Disorganization in mice and humans

Active inference, morphogenesis, and computational psychiatry

Active inference is a leading theory in neuroscience that provides a simple and neuro-biologically plausible account of how action and perception are coupled in producing (Bayes) optimal behavior; and has been recently used to explain a variety of psychopathological conditions. In parallel, morphogenesis has been described as the behavior of a (non-neural) cellular collective intelligence solving problems in anatomical morphospace. In this article, we establish a link between the domains of cell biology and neuroscience, by analyzing disorders of morphogenesis as disorders of (active) inference. The aim of this article is three-fold. We want to: (i) reveal a connection between disorders of morphogenesis and disorders of active inference as apparent in psychopathological conditions; (ii) show how disorders of morphogenesis can be simulated using active inference; (iii) suggest that active inference can shed light on developmental defects or aberrant morphogenetic processes, seen as disorders of information processing, and perhaps suggesting novel intervention and repair strategies. We present four simulations illustrating application of these ideas to cellular behavior during morphogenesis. Three of the simulations show that the same forms of aberrant active inference (e.g., deficits of sensory attenuation and low sensory precision) that have been used to explain psychopathological conditions (e.g., schizophrenia and autism) also produce familiar disorders of development and morphogenesis when implemented at the level of the collective behavior of a group of cells. The fourth simulation involves two cells with too high precision, in which we show that the reduction of concentration signaling and sensitivity to the signals of other cells treats the development defect. Finally, we present the results of an experimental test of one of the model's predictions in early Xenopus laevis embryos: thioridazine (a dopamine antagonist that may reduce sensory precision in biological systems) induced developmental (anatomical) defects as predicted. The use of conceptual and empirical tools from neuroscience to understand the morphogenetic behavior of pre-neural agents offers the possibility of new approaches in regenerative medicine and evolutionary developmental biology.

A missense mutation in TRAPPC6A leads to build-up of the protein, in patients with a neurodevelopmental syndrome and dysmorphic features

Childhood onset clinical syndromes involving intellectual disability and dysmorphic features, such as polydactyly, suggest common developmental pathways link seemingly unrelated phenotypes. We identified a consanguineous family of Saudi origin with varying complex features including intellectual disability, speech delay, facial dysmorphism and polydactyly. Combining, microarray based comparative genomic hybridisation (CGH) to identify regions of homozygosity, with exome sequencing, led to the identification of homozygous mutations in five candidate genes (RSPH6A, ANKK1, AMOTL1, ALKBH8, TRAPPC6A), all of which appear to be pathogenic as predicted by Proven, SIFT and PolyPhen2 and segregate perfectly with the disease phenotype. We therefore looked for differences in expression levels of each protein in HEK293 cells, expressing either the wild-type or mutant full-length cDNA construct. Unexpectedly, wild-type TRAPPC6A appeared to be unstable, but addition of the proteasome inhibitor MG132 stabilised its expression. Mutations have previously been reported in several members of the TRAPP complex of proteins, including TRAPPC2, TRAPPC9 and TRAPPC11, resulting in disorders involving skeletal abnormalities, intellectual disability, speech impairment and developmental delay. TRAPPC6A joins a growing list of proteins belonging to the TRAPP complex, implicated in clinical syndromes with neurodevelopmental abnormalities.

Sixteenth-century German woodcut of a male infant with possible disorganization

History has preserved a beautiful 16th century woodcut print, which depicts an infant with several malformations. The German inscription describes the infant's hypotonia and ectopic growths, and the image itself shows a child with an ectopic accessory third lower limb, a large papilla, and an omphalocele-like growth. The 'case' bears striking similarity to reported human cases of the disorganization (Ds) syndrome. This article describes the woodcut, describes Ds, and then explains how the image may represent the earliest depiction of Ds in history.

Congenital upper eyelid coloboma: embryologic, nomenclatorial, nosologic, etiologic, pathogenetic, epidemiologic, clinical, and management perspectives

Purpose:

To review the recent literature and describe the authors’ experience with congenital upper eyelid coloboma.

Methods:

In this review, we will summarize the embryologic and etiopathogenetic bases of congenital upper eyelid coloboma, and study the published clinical reports. We will also attempt to briefly shed some light on the rarer syndromic curiosities associated with upper eyelid coloboma.

Results:

Congenital upper eyelid colobomas are one of the few nontraumatic oculoplastic emergencies that may occasionally present in the first few days of life with a corneal ulcer and may even present with impending perforation. They can present with or without corneopalpebral adhesions, may be isolated findings or a part of a larger spectrum of congenital anomalies as in the case of Fraser syndrome or Goldenhar syndrome, or could be associated with other rare curiosities that could challenge the clinician with a huge diagnostic dilemma.

Conclusions:

Existing literature dealing with congenital colobomas of the upper eyelid is fraught with nosologic problems, confusing etiologies, and overlapping clinical features. We attempted to clarify the salient clinical features, outline the management principles, and until a time in the not-so-distant future where advances in molecular genetic testing would help redefine the etiology and the diverse clinical spectrum of genetic diseases associated with upper eyelid colobomas, we propose a simplified classification scheme based on the relation of the coloboma to the cornea, the presence or absence of systemic features, and all the syndromic and nonsyndromic associations of congenital coloboma of the upper eyelid known today.

In this review, the authors will describe the pathogenesis of upper eyelid coloboma, suggest a new simplified classification system, describe the clinical picture in detail, clarify the various syndromic associations of upper eyelid coloboma, and lay out the basic surgical principles of management.

Limb body wall complex, amniotic band sequence, or new syndrome caused by mutation in IQ Motif containing K (IQCK)?

Limb body wall complex (LBWC) and amniotic band sequence (ABS) are multiple congenital anomaly conditions with craniofacial, limb, and ventral wall defects. LBWC and ABS are considered separate entities by some, and a continuum of severity of the same condition by others. The etiology of LBWC/ABS remains unknown and multiple hypotheses have been proposed. One individual with features of LBWC and his unaffected parents were whole exome sequenced and Sanger sequenced as confirmation of the mutation. Functional studies were conducted using morpholino knockdown studies followed by human mRNA rescue experiments. Using whole exome sequencing, a de novo heterozygous mutation was found in the gene IQCK: c.667C>G; p.Q223E and confirmed by Sanger sequencing in an individual with LBWC. Morpholino knockdown of iqck mRNA in the zebrafish showed ventral defects including failure of ventral fin to develop and cardiac edema. Human wild-type IQCK mRNA rescued the zebrafish phenotype, whereas human p.Q223E IQCK mRNA did not, but worsened the phenotype of the morpholino knockdown zebrafish. This study supports a genetic etiology for LBWC/ABS, or potentially a new syndrome.

The "Stars and Stripes" Metaphor for Animal Regeneration-Elucidating Two Fundamental Strategies along a Continuum

A number of challenges have hindered the development of a unified theory for metazoan regeneration. To describe the full range of complex regeneration phenomena in Animalia, we suggest that metazoans that regenerate missing body parts exhibit biological attributes that are tailored along a morpho-spatial regeneration continuum, illustrated in its polar scenarios by the USA “stars and stripes” flag. Type 1 organisms (“T1, ‘stars’”) are typical colonial organisms (but contain unitary taxa) that are able to regenerate “whole new stars”, namely, whole bodies and colonial modules, through systemic induction and sometimes multiple regeneration foci (hollow regeneration spheres, resembling the blastula) that compete for dominance. They regenerate soma and germ constituents with pluripotent adult stem cells and exhibit somatic-embryogenesis mode of ontogeny. Type 2 organisms (“T2, ‘stripes’”) are capable of limited regeneration of somatic constituents via fate-restricted stem cells, and regenerate through centralized inductions that lead to a single regeneration front. T2 organisms are unitary and use preformistic mode of ontogeny. T1 and T2 organisms also differ in interpretation of what constitutes positional information. T2 organisms also execute alternative, less effective, regeneration designs (i.e., scar formation). We assigned 15 characteristics that distinguish between T1/T2 strategies: those involving specific regeneration features and those operating on biological features at the whole-organism level. Two model organisms are discussed, representing the two strategies of T1/T2 along the regeneration continuum, the Botrylloides whole body regeneration (T1) and the mouse digit-tip regeneration (T2) phenomena. The above working hypothesis also postulates that regeneration is a primeval attribute of metazoans. As specified, the “stars and stripes” paradigm allows various combinations of the biological features assigned to T1 and T2 regeneration strategies. It does not consider any concentration gradient or thresholds and does not refer to the “epimorphosis” and “morphallaxis” terms, regeneration types across phyla or across body plans. The “stars and stripes” paradigm also ignores, at this stage of analysis, cases of regeneration loss that may obscure biological trajectories. The main advantage of the “stars and stripes” paradigm is that it allows us to compare T1/T2 regeneration, as well as other modes of regeneration, through critical determining characteristics.

Morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning

Establishment of shape during embryonic development, and the maintenance of shape against injury or tumorigenesis, requires constant coordination of cell behaviors toward the patterning needs of the host organism. Molecular cell biology and genetics have made great strides in understanding the mechanisms that regulate cell function. However, generalized rational control of shape is still largely beyond our current capabilities. Significant instructive signals function at long range to provide positional information and other cues to regulate organism-wide systems properties like anatomical polarity and size control. Is complex morphogenesis best understood as the emergent property of local cell interactions, or as the outcome of a computational process that is guided by a physically encoded map or template of the final goal state? Here I review recent data and molecular mechanisms relevant to morphogenetic fields: large-scale systems of physical properties that have been proposed to store patterning information during embryogenesis, regenerative repair, and cancer suppression that ultimately controls anatomy. Placing special emphasis on the role of endogenous bioelectric signals as an important component of the morphogenetic field, I speculate on novel approaches for the computational modeling and control of these fields with applications to synthetic biology, regenerative medicine, and evolutionary developmental biology.

Are abdominal wall defects and external genitalia anomalies randomly expressed in some families?

Familial cases of isolated abdominal wall defects with variable expressivity in more than one generation have rarely been observed. We report four affected individuals within a small three-generation family with either variable non-syndromic abdominal wall defects or external genital anomalies. We discuss the possible transmission of non-syndromic abdominal wall defects. It could be hypothesized that similar developmental defects may result in anomalies like hypospadias in males or developmental anomalies of the labia minora or labia majora in females.

Piwi positive cells that line the vasculature epithelium, underlie whole body regeneration in a basal chordate

The colonial tunicate Botrylloides leachi can regenerate functional adults from minute vasculature fragments, in a poorly understood phenomenon termed Whole Body Regeneration (WBR). Using Piwi expression (Bl-Piwi), blood cell labeling and electron microscopy, we show that WBR develops through activation, mobilization and expansion of 'dormant' cells which normally line the internal vasculature epithelium of blood vessels. Following a mechanical insult, these cells express Bl-Piwi de novo, change morphology and invade niches of the vasculature lumen, where they proliferate and differentiate, regenerating a functional organism. Mitomycin C treatments and siRNA knockdown of Bl-Piwi result in deficient cells incapable of expanding or differentiating and to subsequent regeneration arrest. Last, we find similar transient mobilization of Piwi(+) cells recurring every week, as part of normal colony development, and also during acute environmental stress. This recurrent activation of Piwi(+) cells in response to developmental, physiological and environmental insults may have enabled the adaptation of colonial tunicates to the imposed varied conditions in the marine, shallow water environment.

What lies at the interface of regenerative medicine and developmental biology?

At a recent Keystone Symposium on `Developmental Biology and Tissue Engineering', new findings in areas ranging from stem cell differentiation,embryonic pattern formation and organ regeneration to engineered cell microenvironments, synthetic biomaterials and artificial tissue fabrication were described. Although these new advances were exciting, this symposium clarified that biologists and engineers often view the challenge of tissue formation from different, and sometimes conflicting, perspectives. These dichotomies raise questions regarding the definition of regenerative medicine,but offer the promise of exciting new interdisciplinary approaches to tissue and organ regeneration, if effective alliances can be established.

A genetic model for cloacal exstrophy, the extreme cloacal malformation

Cloacal exstrophy (CE) or vesicointestinal fissure is an uncommon but well known anomaly that represents the extreme cloacal malformation. It is most often seen as an isolated anomaly, or as part of the OEIS complex (omphalocele, exstrophy, imperforate anus, spinal defects). Limb anomalies are also seen with CE. Unlike the OEIS complex, limb anomalies occur as independent malformations. Here, we present two cases of CE with limb anomalies that are consistent with the phenotype seen in Disorganization (Ds), an unusual human malformation syndrome. From reviewing the mouse model, it may be that the Ds gene is a candidate for isolated CE as well.

A phylogenetic approach to mapping cell fate

Recent, surprising, and controversial discoveries have challenged conventional concepts regarding the origins and plasticity of stem cells, and their contributions to tissue regeneration, and highlight just how little is known about mammalian development in comparison to simpler model organisms. In the case of the transparent worm, Caenorhabditis elegans, Sulston and colleagues used a microscope to record the birth and death of every cell during its life, and the compilation of this "fate map" represents a milestone achievement of developmental biology. Determining a fate map for mammals or other higher organisms is more complicated because they are opaque, take a long time to mature, and have a tremendous number of cells. Consequently, fate mapping experiments have relied on tagging a progenitor cell with a dye or genetic marker in order to later identify its descendants. This approach, however, extracts little information because it demonstrates that a population of cells, all having inherited the same label, shares a common ancestor, but it does not reveal how cells in that population are related to one another. To avoid that problem, as well as technical limitations of current methods for mapping cell fate, we, and others, have developed a new strategy for retrospectively deriving cell fate maps by using phylogenetics to infer the order in which somatic mutations have arisen in the genomes of individual cells during development in multicellular organisms. DNA replication inevitably introduces mutations, particularly at repetitive sequences, every time a cell divides. It is thus possible to deduce the history of cell divisions by cataloging somatic mutations and phylogenetically reconstructing cell lineage. This approach has the potential to produce a complete mammalian cell fate map that, in principle, could describe the developmental lineage of any cell and help resolve outstanding questions of stem cell biology, tissue repair and maintenance, and aging.

Finally, a sense of closure? Animal models of human ventral body wall defects

Malformations concerning the ventral body wall constitute one of the leading categories of human birth defects and are present in about one out of every 2000 live births. Although the occurrence of these defects is relatively common, few detailed experimental studies exist on the development and closure of the ventral body wall in mouse and human. This field is further complicated by the array of theories on the pathogenesis of body wall defects and the likelihood that there is no single cause for these abnormalities. In this review, we summarize what is known concerning the mechanisms of normal ventral body wall closure in humans and mice. We then outline the theories that have been proposed concerning human body wall closure abnormalities and examine the growing number of mouse mutations that impact normal ventral body wall closure. Finally, we speculate how studies in animal models such as mouse and Drosophila are beginning to provide a much-needed mechanistic framework with which to identify and characterize the genes and tissues required for this vital aspect of human embryogenesis.

Clefting, amniotic bands, and polydactyly: A distinct phenotype that supports an intrinsic mechanism for amniotic band sequence

Amniotic band sequence (ABS) is a well-described condition involving a variety of congenital anomalies in association with fibrous bands. However, many cases are associated with birth defects that are not readily explained by the mechanism of fibrous strings entangling body parts and causing disruption of the fetal structures. The most common of these is typical cleft lip and palate (CLP). Here we describe such a case, with typical ABS limb defects and constriction bands, along with CLP, supernumerary left nipple, polydactyly, and a skin papilla. This case is nearly identical to a child previously described by Guion-Almieda and Richieri-Costa [2000] and may, therefore, represent a previously unrecognized syndrome that overlaps with ABS. Furthermore it may be that cases with ABS-like anomalies associated with CLP represent a different condition, possibly caused by mutations in the genes Disorganization, p63, or IRF6.

Human disorganization complex, as a polytopic blastogenesis defect: a new case

We describe a baby girl of 4,000 g and 55 cm with supernumerary, malformed, and partially duplicated lower limbs, malformed and partially duplicated pelvis, spina bifida, coccygeal dermal sinus, ectopic anus located in the right buttock, duplicated internal genitalia, rectovaginal fistula, ileal atresia, Meckel diverticulum, and various renal system anomalies. We think that this phenotype is a new case of disorganization in humans (DsH) and postulate that this condition constitutes a polytopic defect of the blastogenesis. In this case, the presence of a malformation pattern involving structures in different parts of the body and organs derived from all of the germ layers, suggests that the pathogenetic event most probably occurred during blastogenesis affecting various progenitors fields.

The novel DNA glycosylase, NEIL1, protects mammalian cells from radiation-mediated cell death

DNA damage mediated by reactive oxygen species generates miscoding and blocking lesions that may lead to mutations or cell death. Base excision repair (BER) constitutes a universal mechanism for removing oxidatively damaged bases and restoring the integrity of genomic DNA. In Escherichia coli, the DNA glycosylases Nei, Fpg, and Nth initiate BER of oxidative lesions; OGG1 and NTH1 proteins fulfill a similar function in mammalian cells. Three human genes, designated NEIL1, NEIL2 and NEIL3, encode proteins that contain sequence homologies to Nei and Fpg. We have cloned the corresponding mouse genes and have overexpressed and purified mNeil1, a DNA glycosylase that efficiently removes a wide spectrum of mutagenic and cytotoxic DNA lesions. These lesions include the two cis-thymineglycol(Tg) stereoisomers, guanine- and adenine-derived formamidopyrimidines, and 5,6-dihydrouracil. Two of these lesions, fapyA and 5S,6R thymine glycol, are not excised by mOgg1 or mNth1. We have also used RNA interference technology to establish embryonic stem cell lines deficient in Neil1 protein and showed them to be sensitive to low levels of gamma-irradiation. The results of these studies suggest that Neil1 is an essential component of base excision repair in mammalian cells; its presence may contribute to the redundant repair capacity observed in Ogg1 -/- and Nth1 -/- mice.

Anomalous anterior midline cervical tube

Anterior midline cervical anomalies, excepting thyroglossal tract abnormalities, are rare. Two unusual and almost identical cases of an anomalous congenital tube connecting the chin to the upper sternum are described; only one previous similar report exists in the literature. In all three cases, the tubes occurred as isolated anomalies in otherwise healthy children.