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    Topic review


    Subjects: Cell Biology
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    Submitted by: Michael Heide


    ARHGAP11B is a human-specific gene that likely played a crucial role in human neocortex evolution by inducing hallmarks of cortical expansion. In contrast to its ancestral paralog, ARHGAP11A, ARHGAP11B does not act as a Rho GTPase Activating Protein in the nucleus but is localized in mitochondria and increases glutaminolysis. This increase is a prerequisite for increased basal progenitor proliferation – one essential basis for cortical expansion.

    1. Evolution of ARHGAP11B

    ARHGAP11B arose by a partial duplication of ARHGAP11A around 5 mya [1][2][3][4]. ARHGAP11A is a ubiquitous gene that is composed of 12 exons and encodes a RhoGAP (Rho GTPase Activating Protein) domain-containing protein [5][6]. The partial duplication of ARHGAP11A resulting in ARHGAP11B encompassed only the first 8 exons of ARHGAP11A [7]. This truncated copy of ARHGAP11A (referred to as ancestral ARHGAP11B) most likely did not contribute to cortical expansion. Indeed, a functional analysis of ancestral ARHGAP11B showed that it lacked the ability to promote BP proliferation [7]. Although the ARHGAP11B gene is only a truncated copy of ARHGAP11A, it contains the full nucleotide sequence of the RhoGAP domain. However, at the protein level, ARHGAP11B features only a truncated RhoGAP domain, lacking the last (C-terminal) 26 amino acids of this domain [7]. In line with this finding, functional analyses showed that ARHGAP11B lacks RhoGAP activity in vivo [8][7]. The truncation of the RhoGAP domain, despite the presence of the full nucleotide sequence for this domain in the ARHGAP11B gene, is due to a single C → G nucleotide substitution in the ARHGAP11B gene, which most likely occurred after the partial gene duplication event. This substitution generated a novel splice donor site in ARHGAP11B, leading to the loss of 55 nucleotides upon ARHGAP11B mRNA splicing. This loss led to a frameshift that resulted in a novel, human-specific 47 amino acid-long C-terminal sequence of ARHGAP11B [7]. In contrast to the ancestral ARHGAP11B gene that lacks the C → G nucleotide substitution and that would encode an ARHGAP11B protein containing a complete RhoGAP domain and exhibiting RhoGAP activity in vivo, the ARHGAP11B gene carrying this substitution, and the truncated RhoGAP domain-containing protein generated from it that can promote BP proliferation (see below), have often been referred to as modern ARHGAP11B/ARHGAP11B [7]. For the sake of simplicity, the latter will from now on be referred to merely as “ARHGAP11B/ARHGAP11B”.

    2. Expression of ARHGAP11B during Corticogenesis

    During fetal human neocortex development, ARHGAP11B is expressed in the VZ and SVZ (including iSVZ and oSVZ), but not in the cortical plate (CP), as shown by in situ hybridization of 13 weeks post-conception (wpc) fetal human neocortex sections [9] and by RNA-seq of micro-dissected germinal zones and CPs of fetal human neocortex ranging from 13 to 16 wpc [10]. Furthermore, RNA-seq data of FACS-isolated cell populations from fetal human neocortex enriched in either apical radial glia (aRG), bRG, or neurons (the latter also containing bRG in G1) showed that ARHGAP11B is expressed at almost equal levels in aRG and bRG, but not in neurons [8]. Notably, in contrast to ARHGAP11A, ARHGAP11B is not expressed in the basal end-feet of radial glia, as shown by in situ hybridization [9][11]. Furthermore, re-analysis of the Florio et al. 2015 RNA-seq data showed that one ARHGAP11B splice variant is specifically expressed in bRG [9].

    3. Function/Role of ARHGAP11B during Corticogenesis

    Functional studies of ARHGAP11B in different model systems revealed a potentially important role of this human-specific gene in neocortical development and evolution (summarized in Table 1). Transient overexpression of ARHGAP11B in mouse embryos by in utero electroporation led to an increase in BP abundance and proliferation, which was accompanied by an increase in SVZ thickness, and in half of the cases, resulted in folding of the normally unfolded mouse neocortex [8]. Furthermore, transient overexpression of ARHGAP11B in ferret embryos by in utero electroporation resulted in an increase in proliferative bRG, in an extension of the neurogenic period and an increase in upper-layer neurons [12]. Finally, and in contrast to the transient overexpression studies, a recent study with transgenic marmoset fetuses that expressed ARHGAP11B under the control of its own human promoter—hence, achieving a physiological-like expression—showed an increased size and the induction of folding of the fetal marmoset neocortex, which at the fetal stage studied, is known to be unfolded [13]. Along with this increase in size and folding, this ARHGAP11B expression resulted in an increase in the thickness of the CP and a specific increase in upper-layer neurons. Moreover, the oSVZ—the germinal zone thought to predominantly contribute to human neocortex expansion—was increased in thickness, which reflected an increase in the abundance of BPs, including that of the—for human neocortex expansion, highly relevant—bRG [13]. In summary, gain-of-function experiments with ARHGAP11B strongly suggest a key role for this gene in human neocortex expansion.
    Table 1. Summary of the main functions of ARHGAP11B and of the NOTCH2NL genes during neocortex development.
    neocortex size ↑ basal progenitors ↑ apical progenitor ↑
    cortical folding ↑ basal intermediate progenitors ↑ cortical progenitor proliferation ↑
    cortical plate thickness ↑   cortical progenitor differentiation ↓
    upper-layer neurons ↑   neuronal output ↑
    oSVZ thickness ↑    
    basal progenitors ↑    
    basal radial glia ↑    
    To corroborate the potentially important role of ARHGAP11B in fetal human neocortex development, loss-of-function experiments are needed. However, due to the high sequence identity between ARHGAP11B and its paralog, ARHGAP11A [7], and the expression of these two genes largely in the same cell types [8][9], it is difficult to find guide RNAs for specific and efficient CRISPR/Cas9-mediated disruption of ARHGAP11B expression, or small hairpin RNAs for specific ARHGAP11B RNAi. To overcome this limitation, it was recently shown that a truncated version of ARHGAP11A that comprises only its N-terminal 220 amino acids (referred to as ARHGAP11A220) can act in a dominant-negative manner on ARHGAP11B’s function [14]. Indeed, inhibition of ARHGAP11B’s function in fetal human neocortex tissue by ex vivo electroporation using ARHGAP11A220 was found to result in a decreased abundance of BPs [14], providing the first loss-of-function evidence for an important role of ARHGAP11B in fetal human neocortex development.
    The same study unraveled the molecular function of ARHGAP11B. In contrast to ARHGAP11A, which is mainly localized in the nucleus, ARHGAP11B is localized in mitochondria due to a functional N-terminal mitochondrial import sequence [14]. Although this mitochondrial import sequence is also present in ARHGAP11A, it appears to be functionally masked in this longer protein. Moreover, ARHGAP11A contains two nuclear localization signals that are not present anymore in the shorter ARHGAP11B protein [14]. In mitochondria, ARHGAP11B interacts with the adenine nucleotide translocase (ANT) and inhibits the opening of the mitochondrial permeability transition pore. As a result, intramitochondrial calcium levels rise, and the metabolic pathway, called glutaminolysis, a hallmark of cancer metabolism [15], is increasingly used [14]. In fact, the ARHGAP11B-induced increase in glutaminolysis was shown to be a prerequisite for the increased BP proliferation upon ARHGAP11B expression [14]. Interestingly, the protein encoded by a known microcephaly gene, MCPH1, was also shown to be associated with mitochondria and to regulate glutaminolysis [16]. Taken together, these data are consistent with the notion that an increase in glutaminolysis is associated with neocortex expansion, whereas a decrease can be a potential cause of microcephaly [17]. In summary, all the findings discussed in this section point to an important role of ARHGAP11B in human neocortex development and most likely in determining its size.

    4. Potential Contribution of ARHGAP11B to Microcephaly

    ARHGAP11B is located on chromosome 15, near the region that is associated with the 15q13.3 microdeletion/microduplication syndrome. The 15q13.3 microdeletion syndrome is characterized by intellectual and developmental disabilities, mostly delays in speech acquisition and in cognitive function linked to cognitive impairments [18][19][20][21]. Moreover, epilepsy/seizures are present in 28% of affected individuals [21], and the occurrence of schizophrenia was found to be increased in cohorts of 15q13.3 microdeletion patients [21][22]. In some cases, affected patients also display reduced brain volumes and microcephaly [23][24][25]. The 15q13.3 microdeletion is typically characterized by a common 2 Mb deletion on chromosome 15, including the genes MTMR15, TRPM1, MTMR10, KLF13, OTUD7A, CHRNA7, and also ARHGAP11B [21]. Some studies have reported homozygous deletion of this chromosomal region [23][25][26][27][28]. However, a closer examination of the coordinates of the deletions suggested that only one copy of ARHGAP11B is included in the deletion, or that ARHGAP11B is only very close to the deletion, or that the sequence of ARHGAP11B’s main isoform is still intact (Table 2).
    Table 2. Genomic coordinates (GRCh37/hg19 assembly) of ARHGAP11B (left) and of patients reported to have a homozygous 15q13.3 microdeletion (see references indicated).
    ARHGAP11B Le Pichon et al., 2010 [26] Endris et al., 2010 [23] Spielmann et al., 2011 [27] Le Pichon et al., 2013 [28] Masurel-Paulet et al., 2014 [25]
    chr15:30,918,879–30,931,023 chr15:30,931,644–32,914,281 chr15:29,085,644–32,511,004 (paternal) 1
    chr15:31,122,986–32,511,004 (maternal) 1
    chr15:30,971,330–32,439,084 chr15:30,931,644–32,914,281 chr15:30,938,215–32,510,863 (three patients)
    1 Patient 2.
    Therefore, ARHGAP11B’s contribution to 15q13.3 microdeletion/microduplication syndrome as well as to microcephaly, in general, remains open. Due to ARHGAP11B’s likely role in human neocortex development and evolution (Table 1), it is conceivable that its mutation or deletion could contribute to microcephaly. Although ARHGAP11B has not been the focus of microcephaly studies in the past, it should be noted that, due to its high sequence homology to ARHGAP11A, mutations in ARHGAP11B in microcephaly patients were perhaps masked by ARHGAP11A. As some cases of 15q13.3 microdeletion display microcephaly and ARHGAP11B is close to one end of the deletion, it would be important to (re-)analyze 15q13.3 microdeletion cases with microcephaly in detail to see if ARHGAP11B is perhaps affected by the deletion.

    The entry is from 10.3390/cells10051209


    1. Riley, B.; Williamson, M.; Collier, D.; Wilkie, H.; Makoff, A. A 3-Mb map of a large segmental duplication overlapping the alpha7-nicotinic acetylcholine receptor gene (CHRNA7) at human 15q13-q14. Genomics 2002, 79, 197–209.
    2. Sudmant, P.H.; Kitzman, J.O.; Antonacci, F.; Alkan, C.; Malig, M.; Tsalenko, A.; Sampas, N.; Bruhn, L.; Shendure, J.; Genomes, P.; et al. Diversity of human copy number variation and multicopy genes. Science 2010, 330, 641–646.
    3. Antonacci, F.; Dennis, M.Y.; Huddleston, J.; Sudmant, P.H.; Steinberg, K.M.; Rosenfeld, J.A.; Miroballo, M.; Graves, T.A.; Vives, L.; Malig, M.; et al. Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nat. Genet. 2014, 46, 1293–1302.
    4. Dennis, M.Y.; Harshman, L.; Nelson, B.J.; Penn, O.; Cantsilieris, S.; Huddleston, J.; Antonacci, F.; Penewit, K.; Denman, L.; Raja, A.; et al. The evolution and population diversity of human-specific segmental duplications. Nat. Ecol. Evol. 2017, 1, 69.
    5. Kagawa, Y.; Matsumoto, S.; Kamioka, Y.; Mimori, K.; Naito, Y.; Ishii, T.; Okuzaki, D.; Nishida, N.; Maeda, S.; Naito, A.; et al. Cell cycle-dependent Rho GTPase activity dynamically regulates cancer cell motility and invasion in vivo. PLoS ONE 2013, 8, e83629.
    6. Zanin, E.; Desai, A.; Poser, I.; Toyoda, Y.; Andree, C.; Moebius, C.; Bickle, M.; Conradt, B.; Piekny, A.; Oegema, K. A conserved RhoGAP limits M phase contractility and coordinates with microtubule asters to confine RhoA during cytokinesis. Dev. Cell 2013, 26, 496–510.
    7. Florio, M.; Namba, T.; Pääbo, S.; Hiller, M.; Huttner, W.B. A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification. Sci. Adv. 2016, 2, e1601941.
    8. Florio, M.; Albert, M.; Taverna, E.; Namba, T.; Brandl, H.; Lewitus, E.; Haffner, C.; Sykes, A.; Wong, F.K.; Peters, J.; et al. Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Science 2015, 347, 1465–1470.
    9. Florio, M.; Heide, M.; Pinson, A.; Brandl, H.; Albert, M.; Winkler, S.; Wimberger, P.; Huttner, W.B.; Hiller, M. Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex. eLife 2018, 7, e32332.
    10. Fietz, S.A.; Lachmann, R.; Brandl, H.; Kircher, M.; Samusik, N.; Schroder, R.; Lakshmanaperumal, N.; Henry, I.; Vogt, J.; Riehn, A.; et al. Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proc. Natl. Acad. Sci. USA 2012, 109, 11836–11841.
    11. Pilaz, L.-J.; Joshi, K.; Liu, J.; Tsunekawa, Y.; Alsina, F.C.; Sethi, S.; Suzuki, I.K.; Vanderhaeghen, P.; Polleux, F.; Silver, D.L. Subcellular mRNA localization and local translation of ARHGAP11A in radial glial cells regulates cortical development. bioRxiv 2020.
    12. Kalebic, N.; Gilardi, C.; Albert, M.; Namba, T.; Long, K.R.; Kostic, M.; Langen, B.; Huttner, W.B. Human-specific ARHGAP11B induces hallmarks of neocortical expansion in developing ferret neocortex. eLife 2018, 7, e41241.
    13. Heide, M.; Haffner, C.; Murayama, A.; Kurotaki, Y.; Shinohara, H.; Okano, H.; Sasaki, E.; Huttner, W.B. Human-specific ARHGAP11B increases size and folding of primate neocortex in the fetal marmoset. Science 2020, 369, 546–550.
    14. Namba, T.; Doczi, J.; Pinson, A.; Xing, L.; Kalebic, N.; Wilsch-Bräuninger, M.; Long, K.R.; Vaid, S.; Lauer, J.; Bogdanova, A.; et al. Human-specific ARHGAP11B acts in mitochondria to expand neocortical progenitors by glutaminolysis. Neuron 2020, 105, 867–881.
    15. Yang, L.; Venneti, S.; Nagrath, D. Glutaminolysis: A hallmark of cancer metabolism. Annu. Rev. Biomed. Eng. 2017, 19, 163–194.
    16. Journiac, N.; Gilabert-Juan, J.; Cipriani, S.; Benit, P.; Liu, X.; Jacquier, S.; Faivre, V.; Delahaye-Duriez, A.; Csaba, Z.; Hourcade, T.; et al. Cell metabolic alterations due to Mcph1 mutation in microcephaly. Cell Rep. 2020, 31, 107506.
    17. Namba, T.; Nardelli, J.; Gressens, P.; Huttner, W.B. Metabolic regulation of neocortical expansion in development and evolution. Neuron 2020, 3, 408–419.
    18. Sharp, A.J.; Mefford, H.C.; Li, K.; Baker, C.; Skinner, C.; Stevenson, R.E.; Schroer, R.J.; Novara, F.; De Gregori, M.; Ciccone, R.; et al. A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nat. Genet. 2008, 40, 322–328.
    19. Ben-Shachar, S.; Lanpher, B.; German, J.R.; Qasaymeh, M.; Potocki, L.; Nagamani, S.C.; Franco, L.M.; Malphrus, A.; Bottenfield, G.W.; Spence, J.E.; et al. Microdeletion 15q13.3: A locus with incomplete penetrance for autism, mental retardation, and psychiatric disorders. J. Med. Genet. 2009, 46, 382–388.
    20. van Bon, B.W.; Mefford, H.C.; Menten, B.; Koolen, D.A.; Sharp, A.J.; Nillesen, W.M.; Innis, J.W.; de Ravel, T.J.; Mercer, C.L.; Fichera, M.; et al. Further delineation of the 15q13 microdeletion and duplication syndromes: A clinical spectrum varying from non-pathogenic to a severe outcome. J. Med. Genet. 2009, 46, 511–523.
    21. Lowther, C.; Costain, G.; Stavropoulos, D.J.; Melvin, R.; Silversides, C.K.; Andrade, D.M.; So, J.; Faghfoury, H.; Lionel, A.C.; Marshall, C.R.; et al. Delineating the 15q13.3 microdeletion phenotype: A case series and comprehensive review of the literature. Genet. Med. 2015, 17, 149–157.
    22. Stefansson, H.; Rujescu, D.; Cichon, S.; Pietilainen, O.P.; Ingason, A.; Steinberg, S.; Fossdal, R.; Sigurdsson, E.; Sigmundsson, T.; Buizer-Voskamp, J.E.; et al. Large recurrent microdeletions associated with schizophrenia. Nature 2008, 455, 232–236.
    23. Endris, V.; Hackmann, K.; Neuhann, T.M.; Grasshoff, U.; Bonin, M.; Haug, U.; Hahn, G.; Schallner, J.C.; Schrock, E.; Tinschert, S.; et al. Homozygous loss of CHRNA7 on chromosome 15q13.3 causes severe encephalopathy with seizures and hypotonia. Am. J. Med Genet. Part A 2010, 152A, 2908–2911.
    24. Hoppman-Chaney, N.; Wain, K.; Seger, P.R.; Superneau, D.W.; Hodge, J.C. Identification of single gene deletions at 15q13.3: Further evidence that CHRNA7 causes the 15q13.3 microdeletion syndrome phenotype. Clin. Genet. 2013, 83, 345–351.
    25. Masurel-Paulet, A.; Drumare, I.; Holder, M.; Cuisset, J.M.; Vallee, L.; Defoort, S.; Bourgois, B.; Pernes, P.; Cuvellier, J.C.; Huet, F.; et al. Further delineation of eye manifestations in homozygous 15q13.3 microdeletions including TRPM1: A differential diagnosis of ceroid lipofuscinosis. Am. J. Med Genet. Part A 2014, 164A, 1537–1544.
    26. Lepichon, J.B.; Bittel, D.C.; Graf, W.D.; Yu, S. A 15q13.3 homozygous microdeletion associated with a severe neurodevelopmental disorder suggests putative functions of the TRPM1, CHRNA7, and other homozygously deleted genes. Am. J. Med. Genet. Part A 2010, 152A, 1300–1304.
    27. Spielmann, M.; Reichelt, G.; Hertzberg, C.; Trimborn, M.; Mundlos, S.; Horn, D.; Klopocki, E. Homozygous deletion of chromosome 15q13.3 including CHRNA7 causes severe mental retardation, seizures, muscular hypotonia, and the loss of KLF13 and TRPM1 potentially cause macrocytosis and congenital retinal dysfunction in siblings. Eur. J. Med. Genet. 2011, 54, e441–e445.
    28. Le Pichon, J.B.; Yu, S.; Kibiryeva, N.; Graf, W.D.; Bittel, D.C. Genome-wide gene expression in a patient with 15q13.3 homozygous microdeletion syndrome. Eur. J. Hum. Genet. EJHG 2013, 21, 1093–1099.