Stem Cell Collection 2020 Why Submit Your Research?

STEM CELL COLLECTION 2020 WHY SUBMIT YOUR RESEARCH?

AN EDITORIAL PROCESS GUIDED EDITORS FROM THE BY YOUR COMMUNITY STEM CELL RESEARCH COMMUNITY At Journal of Cell Biology (JCB) and Journal of Experimental Medicine (JEM), all editorial decisions on research manuscripts are made through collaborative consultation between JCB professional scientific editors and the academic editorial board. Elaine Fuchs Ana Pombo Carien Niessen Juergen Knoblich Cedric Blanpain Submission or transfer Academic and scientific Michael Rudnicki editors review Thomas Rando Yukiko Gotoh

JEM If appropriate, sent to Academic and scientific Informed decisions peer review editors review comments sent to authors Emmanuelle Passegue Elaine Dzierzak Paul Frenette Margaret (Peggy) Goodell Bertie Gottgens Revised manuscript Academic and scientific 97% of invited revisions submission and rereview editors review accepted at JCB and Hanna Mikkola 92% at JEM.* Sean J. Morrison Ulrich Steidl Leonard Zon Patricia Ernst Published online 1-2 days after Circulated via alerts and social media Toshio Suda author proofs returned to readers around the world

*Median 2019

Format Neutral Transfer Policy Fair and Fast Open Access Options You may submit We welcome submissions that include We limit rounds of revision, and Our options include your papers in reviewer comments from another journal. You we strive to provide clear, detailed Immediate Open Access ANY format. may also request manuscript transfer between decisions that illustrate what is (CC-BY) and open access Rockefeller University Press journals, and we expected in the revisions. Articles six months after publication can confidentially send reviewer reports and appear online one to two days (CC-BY-NC-SA). identities to another journal beyond RUP. after author proofs are returned.

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ournal of Cell Biology (JCB) and Journal of Experimental Medicine (JEM) editors are delighted to present this selection of recent, cutting-edge stem cell research. JCB publishes new cellular and molecular advances in any area of basic cell biology as well as papers that describe applied cell biology to translational fields such as stem cells. JEM is interested Jin original findings on all aspects of disease pathogenesis, including both hematopoietic stem cell and non-hematopoietic stem cell physiopathology. This collection includes some of our most highly read papers and articles selected to reflect the breadth of stem cell research published in our journals. We hope you enjoy these articles that delve into the cell biology of regeneration, stem cell division, fate decision, and their links to various diseases and innovative therapies.

Visit jcb.org and jem.org to learn about our editorial policies and members of our editorial boards. We welcome your feedback and questions via Twitter (@JCellBiol and @JExpMed). You can also email JCB at jcellbiol@rockefeller. edu and JEM at [email protected] (regarding general stem cell studies) and [email protected] (for studies with a cancer research angle).

6 Myc regulates retinal regeneration Study identifies multiple roles for Myc in controlling the induction and proliferation of Muller glia–derived progenitor cells upon retinal injury in zebrafish Soumitra Mitra … Rajesh Ramachandran

7 The RNA exosome restrains hESC differentiation The nuclease complex degrades a variety of RNAs to maintain pluripotency and suppress the differentiation of human embryonic stem cells Cedric Belair … Sandra L. Wolin

8 Hair follicles restrict cancer growth Normal skin corrals cancer-causing mutations and reveals how tissue can subvert tumorigenesis Cristiana M. Pineda … Valentina Greco

9 Centromeres drive asymmetric stem cell division Asymmetric incorporation of the centromeric histone CENP-A during G2/M regulates the fate of Drosophila female germline stem cells Anna Ada Dattoli … Elaine M. Dunleavy

10 NCAM regulates neural progenitor cell fate Neural cell adhesion molecule controls the proliferation and differentiation of cortical progenitors by binding to the actin polymerization regulator profilin2 Rui Huang, De-Juan Yuan, Shao Li … Quan-Hong Ma, Quan-Hong Ma

11 Glutamylation regulates HSC self-renewal Reversible modification of the tumor suppressor BAP1 controls hematopoietic stem cell self-renewal and blood cell formation Zhen Xiong, Pengyan Xia, Xiaoxiao Zhu … Yong Tian, Zusen Fan

12 The chromatin landscape of glioblastoma Profiling of glioblastoma stem cells and primary tumor samples identifies subgroup-specific transcriptional regulatory circuits and novel therapeutic targets Stephen C. Mack, Irtisha Singh, Xiuxing Wang … Charles Y. Lin, Jeremy N. Rich

13 Primitive HSCs continue cycling into adulthood Brochure articles: Ben Short, PhD and Study reveals that, contrary to a previous report, the most primitive hematopoietic stem cells do not become permanently quiescent and, instead, show continuous mitotic activity in adult mice Christina Szalinski, PhD Mina N.F. Morcos, Thomas Zerjatke ... Alexander Gerbaulet Design: Christine Candia 14 Distinguishing physiologic and oncogenic Wnt signals On the cover: Two-photon images of Profiling of isogenic human colon organoids reveals differences between oncogenic Wnt activation and normal Wnt HrasG12V/+ hair follicles during the “second rest signaling essential for stem cell maintenance phase” (P55). Mosaic activation of Hras using lentiviral-Cre delivery demonstrates that wild- Birgitta E. Michels, Mohammed H. Mosa … Henner F. Farin type follicles (green) within the HrasG12V/+ skin reenter the growth phase precociously along 15 Leukemia hijacks myeloid regeneration pathways with their Hras mutant (red) neighbors. Image Correcting aberrant Notch and Wnt signaling in leukemic stem cells might normalize myeloid cell production in a © 2019 Pineda et al. Read “Hair follicles restrict number of different leukemias cancer growth,” page 8. Yoon-A Kang, Eric M. Pietras, Emmanuelle Passegué 3 Editor-In-Chief Editorial Board Jodi Nunnari John Aitchison Rebecca Heald Elior Peles Executive Editor Johan Auwerx Martin Hetzer Will Prinz Tim Spencer Manuela Baccarini Erika Holzbaur Thomas Rando email: [email protected] Tamas Balla Martin Humphries Samara Reck-Peterson Editors Maureen Barr James Hurley Daniel B. Rifkin Arshad Desai Bill Bement Fumiyo Ikeda Michael Rout Pier Paolo Di Fiore Vann Bennett Luisa Iruela-Arispe Craig Roy Elaine Fuchs Dominique Bergmann Nancy Ip Michael Rudnicki Anna Huttenlocher Monica Bettencourt-Dias Johanna Ivaska Erik Sahai Ian Macara Joerg Bewersdorf Tarun Kapoor Martin Schwartz Ira Mellman Magdalena Bezanilla Gerard Karsenty Shu-ou Shan Ana Pombo Cédric Blanpain Scott Keeney Andrey Shaw Louis F. Reichardt Julius Brennecke Alexey Khodjakov Zu-Hang Sheng Kenneth M. Yamada Tony Bretscher Hiroshi Kimura Agata Smogorzewska Richard Youle Marianne Bronner Jürgen Knoblich Joan Steitz Valérie Castellani Alberto R. Kornblihtt Harald Stenmark Senior Scientific Editor Daniela Cimini Thomas Langer Aaron Straight Melina Casadio Karlene Cimprich Ana Maria Lennon-Dumenil Maria-Elena Torres-Padilla email: [email protected] Don W. Cleveland Andres Leschziner Billy Tsai Scientific Editor, Reviews Nika Danial Danny Lew Bas van Steensel Andrea Marat William Earnshaw Jens Lykke-Andersen Patrik Verstreken email: [email protected] Jan Ellenberg Vivek Malhotra Mark von Zastrow Scientific Editors Scott Emr Brendan Manning Erwin Wagner Marie Anne O'Donnell Anne Ephrussi Joan Massague John Wallingford email: [email protected] Jeffrey Esko Satyajit Mayor Tobias Walther Dan Simon Sandrine Etienne-Manneville Frauke Melchior Xiaochen Wang email:[email protected] Marc Freeman Tobias Meyer Lois Weisman Managing Editor Judith Frydman Liz Miller Min Wu Lindsey Hollander Hironori Funabiki Alex Mogilner Tim Yen Phone: 212-327-8588 email: [email protected] Melissa Gardner Sean Munro Tamotsu Yoshimori Larry Gerace Maxence Nachury Li Yu David Gilbert Karla Neugebauer Xiang Yu Bruce Goode Carien Niessen Junying Yuan Yukiko Gotoh Eva Nogales Marino Zerial Roger Greenberg Karen Oegema Hong Zhang Marcia Haigis Ewa Paluch Yixian Zheng Ulrich Hartl Mark Peifer

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Compared with humans and other ation of many cell types to form induced mammals, zebrafish have a much pluripotent stem cells. greater capacity to regenerate dam- aged tissues after injury. Damage to the Mitra et al. found that, upon retinal injury, zebrafish retina, for example, causes the two zebrafish Myc genes, myca Muller glial cells to dedifferentiate into and mycb, were rapidly induced in both multipotent progenitor cells that prolif- Muller glia-derived progenitor cells (MG- erate and eventually redifferentiate into PCs) and neighboring cells at the injury many different retinal cell types, thereby site. Knocking down or inhibiting Myc Four days after injury, the number enabling the tissue’s regeneration. impaired the dedifferentiation of Muller of proliferative MGPCs (labeled glia into MGPCs and blocked MGPC with GFP, green, and PCNA, red) is Muller glia with some stem cell–like proliferation and retinal regeneration. reduced in a zebrafish retina treated characteristics have been identified in with 10058-F4, a drug that inhibits mammalian retina, but their regener- The researchers found that mycb pro- the interaction between Myc and its ative capacity appears to be limited. motes the generation and proliferation obligatory transcriptional partner Max. “Unraveling the complete cascade of of MGPCs by inducing the expression of Credit: Mitra et al., 2019 gene regulatory networks induced by ascl1a, leading, in turn, to the production retina injury in zebrafish could help in of lin28a. (This gene regulatory cascade deciphering the lack of efficient regen- is tightly controlled: while Ascl1a feeds Though the precise details remain to eration in mammals,” explains Rajesh back to promote further mycb expression, be determined, Mycb therefore func- Ramachandran from the Indian Institute another transcriptional target of Ascl1a, tions as both a transcriptional activator of Science Education and Research in Insm1a, represses mycb). and repressor to finetune the extent of Mohali. In neighboring cells, however, Mycb lin28a expression and MGPC formation in response to retinal injury. Ramachandran has previously identified recruits the histone deacetylase Hdac1 important roles for several factors in to repress the lin28a promoter and limit “Our study suggests that Mycs are part Muller glia dedifferentiation and retinal lin28a expression. This may help prevent of a gene regulatory network essential regeneration, such as the transcriptional MGPCs from forming throughout the ret- for retina regeneration, and provides activator Ascl1a and one of its targets, ina and restrict their appearance to the insights that could ultimately help lin28a. In their latest study, Ramach- immediate site of injury. The researchers improve Muller glia reprogramming in andran and colleagues, including first found that Notch signaling plays a key injured human retina and enable suc- author Soumitra Mitra, investigated a role in this restriction by inducing the ex- cessful repair,” Ramachandran says. potential role for the transcription factor pression of an effector called her4.1 (itself Myc, which, among many biological a target for Mycb and Hdac1). functions, can promote the dedifferenti-

RESEARCHER DETAILS ORIGINAL PAPER Mitra, S., P. Sharma, S. Kaur, M.A. Khursheed, S. Gupta, M. Chaudhary, A.J. Kurup, and R. Ramachandran. 2019. Dual regulation of lin28a by Myc is necessary during zebrafish retina regeneration. J. Cell Biol. 218:489–507. https://doi.org/10.1083/jcb.201802113

Soumitra Mitra Rajesh Ramachandran Graduate student Associate Professor IISER Mohali IISER Mohali [email protected] 6 THE RNA EXOSOME RESTRAINS HESC DIFFERENTIATION The nuclease complex degrades a variety of RNAs to maintain pluripotency and suppress the differentiation of human embryonic stem cells

Human embryonic stem cells (hESCs) EXOSC3-deficient hESCs expressed can differentiate into all three embryon- increased levels of endodermal, me- ic germ layers: the endoderm, meso- sodermal, and ectodermal markers, derm, and ectoderm. This pluripotent suggesting that loss of the RNA exo- state is maintained by a network of some expedites hESC differentiation transcriptional regulators and epigene- into all three germ layers. Accordingly, tic factors that allow the cells to self-re- the researchers found, wild-type hESCs new indefinitely while remaining poised downregulate several subunits of the to differentiate rapidly when required. nuclease complex during differentiation. For example, the chromatin in hESCs Conversely, differentiated cells upreg- is in a less condensed “open” state ulate these subunits when they are amenable to gene expression. reprogrammed into induced pluripotent stem cells. “hESCs must balance the need to keep Depletion of the RNA exosome has many genes transcriptionally competent Wolin and colleagues identified RNAs of little effect on the appearance (or with the need to protect themselves various classes that bind to the exo- pluripotency) of hESC colonies. Upon from deleterious consequences of some in hESCs and are upregulated differentiation, however, endoderm, promiscuous transcription,” explains when the nuclease complex is depleted. mesoderm, and ectoderm markers Sandra Wolin from the National Cancer These direct targets of the exosome are all increased in the absence of the Institute. Various RNA surveillance and include LINE-1 retrotransposons and a exosome, indicating that the nuclease degradation pathways might limit the long noncoding RNA that regulates the complex restrains hESC differentia- damage of any prematurely expressed transcription start site of a transcription tion into all three germ layers. RNAs in hESCs. The RNA exosome, factor important for hESC pluripotency. Credit: Belair et al., 2019 for example, is a multiprotein nuclease The RNA exosome also restricts the lev- complex involved in RNA quality control els of a primary microRNA, pri-miR-205, that has also been proposed to regulate that is linked to endoderm developing that the exosome restrains mesen- the levels of specific mRNAs involved in ment and numerous mRNAs encoding doderm formation by degrading FOXH1 cell proliferation and development. But developmental regulators such as the mRNA. whether it helps maintain hESC pluripo- transcription factor FOXH1. tency was unknown. “Our data support a model in which the hESCs require FOXH1 to induce forma- exosome contributes to hESC pluripo- Wolin and colleagues, including first tion of the mesendoderm, the precursor tency by degrading RNAs that encode author Cedric Belair, depleted the RNA to the mesodermal and endodermal key developmental regulators,” Wolin exosome from hESCs by targeting germ layers. Wolin and colleagues says. “Moreover, because the exosome one of the complex’s core subunits, found that, in the absence of the RNA can undergo rapid inactivation, it may EXOSC3. hESCs lacking EXOSC3 still exosome, the transcriptional targets function as a developmental switch that expressed the pluripotency markers of FOXH1 are elevated during hESC allows hESCs to quickly increase levels OCT4, NANOG, and SOX2. When differentiation, but these increases were of important RNAs.” induced to differentiate, however, abolished by FOXH1 depletion, indicat-

RESEARCHER DETAILS ORIGINAL PAPER Belair, C., S. Sim, K.-Y. Kim, Y. Tanaka, I.-H. Park, and S.L. Wolin. 2019. The RNA exosome nuclease complex regulates human embryonic stem cell differentiation. J. Cell Biol. 218:2564–2582. https://doi.org/10.1083/jcb.201811148

Cedric Belair Sandra L. Wolin Research Fellow Chief, RNA Biology Laboratory National Cancer Institute National Cancer Institute (Currently a Biologist at the [email protected] National Institute of Aging) 7 HAIR FOLLICLES RESTRICT CANCER GROWTH Normal skin corrals cancer-causing mutations and reveals how tissue can subvert tumorigenesis

Normal aged skin contains cancer-causing mutations, recent research has shown, but how these mutations are prevented from forming tumors was a mystery. Christiana M. Pineda, Valentina Greco, and colleagues at Yale University used unique live-tissue imaging to track mouse skin cells after inducing cancer-causing mutations. They found that protection against skin cancer comes from a surprising place: hair follicles.

About 30% of all cancers contain a Ras mutation, but these same mutations have been found in non-cancerous skin epithelia. Pineda and colleagues induced Ras mutations in mouse hair follicle cells along with a glowing red reporter to track the mutant stem cells Two-photon images of the ear skin from the same mouse at day 0 and 4 months and their progeny. The cells persisted in after Ras activation reveal normal follicular architecture despite the persistent pres- the epithelium, revealing that the body ence of mutant cells (red). doesn’t just eliminate mutant cells. Credit: Pineda et al., 2019

Pineda and colleagues found that when they induced mutations in hair follicle induce some tumors, typically at sites “Our results indicate that the hair stem cells, they outcompeted wild-type of high grooming or scratching. Imag- follicle has a unique ability to cope with neighboring cells. They still responded ing revealed that those tumors arose Ras-activated cells. This organ is able to normal tissue constraints, such as after an injury caused them to exit the to integrate the mutant epithelial cells resting phase cues, however. Even after follicular niche. To test whether injury while remaining clinically normal,” Pine- a year, the transformed cells did not de- can promote tumorigenesis within the da says. There’s still much to learn about velop into tumors. In contrast, targeting follicle, they ablated hair follicle bulbs what’s going on in the skin that could be the Ras mutation to the upper non-cy- and the double mutant cells showed applied to other cancers. “Manipulation cling region of the skin epithelium led to rapid, and normal, regeneration. “Once of certain cell types or signaling path- benign outgrowths. out of the follicular niche, Hras mutant ways may enable and/or enhance the cells can no longer be controlled and ability of other epithelial tissues to also Introducing a second mutation that contained through hair regeneration suppress oncogenic growth.” results in the loss of TGFβ signaling into programs,” Pineda says. Ras-mutant hair follicle stem cells did

RESEARCHER DETAILS ORIGINAL PAPER Pineda, C.M., D.G. Gonzalez, C. Matte-Martone , J. Boucher , E. Lathrop , S. Gallini , N.R. Fons, T. Xin , K. Tai, E. Marsh , D. X. Nguyen , K.C. Suozzi , S. Beronja , and V. Greco. 2019. Hair follicle regeneration suppresses Ras-driven oncogenic growth. J. Cell Biol. 218:3212-3222. https://doi.org/10.1083/jcb.201907178

Cristiana M. Pineda Valentina Greco Graduate Student Professor Yale University Yale University [email protected] 8 CENTROMERES DRIVE ASYMMETRIC STEM CELL DIVISION Asymmetric incorporation of the centromeric histone CENP-A during G2/M regulates the fate of Drosophila female germline stem cells

Stem cells divide asymmetrically to pro- deposited at centromeres after DNA duce one new daughter stem cell and replication but before chromosome one daughter cell that will subsequently segregation (i.e., during the G2/M differentiate. One mechanism that has transition). The researchers saw similar been proposed to contribute to this dynamics in Drosophila neural stem asymmetry is the selective inheritance cells as well. of sister chromatids that carry specific epigenetic marks between the stem and Dattoli, Dunleavy, and colleagues found daughter cell. Upon division, distinct that the cell cycle regulator CYCLIN A epigenetic marks on sister chromatids promotes CENP-A deposition in GSCs, Superresolution image of a meta- can result in differential gene expres- whereas CYCLIN B, and its down- phase GSC (captured using the sion in the two resulting daughter cells. stream target HASPIN kinase, prevent H3T3P marker, green) shows asym- According to this “silent sister hypothe- excessive CENP-A incorporation. But metric levels of CENP-A (red) at the sis,” the centromeric regions of each sis- CENP-A isn’t deposited evenly on each centromeres of sister chromatids. ter chromatid—which are crucial for cell set of sister chromatids: superresolution Centromeres of the chromatids division and are epigenetically defined microscopy revealed that more CENP-A destined for the daughter GSC have by the histone H3 variant CENP-A— is incorporated into the centromeres approximately 20% more CENP-A would also be distinct to facilitate their of chromatids that are destined to be compared to centromeres of the chromatids destined to be inherited selective segregation. segregated into the daughter cell that maintains its stem cell identity. Accord- by the cystoblast (CB) that will undergo differentiation. In human cells, CENP-A is assembled ingly, these chromatids assembled larg- into centromeres at the end of mito- er kinetochores on their centromeres Credit: Dattoli et al., 2020 sis. “However, centromere assembly and captured more spindle microtu- dynamics can differ among metazoans bules, providing a potential mechanism and also among different cell types in to bias chromosome segregation. “Our results provide the first functional the same organism,” says Elaine Dun- evidence that centromeres have a role leavy from the National University of Overexpressing CENP-A in GSCs, in the epigenetic pathway that specifies Ireland Galway. “To date, little is known or depleting HASPIN kinase, caused stem cell identity,” Dunleavy says. “Fur- about centromere assembly dynamics CENP-A to be evenly deposited on thermore, our data support the silent and functions during stem cell asym- sister chromatids. This is likely to result sister hypothesis in which centromeres metric divisions.” in the random segregation of sister drive the selective segregation of sister chromatids, which, according to the chromatids and the asymmetric division Dunleavy’s team, including first author silent sister hypothesis, would promote of stem cells.” Ada Dattoli, followed the dynamics of stem cell self-renewal. Indeed, overex- centromere assembly in Drosophila pressing CENP-A or depleting HASPIN female germline stem cells (GSCs) and increased the overall number of GSCs found that, in these cells, CENP-A is in fly ovaries.

RESEARCHER DETAILS ORIGINAL PAPER Dattoli, A.A., B.L. Carty, A.M. Kochendoerfer, C. Morgan, A.E. Walshe, and E.M. Dunleavy. 2020. Asymmetric assembly of centromeres epigenetically regulates stem cell fate. J. Cell Biol. 219:e201910084. https://doi.org/10.1083/jcb.201910084

Anna Ada Dattoli (current affiliation) Elaine M. Dunleavy Senior Postdoctoral Fellow Senior Lecturer in Biochemistry University of Pennsylvania Perelman School Centre for Chromosome Biology, National of Medicine University of Ireland Galway [email protected] [email protected] 9 NCAM REGULATES NEURAL PROGENITOR CELL FATE Neural cell adhesion molecule controls the proliferation and differentiation of cortical progenitors by binding to the actin polymerization regulator profilin2

Development of the cerebral cortex entiation, the researchers performed a depends on a precisely coordinated yeast two-hybrid screen and found that program of neural progenitor cell (NPC) an intracellular region of NCAM140, a proliferation, migration, and differenti- splice variant of NCAM, binds to profil- ation. The developmental program ini- in2, a key regulator of actin polymeriza- tially generates cortical neurons before tion. Profilin2 showed a similar dynamic switching to the production of astro- expression pattern in NPCs during cytes and, after birth, oligodendrocytes. cortical development, and depleting the protein altered NPC proliferation Neural cell adhesion molecule (NCAM) and differentiation in vitro, favoring glial At embryonic day 16, there are many has a variety of functions within the cell formation at the expense of neuron more glial fibrillary acidic protein– nervous system and misexpression of production. positive (GFAP+) astrocytes (green) this protein can alter the proliferation in the developing cortex of a mouse and differentiation of NPCs. “Howev- Li and colleagues confirmed that NCAM whose NPCs lack NCAM (right). er, it was unknown whether NCAM is regulates the proliferation and fate Credit: Huang et al., 2020 an intrinsic modulator of NPCs during of NPCs by binding to profilin2 and cortical development,” says Shen Li promoting actin polymerization. F-actin from Dalian Municipal Central Hospital levels were reduced in NCAM-de- in China. ficient NPCs and an NCAM mutant tal diseases associated with abnormal unable to bind to profilin2 was unable NCAM function,” Li says. “Understand- Li and colleagues, including co-corre- to rescue actin dynamics or normalize ing the molecular mechanisms under- sponding author Quan-Hong Ma from NPC proliferation and differentiation. lying these abnormalities may help in Soochow University, found that NCAM NCAM-modulated actin dynamics may the design of future strategies aimed at is prominently expressed in mouse influence NPCs in several ways. One correcting neural differentiation in the NPCs during the early, neurogenic effect noticed by Li and colleagues is affected brain.” stages of cortical development, but its that mitotic NPCs fail to round up in levels decline during the later, gliogenic NCAM-deficient mice, which is likely to periods when astrocytes and oligoden- impair the cells’ progression through drocytes are produced. NPC-specific the cell cycle. deletion of the NCAM gene caused a transient reduction in NPC proliferation Single nucleotide polymorphisms in the and a delay in cortical neuron genera- NCAM gene and/or defects in NCAM tion, while astrocyte and oligodendro- proteolysis or glycosylation have been cyte formation occurred earlier than linked to a variety of neurological normal. disorders, including autism. “Our study suggests that abnormalities in temporal To understand how NCAM might NPC fate decision may contribute to the regulate NPC proliferation and differ- pathophysiology of neurodevelopmen-

RESEARCHER DETAILS ORIGINAL PAPER Huang, R., D.-J. Yuan, S. Li, X.-S. Liang, Y. Gao, X.-Y. Lan, H.-M. Qin, Y.-F. Ma, G.-Y. Xu, M. Schachner, V. Sytnyk, J. Boltze, Q.-H. Ma, and S. Li. 2020. NCAM regulates temporal specification of neural progenitor cells via profilin2 during corticogenesis. J. Cell Biol. 219:e201902164. https://doi.org/10.1083/jcb.201902164 Rui Huang De-Juan Yuan Shao Li Quan-Hong Ma Shen Li Graduate student Graduate student Professor Professor Professor Dalian Medical Dalian Medical Dalian Medical Soochow University Dalian Municipal Cen- University University University maquanhong@suda. tral Hospital affiliated edu.cn with Dalian Medical 10 University listenlishen@hotmail. com GLUTAMYLATION REGULATES HSC SELF- RENEWAL Reversible modification of the tumor suppressor BAP1 controls hematopoietic stem cell self-renewal and blood cell formation

The functions of proteins within cells The researchers identified the nuclear can be altered by a wide range of re- deubiquitinase BAP1 as a key target of versible, posttranslational modifications, CCP3 in HSCs. The team found that such as methylation, phosphorylation, glutamylation of BAP1 by the enzymes and ubiquitination. Protein glutamyla- TTLL5 and TTLL7 accelerates the pro- tion—in which glutamate side chains tein’s degradation, whereas deglutamy- are added to the γ-carboxyl groups of lation by CCP3 stabilizes BAP1. glutamic acid residues—was original- ly shown to regulate the dynamics of BAP1 is a tumor suppressor linked to microtubules. More recently, however, a range of cancers as well as the rare the tubulin tyrosine ligase-like (TTLL) blood disorder myelodysplastic syn- enzymes that add glutamate side drome. Fan and colleagues found that chains, and the cytosolic carboxypepti- BAP1 promotes HSC self-renewal and dase (CCP) enzymes that remove them, hematopoiesis by facilitating expres- Compared with wild-type (left), the have been shown to target a variety of sion of the transcription factor Hoxa1. bone marrow of mice lacking the proteins and regulate a range of cellular BAP1 and Hoxa1 levels are reduced in glutamylating enzymes TTLL5 and processes. Ccp3-deficient HSCs, limiting the stem TTLL7 (DKO, right) contains an cells’ ability to remain quiescent and increased number of cells due to an For example, Zusen Fan, Yong Tian, and self-renew. The HSC pool is therefore increase in BAP1 levels that promotes colleagues at the Institute of Biophysics, soon exhausted, impairing hematopoie- HSC self-renewal and hematopoiesis. Chinese Academy of Sciences, have sis in Ccp3-knockout mice. Credit: Xiong et al., 2020 previously shown that glutamylation regulates the development of both In contrast, HSCs from mice lacking megakaryocytes and group 3 innate TTLL5 and TTLL7 showed increased lymphoid cells. “However, how glutam- levels of BAP1 and Hoxa1, promoting ylation regulates hematopoietic stem HSC quiescence and self-renewal, as cells (HSCs), which give rise to all blood well as boosting hematopoiesis. cell lineages, is unclear,” says Fan. “Therefore, glutamylation and deglu- Fan and colleagues found that the tamylation of BAP1 play a critical role deglutamylating enzyme CCP3 is highly in the regulation of HSC self-renewal expressed in mouse HSCs. Inhibiting and hematopoiesis,” Fan says. “We are this enzyme, or deleting the Ccp3 gene, currently exploring the molecular mech- impaired HSC self-renewal and hemato- anism by which BAP1 glutamylation poiesis, resulting in reduced HSC num- modulates Hoxa1 expression in a direct bers in the bone marrow and decreased or indirect manner in HSCs.” peripheral blood cell counts.

RESEARCHER DETAILS ORIGINAL PAPER Xiong, Z., P. Xia, X. Zhu, J. Geng, S. Wang, B. Ye, X. Qin, Y. Qu, L. He, D. Fan, Y. Du, Y. Tian, and Z. Fan. 2020. Glutamylation of deubiquitinase BAP1 controls self-renewal of hematopoietic stem cells and hematopoiesis. J. Exp. Med. 217:e20190974. https://doi.org/10.1084/jem.20190974

Zhen Xiong Yong Tian Zusen Fan Photo not available Photo not available Graduate student Professor Professor Pengyan Xia Xiaoxiao Zhu Institute of Biophysics Institute of Biophysics Institute of Biophysics Postdoctoral re- Postdoctoral re- Chinese Academy of Chinese Academy of Chinese Academy of searcher searcher Sciences Sciences Sciences Institute of Biophysics Institute of Biophysics [email protected] [email protected] Chinese Academy of Chinese Academy of 11 Sciences Sciences THE CHROMATIN LANDSCAPE OF GLIOBLASTOMA Profiling of glioblastoma stem cells and primary tumor samples identifies subgroup- specific transcriptional regulatory circuits and novel therapeutic targets

Glioblastoma is the most common form high expression of this GSC signature of primary brain tumor and is largely showed increased malignancy and poor incurable. Driven by therapy-resistant prognosis. Moreover, knocking down glioblastoma stem cells (GSCs), glio- many of these SE-regulated genes im- blastomas show high levels of pheno- paired GSC proliferation in vitro. typic heterogeneity both between and within individual tumors. In addition to this core signature common to the vast majority of GSCs, Cellular states are generally defined by further analysis revealed that pa- a small number of master transcription tient-derived GSCs cluster into at factors that bind to super-enhancers least two different groups with distinct (SEs), driving the expression of numer- chromatin signatures defined by unique ous genes essential for establishing SE activities and transcription factors. cellular identity, including the master These different GSC states could also transcription factors themselves. To be identified in primary tumor samples define the core regulatory circuits that from glioblastoma patients. define glioblastoma cell states, a team Mapping histone H3 acetylation of researchers led by Jeremy Rich and Knocking down group-specific tran- reveals the distinct patterns of SE Xiuxing Wang at the University of Cali- scription factors had group-specific activity in group 1 and group 2 GSCs. effects. For example, knocking down fornia, San Diego, and Charles Lin, Ste- Credit: Mack et al., 2019 phen Mack, and Irtisha Singh at Baylor RUNX2, a transcription factor uniquely College of Medicine, profiled a large active in group 2 GSCs, inhibited the cohort of patient-derived GSCs and growth of tumors derived from group primary glioblastoma tumor samples. 2 GSCs, but had no effect on tumors “In sum, our data reveal the existence derived from group 1 GSCs. of distinct GSC populations defined by “We mapped active enhancer land- unique chromatin signatures aris- scapes and integrated this with profiles “Transcription factors are notoriously ing from specific regulatory circuits of gene expression, DNA methylomes, challenging to target therapeutically,” composed of SEs and SE-associated copy number variations, and whole says Rich. “However, because these transcription factors,” Rich says. “These exomes to identify the core transcrip- transcription factors are associated with SE programs that regulate GSC identity tion factors and other SE-associated SEs, we were able to identify other es- (both core and group specific) can be genes that establish and maintain GSC sential genes that are more amenable to used for the discovery of new therapeu- identity,” Rich explains. therapeutic targeting.” For example, the tic targets.” researchers found that group 1 GSCs The researchers uncovered a set of show SE-mediated activation of MAPK/ SEs and genes active in >75% of GSCs, ERK signaling and can thus be spe- allowing them to derive a core gene cifically targeted by a small molecule signature for these cells. Tumors with inhibitor against this pathway.

RESEARCHER DETAILS ORIGINAL PAPER Mack, S.C., I. Singh, X. Wang, R. Hirsch, Q. Wu, R. Villagomez, J.A. Bernatchez, Z. Zhu, R.C. Gimple, L.J.Y. Kim, A. Morton, S. Lai, Z. Qiu, B.C. Prager, K.C. Bertrand, C. Mah, W. Zhou, C. Lee, G.H. Barnett, M.A. Vogelbaum, A.E. Sloan, L. Chavez, S. Bao, P.C. Scacheri, J.L. Siqueira-Neto, C.Y. Lin, and J.N. Rich. 2019. Chromatin landscapes reveal developmentally Stephen C. Mack Charles Y. Lin Photo not available Photo not available Photo not available encoded transcriptional states that define human Assistant Professor Assistant Professor Irtisha Singh Xiuxing Wang Jeremy N. Rich glioblastoma. J. Exp. Med. 216:1071–1090. Baylor College of Baylor College of Postdoc fellow Postdoctoral re- Professor of Medicine https://doi.org/10.1084/jem.20190196 Medicine Medicine Baylor College of searcher University of California, [email protected] [email protected] Medicine University of California, San Diego 12 (Currently an assistant San Diego drjeremyrich@gmail. professor at Texas com A&M University) PRIMITIVE HSCS CONTINUE CYCLING INTO ADULTHOOD Study reveals that, contrary to a previous report, the most primitive hematopoietic stem cells do not become permanently quiescent and, instead, show continuous mitotic activity in adult mice

Hematopoietic stem cells (HSCs) are responding author Thomas Zerjatke, multipotent adult stem cells that can found that in three different H2B-FP give rise to every type of blood cell mouse strains—including the one used throughout an individual’s lifetime. The in the 2016 study—leaky expression mitotic activity of HSCs can be tracked even in the absence of induction causes in vivo using an inducible “pulse” of fluorescent histone label to gradually fluorescent histone fusion protein (H2B- accumulate in HSCs. This age-depen- FP) which labels the cells’ chromatin. dent background fluorescence accu- This is followed by a “chase” period mulation was particularly prominent in during which quiescent HSCs retain quiescent HSCs with high repopulating the fluorescent label while proliferating activity. “We argue that this accumulat- HSCs pass it on to their daughters, ed background can be easily misinter- gradually diluting the fluorescent signal preted as stable retention of induced within a few cell divisions. label,” Zerjatke says.

In 2016, a high-profile study used this On the other hand, Gerbaulet and approach in mice to identify a small colleagues found that the half-life of flu- Scheme recapitulates key features of population of primitive HSCs containing orescent histones is within the range of pulse-chase experiments to identify all of the HSC compartment’s long- 2–6 weeks, meaning that protein degra- quiescent HSCs retaining H2B-GFP term repopulating activity. These cells dation represents the major contributor label. Infrequently dividing HSCs appeared to undergo four self-renewing to loss of fluorescenct label in rarely dilute fluorescent label mostly by pro- divisions during the first year of life dividing cells. “This precludes very long tein degradation. In parallel, continu- before entering a state of permanent chase periods and neglecting label ous leaky background expression of quiescence, apparently allowing them degradation will result in a massive H2B-FP progressively accumulates in to retain fluorescent histone labeling for overestimation of the divisional activity quiescent HSCs and could be mistak- as long as 22 months. Based on this, the of quiescent HSCs,” says Morcos. en for permanent quiescence. authors hypothesized that HSCs count Credit: Morcos et al., 2020 and remember cell divisions. “Howev- The researchers built a new mathe- er, their model considered neither the matical model for pulse-chase labeling impact of continuous leaky background of HSCs with fluorescent histones, baulet and colleagues saw no evidence expression of the fluorescent histone incorporating the impact of leaky for HSCs counting and remembering a label, nor the division-independent loss background expression and protein set number of divisions before abrupt- of fluorescence due to protein degrada- degradation. The model successfully rely entering permanent quiescence. tion,” says Alexander Gerbaulet from the capitulated experimental observations, “Instead, our data suggest that primitive Institute for Immunology at TU Dresden. including the preferential accumulation HSCs continue to cycle in aged mice, of background fluorescence in more undergoing infrequent but steady mitot- Gerbaulet and colleagues, including quiescent HSCs. Using their model to ic divisions,” Gerbaulet says. first author Mina Morcos and co-cor- infer the mitotic activity of HSCs, Ger-

RESEARCHER DETAILS ORIGINAL PAPER Alexander Gerbaulet Morcos, M.N.F., T. Zerjatke, I. Glauche, C.M. Munz, Y. Ge, A. Petzold, S. Reinhardt, A. Group Leader Dahl, N.S. Anstee, R. Bogeska, M.D. Milsom, P. Säwén, H. Wan, D. Bryder, A. Roers, Institute for Immunology, Carl Gustav Carus and A. Gerbaulet. 2020. Continuous mitotic activity of primitive hematopoietic stem Faculty of Medicine, TU Dresden [email protected] cells in adult mice. J. Exp. Med. 217:e20191284. Mina N.F. Morcos https://doi.org/10.1084/jem.20191284 PhD student Institute for Immunology, Carl Gustav Carus Faculty of Medicine, TU Dresden Thomas Zerjatke PhD student Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden 13 [email protected] DISTINGUISHING PHYSIOLOGIC AND ONCOGENIC WNT SIGNALS Profiling of isogenic human colon organoids reveals differences between oncogenic Wnt activation and normal Wnt signaling essential for stem cell maintenance

Around 80% of colorectal cancers signaling (induced by exogenous Wnt (CRCs) carry truncating mutations in Ad- ligands) upregulate distinct sets of genes enoma polyposis coli (APC). Loss of the and proteins, no matter how strongly the APC protein stabilizes the transcriptional two signaling pathways are activated. coactivator β-catenin, a key component of the Wnt signaling pathway, leading Many of the proteins specifically upregu- to constitutive Wnt signaling and the lated by physiological Wnt signaling are formation of benign adenomas that can expressed in intestinal crypts, suggest- progress into CRC upon the acquisition ing that they could be new markers for of further mutations. CRC cells rely on normal intestinal stem cells. On the other Wnt signaling to continue proliferating hand, many of the proteins specifically but, because Wnt activity also regulates upregulated in response to oncogenic the proliferation and renewal of intestinal Wnt signaling are only expressed in tu- stem cells critical for maintaining gut mors, and could therefore represent new homeostasis, inhibiting this pathway has biomarkers or even therapeutic targets. highly toxic side effects in patients. Some studies have shown that high Developing successful therapies might Wnt activity is associated with favorable therefore require identifying differences outcomes in CRC, whereas other studies between normal Wnt signaling and the have suggested that the presence of To distinguish physiological and constitutive activation induced by onco- Wnt-active stem cells correlates with oncogenic Wnt signaling, Farin and genic mutations in APC or other genes. increased tumor invasiveness and higher colleagues profiled isogenic pairs of “We set out to catalog the physiological rates of relapse. “We therefore wanted colon organoids, cultured in the pres- and oncogenic Wnt responses in primary to test if our organoid-derived signatures ence or absence of Wnt ligands, and carrying either wild-type or truncated human colon epithelial cells on the are associated with distinct clinical out- versions of the APC gene. transcriptome and proteome level,” says comes in CRC,” says Farin. Henner Farin from the German Cancer Credit: Michels et al., 2019 Consortium and Georg-Speyer-Haus, Farin and colleagues found that the Goethe University Frankfurt. oncogenic Wnt signature was associated with good prognosis in the canonical “Oncogenic and physiological Wnt Farin and colleagues, including co-first CRC subtype CMS2, consistent with the responses therefore represent two authors Birgitta Michels and Mohammed role of APC mutations in this subtype independent and opposing prognostic Mosa, analyzed isogenic colon organoids and possibly reflecting an increased determinants in CRC,” Farin says. “Rather grown from intestinal cells isolated from resemblance to benign adenomas. In than Wnt activity per se, stratification healthy human subjects. RNA sequenc- contrast, the physiological Wnt signature of specific downstream responses may ing and quantitative mass spectrometry predicted poor outcomes in CMS4 CRC, be more informative on the status of revealed that oncogenic Wnt signaling possibly reflecting tumors with increased tumors.” (induced by the CRISPR/Cas9-mediated stemness and invasiveness. truncation of APC) and physiological

RESEARCHER DETAILS ORIGINAL PAPER Michels, B.E., M.H. Mosa, B.M. Grebbin, D. Yepes, T. Darvishi, J. Hausmann, H. Urlaub, S. Zeuzem, H.M. Kvasnicka, T. Oellerich, and H.F. Farin. 2019. Human colon organoids reveal distinct physiologic and oncogenic Wnt responses. J. Exp. Med. 216:704–720. https://doi.org/10.1084/jem.20180823

Birgitta E. Michels Mohammed H. Mosa Henner F. Farin Graduate student Postdoctoral researcher Group Leader German Cancer Consortium German Cancer Consortium German Cancer Consortium Georg-Speyer-Haus Georg-Speyer-Haus Georg-Speyer-Haus Goethe University Frankfurt Goethe University Frankfurt Goethe University Frankfurt 14 Photo © Georg-Speyer-Haus Photo © Georg-Speyer-Haus [email protected] Photo © Georg-Speyer-Haus LEUKEMIA HIJACKS MYELOID REGENERATION PATHWAYS Correcting aberrant Notch and Wnt signaling in leukemic stem cells might normalize myeloid cell production in a number of different leukemias

In 2015, Emmanuelle Passegué and pathways. Passegué and colleagues colleagues described how hematopoi- determined that, at steady state, Notch etic stem cells (HSCs) maintain blood activity is high and Wnt activity is low production at steady state by giving in HSCs and MPP4s. MPP3s, in con- rise to a mix of multipotent progenitors trast, show low Notch and high Wnt (MPPs). Some, known as MPP2 and activity. Accordingly, inhibiting Notch MPP3, are biased toward producing or boosting Wnt signaling triggered the myeloid lineage cells such as macro- early stages of myeloid regeneration Staining for nuclear β-catenin (red) phages and neutrophils, while others, by promoting the production of MPP3s shows that activity of the Wnt signal- known as MPP4, are biased toward from HSCs. ing pathway is high in myeloid-biased lymphoid lineage cells like T and B MPP3 cells but low in normal HSCs cells. They also showed that in times Myeloid leukemias are driven by leu- and lymphoid-biased MPP4 cells. of stress, (following HSC transplanta- kemic stem cells (LSCs) that are often Credit: Kang et al., 2020 tion, for example), HSCs regenerate the resistant to treatment and can pro- blood system by inducing emergency mote tumor recurrence. Passegué and colleagues found that Notch activity is myelopoiesis pathways that gener- new treatment options to limit aberrant reduced and Wnt signaling is elevated ate more MPP2 and MPP3 cells than myeloid cell production,” Passegué says. in LSCs in mice, further supporting normal, and reprogram MPP4 cells to “This is particularly relevant for patients the idea that myeloid leukemias hijack produce more myeloid lineage cells. with no identified driver mutations or myeloid regeneration pathways and who relapsed with resistance muta- Together with Yoon-A Kang and Eric Pi- providing therapeutic targets. “We tions. The next step will be to identify etras, Passegué wondered whether this found that increasing Notch activity or druggable targets that could appro- myeloid regeneration pathway might decreasing Wnt activity in mouse LSCs priately increase Notch activity while be constitutively activated in myeloid has very similar effects in correcting limiting Wnt activity, providing a specific leukemias. “Using several different myeloid cell production, delaying dis- anti-LSC therapy that could block their mouse models, we found that MPP3 ex- ease progression, and improving overall enhanced and overly biased myeloid pansion and myeloid reprogramming of survival,” Passegué says. differentiation potential.” MPP4 are common features of myeloid leukemia and reflect the hijacking of a Notably, similar attempts to increase normally transiently activated pathway Notch or decrease Wnt activity in of emergency myelopoiesis,” Passegué normal HSCs had no effect, with says. compensatory crosstalk between the two signaling pathways appearing to The molecular mechanisms regulating prevent abnormal MPP function and the production of different MPPs from blood production. “Our results identify HSCs are unknown but are likely to a common mechanism for myeloid leu- involve the Notch and Wnt signaling kemia development that could provide

RESEARCHER DETAILS ORIGINAL PAPER Kang, Y.-A., E.M. Pietras, and E. Passegué. 2020. Deregulated Notch and Wnt signaling activates early-stage myeloid regeneration pathways in leukemia. J. Exp. Med. 217:e20190787. https://doi.org/10.1084/jem.20190787

Yoon-A Kang Eric M. Pietras Emmanuelle Passegué Postdoctoral Fellow Assistant Professor Professor of Genetics and Columbia University University of Colorado An- Development schutz Medical Campus Director, Columbia Stem Cell Initiative Columbia University Irving 15 Medical Center [email protected]