delineating mechanisms of age specificity in leukemia could improve disease models and uncover new therapeutic approaches. Here, we used heterochronic transplantation of leukemia driven by / translocations to investigate the contribution of the age of the hematopoietic microenvironment to age-specific leukemia phenotypes. When driven by , leukemia cells in the adult microenvironment sustained a myeloid phenotype, whereas the neonatal microenvironment supported genesis of mixed early B cell/myeloid leukemia. In leukemia, the neonatal microenvironment potentiated B-lymphoid differentiation compared with the adult. Ccl5 elaborated from adult marrow stroma inhibited B-lymphoid differentiation of leukemia cells, illuminating a mechanism of age-specific lineage commitment. Our study illustrates the contribution of the developmental stage of the hematopoietic microenvironment in defining the age specificity of leukemia.
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http://dx.doi.org/10.1084/jem.20181765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400531PMC
March 2019

The Lin28/let-7 Pathway Regulates the Mammalian Caudal Body Axis Elongation Program.

Dev Cell 2019 02 17;48(3):396-405.e3. Epub 2019 Jan 17.

Division of Pediatric Hematology/Oncology, Children's Hospital Boston, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA. Electronic address:

The heterochronic genes Lin28a/b and let-7 regulate invertebrate development, but their functions in patterning the mammalian body plan remain unexplored. Here, we describe how Lin28/let-7 influence caudal vertebrae number during body axis formation. We found that FoxD1-driven overexpression of Lin28a strikingly increased caudal vertebrae number and tail bud cell proliferation, whereas its knockout did the opposite. Lin28a overexpression downregulated the neural marker Sox2, causing a pro-mesodermal phenotype with a decreased proportion of neural tissue relative to nascent mesoderm. Manipulating Lin28a and let-7 led to opposite effects, and manipulating Lin28a's paralog, LIN28B caused similar yet distinct phenotypes. These findings suggest that Lin28/let-7 play a role in the regulation of tail length through heterochrony of the body plan. We propose that the Lin28/let-7 pathway controls the pool of caudal progenitors during tail development, promoting their self-renewal and balancing neural versus mesodermal cell fate decisions.
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http://dx.doi.org/10.1016/j.devcel.2018.12.016DOI Listing
February 2019

After the Storm - A Responsible Path for Genome Editing.

N Engl J Med 2019 Mar 16;380(10):897-899. Epub 2019 Jan 16.

From Harvard Medical School, Boston (G.Q.D.); the Francis Crick Institute, London (R.L.-B.); and Université Paris Descartes, Imagine Inserm UMR1163, Service de Génétique Moléculaire, Hôpital Necker-Enfants Malades, Paris (J.S.).

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http://dx.doi.org/10.1056/NEJMp1900504DOI Listing
March 2019

Lin28 and let-7 regulate the timing of cessation of murine nephrogenesis.

Nat Commun 2019 01 11;10(1):168. Epub 2019 Jan 11.

Division of Pediatric Hematology/Oncology, Children's Hospital Boston, Boston, MA, 02115, USA.

In humans and in mice the formation of nephrons during embryonic development reaches completion near the end of gestation, after which no new nephrons are formed. The final nephron complement can vary 10-fold, with reduced nephron number predisposing individuals to hypertension, renal, and cardiovascular diseases in later life. While the heterochronic genes lin28 and let-7 are well-established regulators of developmental timing in invertebrates, their role in mammalian organogenesis is not fully understood. Here we report that the Lin28b/let-7 axis controls the duration of kidney development in mice. Suppression of let-7 miRNAs, directly or via the transient overexpression of LIN28B, can prolong nephrogenesis and enhance kidney function potentially via upregulation of the Igf2/H19 locus. In contrast, kidney-specific loss of Lin28b impairs renal development. Our study reveals mechanisms regulating persistence of nephrogenic mesenchyme and provides a rationale for therapies aimed at increasing nephron mass.
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http://dx.doi.org/10.1038/s41467-018-08127-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329821PMC
January 2019

regulates age-dependent differences in murine platelet function.

Blood Adv 2019 01;3(1):72-82

Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester Medical Center, Rochester NY.

Platelets are essential for hemostasis; however, several studies have identified age-dependent differences in platelet function. To better understand the origins of fetal platelet function, we have evaluated the contribution of the fetal-specific RNA binding protein in the megakaryocyte/platelet lineage. Because activated fetal platelets have very low levels of P-selectin, we hypothesized that the expression of platelet P-selectin is part of a fetal-specific hematopoietic program conferred by Lin28b. Using the mouse as a model, we find that activated fetal platelets have low levels of P-selectin and do not readily associate with granulocytes in vitro and in vivo, relative to adult controls. Transcriptional analysis revealed high levels of and in fetal, but not adult, megakaryocytes. Overexpression of in adult mice significantly reduces the expression of P-selectin in platelets, and therefore identifies as a negative regulator of P-selectin expression. Transplantation of fetal hematopoietic progenitors resulted in the production of platelets with low levels of P-selectin, suggesting that the developmental regulation of P-selectin is intrinsic and independent of differences between fetal and adult microenvironments. Last, we observe that the upregulation of P-selectin expression occurs postnatally, and the temporal kinetics of this upregulation are recapitulated by transplantation of fetal hematopoietic stem and progenitor cells into adult recipients. Taken together, these studies identify as a new intrinsic regulator of fetal platelet function.
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http://dx.doi.org/10.1182/bloodadvances.2018020859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325299PMC
January 2019

Retraction Note: NF-κB activation impairs somatic cell reprogramming in ageing.

Nat Cell Biol 2019 Mar;21(3):410

Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006, Oviedo, Spain.

We, the authors, are retracting this Article due to issues that have come to our attention regarding data availability, data description and figure assembly. Specifically, original numerical data are not available for the majority of the graphs presented in the paper. Although original data were available for most EMSA and immunoblot experiments, those corresponding to the published EMSA data of Supplementary Fig. 8a, the independent replicate immunoblots of Fig. 8b and Supplementary Fig. 1e, and the independent replicate EMSA data of Supplementary Figs 6e, 8b, 8c and 8d, are unavailable. Mistakes were detected in the presentation of Figs 3c, 4i and Supplementary Figs 6a, 8a, 8d, 9, and in some cases the β-actin immunoblots were erroneously described in the figure legends as loading controls, rather than as sample processing controls that were run on separate gels. Although we, the authors, believe that the key findings of the paper are still valid, given the issues with data availability we have concluded that the most appropriate course of action is to retract the Article. We deeply regret these errors and apologize to the scientific community for any confusion this publication may have caused. All authors agree with the retraction.
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http://dx.doi.org/10.1038/s41556-018-0259-0DOI Listing
March 2019

Small-Molecule Inhibitors Disrupt let-7 Oligouridylation and Release the Selective Blockade of let-7 Processing by LIN28.

Cell Rep 2018 06;23(10):3091-3101

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA. Electronic address:

LIN28 is an RNA-binding protein that regulates the maturation of the let-7 family of microRNAs by bipartite interactions with let-7 precursors through its two distinct cold shock and zinc-knuckle domains. Through inhibition of let-7 biogenesis, LIN28 functions as a pluripotency factor, as well as a driver of tumorigenesis. Here, we report a fluorescence polarization assay to identify small-molecule inhibitors for both domains of LIN28 involved in let-7 interactions. Of 101,017 compounds screened, six inhibit LIN28:let-7 binding and impair LIN28-mediated let-7 oligouridylation. Upon further characterization, we demonstrate that the LIN28 inhibitor TPEN destabilizes the zinc-knuckle domain of LIN28, while LI71 binds the cold shock domain to suppress LIN28's activity against let-7 in leukemia cells and embryonic stem cells. Our results demonstrate selective pharmacologic inhibition of individual domains of LIN28 and provide a foundation for therapeutic inhibition of the let-7 biogenesis pathway in LIN28-driven diseases.
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http://dx.doi.org/10.1016/j.celrep.2018.04.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511231PMC
June 2018
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