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Inherited disposition to cardiac myxoma development.

Carney complex is a genetic condition in which affected individuals develop benign tumours in various tissues, including the heart. Most individuals with Carney complex have a mutation in the PRKAR1A gene, which encodes the regulatory R1alpha subunit of protein kinase A - a significant component of the cyclic-AMP signalling pathway. Genetically engineered mutant Prkar1a mouse models show an increased propensity to develop tumours, and have established a role for R1alpha in initiating tumour formation and, potentially, in maintaining cell proliferation. Ongoing investigations are exploring the intersection of R1alpha-dependent cell signalling with other gene products such as perinatal myosin, mutation of which can also cause cardiac myxomas.

Animals↗

From phenotype to genotype.

Advances in the field of genomics have made it possible to decipher the genetic and transcriptional changes that underlie differences among organisms. Here we discuss the merits and drawbacks of these strategies as they relate to evolutionary biology. We suggest that the molecular basis of natural variation can best be interpreted via the intersection of genomic and transcriptome approaches. We outline how this might be accomplished in practice and assemble the components of a method to comprehend the evolutionary interplay between genotype and phenotype.

Biological Evolution↗

Research and practice opportunities at the intersection of health education, health behavior, and genomics.

Researchers and practitioners in health behavior and health education (HBHE) can play a pivotal leadership role in the integration of genomic advances to improve the public's health. The purpose of this article is to outline research and practice opportunities at the intersection of genomics and HBHE. We begin this article by briefly summarizing the existing evidence in the literature pertaining to the public's use of genetic services, the effectiveness of genetic counseling, and the impact of genetic testing. Following this, we outline and expand on several areas that we believe are ripe for further exploration, understanding, and public health application:(a) public understanding of genetic information, (b) interventions for health behavior change, and (c) public health assurance and advocacy. This analysis has identified the need to consider potential application efforts in genomics and HBHE from an ecological perspective, with an emphasis on multiple levels of intervention and analysis.

Genetic Counseling↗

Spindle epithelial tumor with thymus-like differentiation of the thyroid: a case report with pathological and molecular genetics study.

We report an unusual case of spindle epithelial tumor with thymus-like differentiation (SETTLE) of the thyroid present in a 6-year-old boy. The tumor, located at both the left lobe and isthmus, was a circumscribed mass with slightly gritty whorled appearance. Microscopically, the lobulated, highly cellular, spindle cell neoplasm was arranged in intersecting bundles and fascicles separated by fibrous bands. Benign-appearing glands entrapped within fibrous bands and foci of squamous differentiation within spindle cells were observed. Immunohistochemically, the spindle cells were diffusely positive for cytokeratins, vimentin, and alpha-smooth muscle actin and patchily reactive for muscle-specific actin and epithelial membrane antigen, exhibiting myoepithelial differentiation. The spindle cells were also patchily immunopositive for p53 protein. Molecular genetic analysis revealed Ki-ras gene mutations at codons 13 (GGC(gly) to AGC(ser)) and 15 (GGC(gly) to AGC(ser)) on the same allele. Mutation of the p53 gene was not detected. This is the first report on Ki-ras oncogene mutations in a case of SETTLE.

Actins↗

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics.

Identifying the genes responsible for human diseases requires combining information about gene position with clues about biological function. The recent availability of whole-genome data sets of RNA and protein expression provides powerful new sources of functional insight. Here we illustrate how such data sets can expedite disease-gene discovery, by using them to identify the gene causing Leigh syndrome, French-Canadian type (LSFC, Online Mendelian Inheritance in Man no. 220111), a human cytochrome c oxidase deficiency that maps to chromosome 2p16-21. Using four public RNA expression data sets, we assigned to all human genes a "score" reflecting their similarity in RNA-expression profiles to known mitochondrial genes. Using a large survey of organellar proteomics, we similarly classified human genes according to the likelihood of their protein product being associated with the mitochondrion. By intersecting this information with the relevant genomic region, we identified a single clear candidate gene, LRPPRC. Resequencing identified two mutations on two independent haplotypes, providing definitive genetic proof that LRPPRC indeed causes LSFC. LRPPRC encodes an mRNA-binding protein likely involved with mtDNA transcript processing, suggesting an additional mechanism of mitochondrial pathophysiology. Similar strategies to integrate diverse genomic information can be applied likewise to other disease pathways and will become increasingly powerful with the growing wealth of diverse, functional genomics data.

Amino Acid Sequence↗

Fostering international collaboration in birth defects research and prevention: a perspective from the International Clearinghouse for Birth Defects Surveillance and Research.

The International Clearing-house for Birth Defects Surveillance and Research, formerly known as International Clearinghouse of Birth Defects Monitoring Systems, consists of 40 registries worldwide that collaborate in monitoring 40 types of birth defects. Clearinghouse activities include the sharing and joint monitoring of birth defect data, epidemiologic and public health research, and capacity building, with the goal of reducing disease and promoting healthy birth outcomes through primary prevention.We discuss 3 of these activities: the collaborative assessment of the potential teratogenicity of first-trimester use of medications (the MADRE project), an example of the intersection of surveillance and research; the international databases of people with orofacial clefts, an example of the evolution from surveillance to outcome research; and the study of genetic polymorphisms, an example of collaboration in public health genetics.

Abnormalities, Drug-Induced↗

Combinatorial signaling codes for the progressive determination of cell fates in the Drosophila embryonic mesoderm.

Mesodermal progenitors arise in the Drosophila embryo from discrete clusters of lethal of scute (l'sc)-expressing cells. Using both genetic loss-of-function and targeted ectopic expression approaches, we demonstrate here that individual progenitors are specified by the sequential deployment of unique combinations of intercellular signals. Initially, the intersection between the Wingless (Wg) and Decapentaplegic (Dpp) expression domains demarcate an ectodermal prepattern that is imprinted on the adjacent mesoderm in the form of a L'sc precluster. All mesodermal cells within this precluster are competent to respond to a subsequent instructive signal mediated by two receptor tyrosine kinases (RTKs), the Drosophila epidermal growth factor receptor (DER) and the Heartless (Htl) fibroblast growth factor receptor. By monitoring the expression of the diphosphorylated form of mitogen-associated protein kinase (MAPK), we found that these RTKs are activated in small clusters of cells within the original competence domain. Each cluster represents an equivalence group because all members initially resemble progenitors in their expression of both L'sc and mesodermal identity genes. Thus, localized RTK activity induces the formation of mesodermal equivalence groups. The RTKs remain active in the single progenitor that emerges from each cluster under the subsequent inhibitory influence of the neurogenic genes. Moreover, DER and Htl are differentially involved in the specification of particular progenitors. We conclude that distinct cellular identity codes are generated by the combinatorial activities of Wg, Dpp, EGF, and FGF signals in the progressive determination of embryonic mesodermal cells.

Animals↗

Differential association of family subsystem negativity on siblings' maladjustment: using behavior genetic methods to test process theory.

This study investigated the family context of adolescent sibling similarity and differentiation in maladjustment (antisocial behavior and depression) by examining negativity in different subsystems. Two hypotheses were proposed: (1) Parental and sibling negativity tends to diffuse through the family system, especially because of the high level of reciprocity in sibling relationships, leading to sibling similarity; and (2) interparental (coparenting) conflict disrupts cohesive functioning and thereby motivates and facilitates sibling differentiation and niche picking. To control for the effects of similar genes between siblings, the authors used behavioral genetic models with a genetically informed sample of 720 two-parent families, each with at least 2 adolescent siblings. Results for the differences in shared environmental influences across groups high and low in each of the domains of family negativity provided partial support for the hypotheses. The results further understanding of influences on individual differences and support a theory of how parent-child and interparental relationships intersect with sibling relationship dynamics.

Adaptation, Psychological↗

Polymorphisms in cytoplasmic serine hydroxymethyltransferase and methylenetetrahydrofolate reductase affect the risk of cardiovascular disease in men.

Genetic variation in folate-regulating enzymes contributes to the risk of cardiovascular disease (CVD). The cytoplasmic serine hydroxymethyltransferase (cSHMT) enzyme is proposed to regulate a key metabolic intersection in folate metabolism. We hypothesized that a variant in cSHMT (cSHMT 1420C-->T) affects CVD risk, and that the effect depends on a linked step in the metabolic pathway catalyzed by methylenetetrahydrofolate reductase (MTHFR). A nested case-control study of incident CVD was conducted within the all-male Normative Aging Study cohort. Of the incident CVD cases, 507 had DNA samples; 2 controls/case were selected by risk set sampling (matched on age and birth year). A significant gene-gene interaction (P-values 0.0013, 0.0064) was found between MTHFR and cSHMT, and there was little or no change in the coefficients in covariate-adjusted models. The effect of MTHFR 677C-->T genotype on CVD risk varied by cSHMT 1420C-->T genotype. Among men with cSHMT 1420C-->T TT genotype, the odds ratios (OR) for CVD risk for MTHFR 677C-->T CT and TT genotypes compared with the MTHFR 677C-->T CC genotype were 3.6 (95% CI, 1.7-7.8) and 10.6 (95% CI, 2.5-46.0), respectively. Among men with the cSHMT 1420C-->T CC/CT genotype, the corresponding ORs were 1.0 (95% CI, 0.8-1.2) and 1.3 (95% CI, 0.9-1.8). Plasma total homocysteine concentrations were highest in the subgroup of men with both polymorphisms, MTHFR 677C-->T TT and cSHMT 1420C-->T TT, consistent with a higher risk of CVD in this subgroup. A more complete understanding of the molecular mechanism awaits identification of the functional effect of the polymorphism.

Adult↗

Quantitative studies of very low density lipoprotein: conversion to low density lipoprotein in normal controls and primary hyperlipidaemic states and the role of direct secretion of low density lipoprotein in heterozygous familial hypercholesterolaemia.

Autologous 131I-labelled very low density lipoprotein (VLDL) and 125I-labelled low density lipoprotein (LDL) were injected into seven normal subjects and twenty-eight genetically classified hyperlipidaemic patients to quantitate lipoprotein interconversion. The apoprotein B specific activity--time curves for VLDl and intermediate density lipoprotein (IDL, density = 1 . 006--1 . 019 g/ml) intersected at or before the IDL-B maximum in thirty-one studies (five normal controls and twenty-six hyperlipidaemic subjects) implying that all IDL-B may be derived from VLDL-B. The fractional conversion of VLDL-B to LDL-B (density 1 . 019--1 . 063 g/ml) following a simultaneous spike injection of 131I-VLDL and 125-LDL was obtained by deconvolution of the 125I and 131I-LDL-B activity curves. 21--65% (mean = 44%) of VLDL-B was converted to LDL-B in twenty-three subjects studied. The mean conversion time ranged from 10 to 24 h in ten normotriglyceridaemic subjects and from 19 to 42 h (mean = 33 h) in twelve hypertriglyceridaemic subjects. In one patient with broad-beta disease the mean conversion time was 55 h. LDL-B production from VLDL-B and total LDL-B synthetic rate were essentially equal in normal controls and normocholesterolaemic subjects and in the patient with broad-beta disease. But in all six patients with familial hypercholesterolaemia LDL-B synthetic rate significantly exceeded LDL-B production from VLDL-B, indicating direct secretion of 20--72% of LDL-B at a rate which correlates positively with plasma LDL concentration. Three of five patients with familial combined hyperlipidaemia showed a lesser but nevertheless significant direct secretion of LDL-B.

Humans↗

Intersecting pathways to neurodegeneration in Parkinson's disease: effects of the pesticide rotenone on DJ-1, alpha-synuclein, and the ubiquitin-proteasome system.

Sporadic Parkinson's disease (PD) is most likely caused by a combination of environmental exposures and genetic susceptibilities, although there are rare monogenic forms of the disease. Mitochondrial impairment at complex I, oxidative stress, alpha-synuclein aggregation, and dysfunctional protein degradation, have been implicated in PD pathogenesis, but how they are related to each other is unclear. To further evaluated PD pathogenesis here, we used in vivo and in vitro models of chronic low-grade complex I inhibition with the pesticide rotenone. Chronic rotenone exposure in vivo caused oxidative modification of DJ-1, accumulation of alpha-synuclein, and proteasomal impairment. Interestingly, the effects become more regionally restricted such that systemic complex I inhibition eventually results in highly selective degeneration of the nigrostriatal pathway. DJ-1 modifications, alpha-synuclein accumulation, and proteasomal dysfunction were also seen in vitro and these effects could be prevented with alpha-tocopherol. Thus, chronic exposure to a pesticide and mitochondrial toxin brings into play three systems, DJ-1, alpha-synuclein, and the ubiquitin-proteasome system, and implies that mitochondrial dysfunction and oxidative stress link environmental and genetic forms of the disease.

Animals↗

Progress towards a biotypic biomarker profile for amyotrophic lateral sclerosis-frontotemporal spectrum disorders.

Determining the optimal timing of disease-modifying therapies for neurodegenerative disorders will necessitate identification of when the underlying pathobiological process becomes active, well in advance of the point at which clinical manifestions appear. Phenoconversion, the emergence of clinically manifest syndomes, may be preceded by years to decades of silent pathobiological activity that can only be mapped by an array of biomarkers. ALS and FTD, traditionally identified as distinct clinical syndromes, are increasingly recognized to exist along a spectrum of clinical syndromes with shared genetic risk and shared underlying pathology. This clinicopathological spectrum is underpinned by cytoplasmic aggregation of TAR DNA-binding protein 43 (TDP-43) as the common neuropathological hallmark. In contrast, the majority of neuropathologically-defined frontotemporal lobar degeneration (FTLD) is associated with alterations in either TDP-43 metabolism (FTLD-TDP) or of the microtubule associated protein tau (FTLD-tau), with a smaller percentage associated with either autosomal dominant genetic mutations or impairments in the ubiquitin proteasome system. As the field of neurodegenerative disorders increasingly shifts towards the frameworks of a pathobiological definition of disease, there is a growing imperative to develop biomarkers that reflect the varied pathobiologies that underly these disorders, and to determine the sensitivity of such biomarkers to detect the presence of these pathobiologies before phenoconversion. To that end, an international workshop was convened in London, Canada in 2025 to review the evidence for existing or evolving biomarkers suitable for (1) the detection of either ALS or FTD pathobiology prior to phenoconversion and/or (2) predict phenoconversion in at risk individuals. Such biomarkers might be conceptualized as "biotypic biomarkers", capturing their ability to describe an underlying pathophysiology whilst being agnostic to the emergent clinical manifestations. Whereas no single biotypic marker is yet able to predict the emergence of ALS, FTD or their intersection, a multimodal approach to developing a biotypic biomarker profile holds promise for the detection of relevant pathobiological processes. The strength of such an approach would be augmented by also addressing issues of resiliency/susceptibility both in terms of genetic risk susceptibility profiles and developing sensitive biomarkers of genomic and cellular aging. By including such nontraditional markers of disease, a more robust picture of not only the degenerative process but also of those factors that might potentially mitigate or drive a heightened probability of disease can be derived.

cryptic exons↗

Defective central tolerance induction in NOD mice: genomics and genetics.

The genetic determinism of type-1 diabetes in NOD mice likely involves complementary defects in central T cell tolerance induction and peripheral immunoregulation. To study the contribution of the NOD genetic background to central tolerance, we followed the behavior of BDC2.5 clonotype thymocytes in fetal thymic organ cultures (FTOC). The NOD genetic background encodes a quantitative deficiency in the ability to delete these self-reactive thymocytes and to divert them to the CD8alphaalpha lineage. In genetic analyses, comparing NOD and B6.H2g7 FTOCs, the NOD defect incorporated the influence of several loci (notably ones on chr1 and 3). Microarray analyses assessing FTOCs from the same two strains argued that the NOD abnormality reflects the combined effects of turning down the gene expression program that provokes apoptosis and turning on a new program promoting cell survival. Intersection of the data from the two approaches points to a small set of attractive candidate genes.

Animals↗

Targeted therapy by disabling crossroad signaling networks: the survivin paradigm.

Embedded in the concept of targeted cancer therapy is the expectation that disabling a single oncogenic pathway will eliminate the tumor cells and leave the normal tissues unscathed. Although validated by clinical responses in certain malignancies, challenges exist to generalize this approach to most tumors, as multiple genetic lesions, chromosomal instability, insensitivity of the cancer stem cell compartment, and emergence of drug resistance complicate the identification and therapeutic exploitation of a single, driving oncogenic pathway. Instead, broader therapeutic prospects may be offered by targeting crossroad signaling networks that are selectively exploited in cancer and oversee multiple aspects of tumor cell maintenance. One such pathway is centered on survivin, a cancer gene that intersects cell proliferation, cell survival, and the cellular stress response. Several clinical trials targeting survivin with a collection of approaches from immunotherapy to small-molecule antagonists are currently under way. By simultaneously disabling multiple signaling circuitries, targeting survivin may provide a novel perspective in rational cancer therapy selective for specific cancer mechanisms but broadly applicable to disparate tumors regardless of their genetic makeup.

Genetic Therapy↗

Carbon and nitrogen sensing and signaling in plants: emerging 'matrix effects'.

Plants, like other organisms, have developed mechanisms that allow them to sense and respond to changes in levels of carbon and nitrogen metabolites. These mechanisms, in turn, regulate the expression of genes and the activities of proteins involved in C and N transport and metabolism, allowing plants to optimize the use of energy resources. Recent studies, which have involved molecular-genetic, genomic, and cell biological approaches, have begun to uncover the signals and components of C:N sensing and signaling mechanisms in plants. For sugar sensing, analysis of Arabidopsis mutants has revealed intersections with hormone and nitrogen signaling. For nitrogen sensing/signaling, recent progress has identified transcriptional and posttranslational mechanisms of regulation. In all, a complex picture is emerging in which C:N signaling systems are subject to a 'matrix effect' in which downstream responses are dependent upon cell-type, developmental, metabolic, and/or environmental conditions.

Anion Transport Proteins↗

Coronary x-ray angiographic reconstruction and image orientation.

We have developed an interactive geometric method for 3D reconstruction of the coronary arteries using multiple single-plane angiographic views with arbitrary orientations. Epipolar planes and epipolar lines are employed to trace corresponding vessel segments on these views. These points are utilized to reconstruct 3D vessel centerlines. The accuracy of the reconstruction is assessed using: (1) near-intersection distances of the rays that connect x-ray sources with projected points, (2) distances between traced and projected centerlines. These same two measures enter into a fitness function for a genetic search algorithm (GA) employed to orient the angiographic image planes automatically in 3D avoiding local minima in the search for optimized parameters. Furthermore, the GA utilizes traced vessel shapes (as opposed to isolated anchor points) to assist the optimization process. Differences between two-view and multiview reconstructions are evaluated. Vessel radii are measured and used to render the coronary tree in 3D as a surface. Reconstruction fidelity is demonstrated via (1) virtual phantom, (2) real phantom, and (3) patient data sets, the latter two of which utilize the GA. These simulated and measured angiograms illustrate that the vessel center-lines are reconstructed in 3D with accuracy below 1 mm. The reconstruction method is thus accurate compared to typical vessel dimensions of 1-3 mm. The methods presented should enable a combined interpretation of the severity of coronary artery stenoses and the hemodynamic impact on myocardial perfusion in patients with coronary artery disease.

Adult↗

Genetic analysis of Pten and Ink4a/Arf interactions in the suppression of tumorigenesis in mice.

Dual inactivation of PTEN and INK4a/ARF tumor suppressor genes is a common feature observed in a broad spectrum of human cancer types. To validate functional collaboration between these genes in tumor suppression, we examined the biological consequences of Pten and/or Ink4a/Arf deficiency in cells and mice. Relative to single mutant controls, Ink4a/Arf-/-Pten+/- mouse embryonic fibroblast cultures exhibited faster rates of growth in reduced serum, grew to higher saturation densities, produced more colonies upon low density seeding, and showed increased susceptibility to transformation by oncogenic H-Ras. Ink4a/Arf deficiency reduced tumor-free survival and shortened the latency of neoplasias associated with Pten heterozygosity, specifically pheochromocytoma, prostatic intraepithelial neoplasia, and endometrial hyperplasia. Compound mutant mice also exhibited an expanded spectrum of tumor types including melanoma and squamous cell carcinoma. Functional synergy between Ink4a/Arf and Pten manifested most prominently in the development of pheochromocytoma, prompting an analysis of genes and loci implicated in this rare human neoplasm. The classical pheochromocytoma genes Ret, Vhl, and Nf-1 remained intact, a finding consistent with the intersection of these genes with pathways engaged by Pten and Ink4a/Arf. Notably, conventional and array-comparative genomic hybridization revealed frequent loss of distal mouse chromosome 4 in a region syntenic to human chromosome 1p that is implicated in human pheochromocytoma. This study provides genetic evidence of collaboration between Pten and Ink4a/Arf in constraining the growth and oncogenic transformation of cultured cells and in suppressing a wide spectrum of tumors in vivo.

Adrenal Gland Neoplasms↗