Genetic mapping and exome sequencing identify variants associated with five novel diseases

The Clinic for Special Children (CSC) has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain) children. Among the Plain people, we have used single nucleotide polymorphism (SNP) microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb) that contain many genes (mean = 79). For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data.

Clinical application of DNA microarrays: molecular diagnosis and HLA matching of an Amish child with severe combined immune deficiency

Amish and Mennonite children with severe combined immune deficiency (SCID) often die without treatment as a result of delayed diagnoses and prohibitive costs of therapy. In this detailed case report, we describe the novel use of DNA microarrays to improve the diagnosis and management of an Amish infant with SCID. Using 10,000 single nucleotide polymorphism (SNP) genotypes from the patient, her parents, and seven siblings, we identified the recombinase activating genes for diagnostic sequencing, and then characterized a novel pathogenic variant in RAG1 (c.2974A>G). The same genotype data were used to identify a sibling stem cell donor who was haplo-identical at human leukocyte antigen (HLA) and blood group (ABO) loci. Autozygosity and linkage analysis of SNP genotypes within a family narrows the search for SCID candidate genes and provides a relatively simple and inexpensive way to identify potential tissue donors among biological siblings.

Abdominal mucinous cystic neoplasm in a male child

Mucinous cystic neoplasms (MCNs) make up a morphologic family of similar appearing tumors arising in the ovary and various extraovarian sites, including the pancreas, hepatobiliary tract, paratesticular soft tissues, and mesentery. Other than the uncommon mucinous cystadenoma of the ovary presenting in adolescence, MCNs are rarely seen by the pediatric pathologist. The present case is a 5-year-old boy with an abdominal mass appearing to arise in the mesentery of the small intestine. Because of its unresectability, a generous biopsy was performed and disclosed a MCN with focal complex papillary architecture in the absence of appreciable cytologic atypia or invasion into the wall. Like other MCNs, this tumor had an inhibin-positive, ovarian-like stroma that was nonreactive for estrogen and progesterone receptors. Only 1 other case of a mesenteric MCN has been reported to date in a child and none in a male. The MCN of the mesentery joins other, somewhat more common cystic lesions of the omentum and mesentery presenting in childhood.

Anatomy and histology of the brain and sense organs of the Antarctic eel cod Muraenolepis microps (Gadiformes; Muraenolepididae)

Brain regions, cranial nerves, and sense organs in Muraenolepis microps, an Antarctic gadiform fish, were examined to determine which features could be attributed to a gadiform ancestry and which to habitation of Antarctic waters. We found that the central nervous system and sense organs are well developed, showing neither substantial regression nor hypertrophy. A detailed drawing of the brain and cranial nerves is provided. The rostral position of the olfactory bulbs and telencephalic size and lobation are common for the order. The optic tectum and corpus cerebelli are smaller than in most other gadiforms. The shape of the corpus cerebelli is not distinctive among gadiforms. The lateral line region is moderately well-developed, but not hypertrophied to the extent seen in deep-sea gadiforms. As is the case in gadids possessing barbels and elongated pelvic rays, Muraenolepis has well-developed facial lobes, although these are smaller and more laterally positioned. The vagal lobes are deeply placed in the rhombencephalon and project into the fourth ventricle. The brain of Muraenolepis resembles that of a phyletically derived gadoid, especially a phycid, more than it resembles the brain of a phyletically basal macrourid. Two histological features of the diencephalon of Muraenolepis appear to be unique among gadiforms: a well-organized thalamic central medial nucleus and subependymal expansions. Muraenolepis has a pure rod retina like many deep-sea species but lacks the superimposed layers of rod outer segments. The histology of the nonvisual sense organs, especially the olfactory and external taste systems, are well-developed in Muraenolepis but not hypertrophied. We relate our findings to what is known about neural morphology in other gadiforms and in phyletically distant notothenioids and liparids that are sympatric with Muraenolepis on the Antarctic shelf. The only feature that reflects an Antarctic existence is the diencephalic subependymal expansions, which within notothenioids mirror the habitation of cold waters and have been found in every Antarctic species examined to date. Although the waters of the Antarctic shelf are cold, dark, and deep, brain and sense organ morphology in Muraenolepis are remarkably free of extreme specialization.

Nervous and sensory system correlates of an epibenthic evolutionary radiation in antarctic notothenioid fishes, genus Trematomus (Perciformes; Nototheniidae)

The perciform suborder Notothenioidei consists of 120 species, with 94 confined to the Antarctic Region of the Southern Ocean. On the Antarctic shelf, this phyletic radiation has been accompanied by a substantial morphological and ecological diversification towards a pelagic existence. For example, the primarily benthic genus Trematomus contains an epibenthic radiation that includes T. loennbergii, T. lepidorhinus, and T. eulepidotus. By comparing these epibenthic species with three congeneric benthic species (T. scotti, T. pennellii, and T. bernacchii) we tested three null hypotheses regarding brain variation in Antarctic trematomids: 1) that there is no difference in brain morphology among the six species; 2) that phylogenetic and ecological factors do not influence brain morphology; and 3) that peripheral sensory structures do not influence brain morphology. We rejected each of these hypotheses, leading us to conclude that Trematomus brains vary interspecifically, between benthic and epibenthic species, and with a species' depth distribution. Further, we conclude that brain variation is correlated with differences in peripheral sensory systems and motor activity. Specifically, epibenthic Trematomus have larger percentages of their brain volume devoted to lateral line mechanoreceptive and motor (cerebellar) structures. Species living at greater depths have low ratios of cones:rods in the retina and larger olfactory structures.

Morphology of the brain and sense organs in the snailfish Paraliparis devriesi: neural convergence and sensory compensation on the Antarctic shelf

The Antarctic snailfish Paraliparis devriesi (Liparidae) is an epibenthic species, inhabiting depths of 500-650 m in McMurdo Sound. Liparids are the most speciose fish family in the Antarctic Region. We examine the gross morphology and histology of the sense organs and brain of P. devriesi and provide a phyletic perspective by comparing this morphology to that of four scorpaeniforms and of sympatric perciform notothenioids. The brain has numerous derived features, including well-developed olfactory lamellae with thick epithelia, large olfactory nerves and bulbs, and large telencephalic lobes. The retina contains only rods and exhibits a high convergence ratio (82:1). Optic nerves are small and nonpleated. The tectum is small. The corpus of the cerebellum is large, whereas the valvula is vestigial. The rhombencephalon and bulbospinal junction are extended and feature expanded vagal and spinal sensory lobes as well as hypertrophied dorsal horns and funiculi in the rostral spinal cord. The lower lobes of the pectoral fins have taste buds and expanded somatosensory innervation. Although the cephalic lateral line and anterior lateral line nerve are well developed, the trunk lateral line and posterior lateral line nerve are reduced. Near-field mechanoreception by trunk neuromasts may have been compromised by the watery, gelatinous subdermal extracellular matrix employed as a buoyancy mechanism. The expanded somatosensory input to the pectoral fin may compensate for the reduction in the trunk lateral line. The brains of P. devriesi and sympatric notothenioids share well-developed olfactory systems, an enlarged preoptic-hypophyseal axis, and subependymal expansions. Although the functional significance is unknown, the latter two features are correlated with habitation of the deep subzero waters of the Antarctic shelf.

Periventricular morphology in the diencephalon of antarctic notothenioid teleosts

We have examined the subependymal region of the diencephalic third ventricle in notothenioid perciforms and report a pattern of neuropil expansions that appears to be phyletically derived for notothenioids and their outgroups but that is otherwise unique among vertebrates. We recognize five types of expansions based on their composition (from less dense neuropil to sacs) and width or protrusion into the third ventricle. In the species with the most elaborate morphology, Trematomus bernacchii, bilateral subependymal expansions fuse along the midline to form a single sac within the ventricular cavity. The extent of these expansions loosely corresponds with phyletic position but also (and perhaps more importantly) is correlated with the habitation of cold water (r2 = 0.48; P = 0.012). Furthermore, subependymal expansion type is positively correlated with the maximum size of the soma of neurons in two hypothalamic nuclei, the preopticus magnocellularis (r2 = 0.54; P = 0.006) and the lateralis tuberis (r2 = 0.40; P = 0.038). These nuclei project to the pituitary and contain cerebrospinal fluid-contacting neurons. In considering the functional consequences of this morphology, we cannot dismiss the possibility that these structures form a specialized enteroceptive system tied to the monitoring of cerebrospinal and extracellular fluid components, including antifreeze glycopeptides and inorganic ions.

Protein content and freezing avoidance properties of the subdermal extracellular matrix and serum of the Antarctic snailfish, Paraliparis devriesi

The Antarctic snailfish, Paraliparis devriesi (Liparididae), occupies an epibenthic habitat at a depth of 500-650 m in the subzero waters of McMurdo Sound, Antarctica. This species has watery (97%) gelatinous subdermal extracellular matrix (SECM) comprising a mean of 33.8% of the body weight, the largest known proportion of any adult fish. The protein concentration of the SECM was found to be 6-7 mg ml(-1) (0.6-0.7% w/v). Separation of the polypeptides of the SECM by SDS-PAGE revealed 11 polypeptides ranging in relative molecular mass (Mr) from 67,000 to 13,000, with other unresolved polypeptides of less than 13,000. The isoelectric points of these proteins ranged from 4.85 to 8.05. Partial N-terminal amino acid sequence data were obtained for four of the major SECM polypeptides. The N-terminal amino acid sequences of three of these were not identical to or homologous with any other known sequences, whereas the N-terminal sequence of one polypeptide (Mr 51,000) was identical to partial sequence from the apolipoprotein A-I precursor of Atlantic salmon (Salmo salar). Although not isolated from either SECM or serum, melting point-freezing point behavior of body fluids suggest that Paraliparis possess modest amounts of a noncolligative antifreeze compound. Since relatively small amounts of antifreeze are present in the serum and even less in the SECM, freezing avoidance results from the combined effects of antifreeze and the elevated osmolality of body fluids. There are no special adaptations to prevent freezing in the superficially located high water content SECM.

Diversification of brain morphology in antarctic notothenioid fishes: basic descriptions and ecological considerations

The Notothenioidei, a perciform suborder of 120 species, dominates the ichthyofauna of the Southern Ocean around Antarctica. Unlike most teleost groups, notothenioids have undergone a corresponding ecological and phyletic diversification and therefore provide an excellent opportunity to study the divergence of the nervous system in an unusual environment. Our goal is to evaluate notothenioid brain variation in light of this diversification. To provide a baseline morphology, we examine the gross morphology and histology of the brain of Trematomus bernacchii, a generalized member of the family Nototheniidae. We then examine the variation in brain gross anatomy (32 species) and histology (10 species) of other notothenioids. Our sample represents about 27% of the species in this group and includes species from each of the six families, as well as species representing diverse ecologies. For comparison we reference the well-studied brains of two species of temperate perciformes (Perca flavescens and Lepomis humilis). Our results show that, in general, notothenioid brains are more similar to the brains of temperate perciforms than to the unusual brains of cave-dwelling and deep-sea fishes. Interspecific variation in gross brain morphology is comparable to that in Old World cyprinids and is illustrated for 17 species. Variation is especially noteworthy in the ecologically and geographically diverse family Nototheniidae. Measurements indicate that sensory regions (olfactory bulbs, eminentia granularis, and crista cerebellaris) exhibit the most pronounced variation in relative surface area. Association areas, including the corpus cerebelli and the telencephalon, exhibit moderate variation in size, shape, and lobation patterns. Regulatory areas of the brain, including the saccus vasculosus and the subependyma of the third ventricle, are also variable. These regions are best developed in species living in the subfreezing water close to the continent. In some species the expanded ependymal lining forms ventricular sacs, not previously described in any other vertebrate. Three species, including two nototheniids (Eleginops maclovinus and Pleuragramma antarcticum) and the only artedidraconid in our sample, have distinctive brains. The unique brain morphology of Pleuragramma is probably related to a sensory (lateral line) specialization for feeding. Within the Nototheniidae, a phyletic effect on cerebellar morphology is evident in the Coriiceps group and in the Pleuragramminae. Neither phyletic position nor ecological factors (water temperature, position in the water column, dietary habits) alone fully explain the pattern of notothenioid brain diversification.

Renal corpuscle development in boreal fishes with and without antifreezes

Light and election microscopy were used to document the degree of renal corpuscle development in boreal telcost fishes that produce peptide or glycopeptide antifreeze compounds on a seasonal or permanent basis. Emphasis was placed on gadids, cottids and pleuronectids from both the North Atlantic and North Pacific Oceans. Based on the classification of Marshall and Smith (1930), corpuscle development ranged from fully glomerular (Type 1) to pauciglomerular (Type III). Unlike the situation in Antarctic notothenioid fishes, there were no aglomerular species among the boreal fishes. Corpuscles were small in diameter in gadids whereas in cottids they ranged from small to large with considerable intraspecific variation. Eight of eleven species with antifreeze had intermediate (Type II-III) or pauciglomerular kidneys with relatively few dense corpuscles (dia. 36-82μm). In some of these species an extensive mesangium and a substantial capillary endothelium contributed to a glomerular filtration barrier that was four to five times thicker than that in Type I kidneys. The corpuscles of other pauciglomerular species were unremarkable and appeared functional at the ultrastructural level. The boreal fish fauna is taxonomically diverse and, compared to the unrelated Antarctic fauna, of relatively recent evolutionary origin. Furthermore, antifreeze is present only during the winter in some species. Hence it is not surprising that the urinary conservation of antifreeze is accomplished by mechanisms other than the evolutionary loss of renal corpuscles.

Preparation of enriched populations of corticotrophs from goldfish rostral pars distalis

A mammalian isolated adrenal cell system was validated as a bioassay for goldfish ACTH; the log dose-response curve for the goldfish hormone is parallel to that for synthetic mammalian ACTH1-24, and the two ACTHs induce the same maximum rate of corticosterone production. Using this assay, it was observed that (1) there is a marked and consistent biphasic change in pituitary ACTH content as related to the length of time the fish are held in laboratory aquaria, and (2) the absolute and relative (to tissue wt) ACTH content of the rostral pars distalis is considerably greater than that of the proximal portion of the gland. Using a trypsin technique, isolated pituitary cells were prepared from both (rostral and proximal) portions of the gland; bioassay data indicate that cell suspensions prepared from the rostral pars distalis are enriched with respect to corticotrophs. The implications of these findings with regard to formulating an advantageous in vitro system for studying ACTH secretion are discussed.

Hepatic ultrastructural specialization in Antarctic fishes

Compared with those of other verebrate animals, the livers of Antarctic fishes have a unique type of perisinusoidal (Ito) cell. These cells were studied in 9 species with emphasis on Dissostichus mawsoni. Perisinusoidal cells are found in large numbers throughout the liver, have long cytoplasmic arms and, in Dissostichus, contain numerous lipid droplets. The extensive rough endoplasmic reticulum and prominent nucleolus are ultrastructural characteristics indicating that these cells are engaged in protein synthesis. An evolutionary specialization, perisinusoidal cells may be partially responsible for the elevated levels of protein synthesis characteristics of fishes in the Antarctic marine environment.

The secondary lamellae of the gills of cold water (high latitude) teleosts. A comparative light and electron microscopic study

The fine structure of the secondary lamellae of gills was examined in two cold-water marine teleosts, the winter flounder, Pseudopleuronectes americanus, and the antarctic cod, Trematomus borchgrevinik. In both species the overall lamellar fine structure is similar to that of other marine teleosts. The major variations in cellular organization involve the distribution of both the "chloride cells" and the mucous cells on the secondary lamellae of P. americanus. At winter water temperatures of +2.5 degrees C, significantly more chloride and mucous cells are present than in summer with water temperatures of +15.2 degrees C. Both cell types are routinely present throughout the length of a secondary lamella as far as the lamellar tip. The chloride cells on the secondary lamellae are always situated in the inner layer of epithelium deep to the outer pavement cells. T. borchgrevinki shows no apparent difference in the distribution of mucous cells either at its normal water temperature of -1.9 degrees C or at a temperature of +4 degrees C, the upper limit of its thermal tolerance to which some specimens were adapted in the aquarium. Chloride cells were never observed on the secondary lamellae of T. borchgrevinki. This suggests that low environmental water temperatures may be related to the distribution of mucous cells and chloride cells on the secondary lamella of the teleost gill.

Renal conservation of antifreeze peptide in Antarctic eelpout, Rhigophila dearborni

In Antarctic notothenioid fishes large amounts (3% w/v) of small molecular weights of 2,600-23,500 and would be expected to be filtered into the urine, they remain in the blood because the kidneys of these fishes contain only aglomerular nephrons. Unlike the situation in most fishes, urine formation is the result of secretion rather than filtration and reabsorption. On the other hand, the peptide antifreezes in Northern Hemisphere fishes such as the winter flounder. Pseudopleuronectes americanus, are retained by the glomerular kidney even though inulin, of comparable weight, is rapidly filtered from the blood into the urine. The Antarctic eelpout (zoarcid), Rhigophila dearborni, which is unrelated to either the Antarctic notothenioids or P. americanus, also uses a peptide antifreeze (molecular weight 6,000) which is maintained at a concentration of 3% (w/v) in the blood plasma. We report here that the lack of antifreeze in the urine of R. dearborni probably reflects the fact that the glomeruli are not functional and cannot filter. We support this conclusion with morphological and physiological evidence and relate our findings to the conservation of biological antifreeze necessary for life in ice-laden polar waters.