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Goldman, J.

Publications and source records attributed to Goldman, J..

3 recordsLinked to original sources

Comparative assessment of genes driving cancer and somatic evolution.

Genetic alterations of somatic cells can drive nonmalignant clone formation and promote cancer initiation. However, the link between these processes remains unclear hampering our understanding of tissue homeostasis and cancer development. Here we collect a literature-based repertoire of 3355 well-known or predicted drivers of cancer and noncancer somatic evolution in 122 cancer types and 12 noncancer tissues. Mapping the alterations of these genes in 7953 pancancer samples reveals that, despite the large size, the known compendium of drivers is still incomplete and biased towards frequently occurring coding mutations. High overlap exists between drivers of cancer and noncancer somatic evolution, although significant differences emerge in their recurrence. We confirm and expand the unique properties of drivers and identify a core of evolutionarily conserved and essential genes whose germline variation is strongly counter-selected. Somatic alteration in even one of these genes is sufficient to drive clonal expansion but not malignant transformation. Our study offers a comprehensive overview of our current understanding of the genetic events initiating clone expansion and cancer revealing significant gaps and biases that still need to be addressed. The compendium of cancer and noncancer somatic drivers, their literature support and properties are accessible at http://www.network-cancer-genes.org/.

cancer biology

Impact of Propionic Acidemia on Brain Astrocytes

Propionic acidemia (PA) is an inborn error of metabolism (IEM) caused by mutations in the enzyme propionyl CoA carboxylase (PCC). It is characterized by the inability to break down branched chain amino acids and odd chain fatty acids, causing a buildup of toxic organic acids in blood. PA affects every organ in the body with particularly severe manifestations in the brain, like hyperammonemia, hypomyelination, seizures, cognitive impairments, optic nerve atrophy and autism spectrum disorders. Dietary management and liver transplantation have helped to ameliorate the acute expression of the disorder, but do not prevent the chronic toxicity that builds up in brain. Despite the severe brain manifestation of the disease, little is known about the mechanisms by which PA affects the nervous system. PCCA and PCCB, the two subunits required for a functional PCC enzyme, are both expressed not only in neurons but also in astrocytes. Using the two rodent genetic models of PA currently available, with mutations in PCCA, we have evaluated the involvement of astrocytes in the neuropathology of propionic acidemia. These mice exhibit cardiac pathology and hyperammonemia, similar to what is observed in patients with PA. We found that wild type (wt) astrocytes positively respond to treatment with L-Carnitine, a therapeutic approach commonly used in patients with PA, by improved survival and more efficient mitochondrial morphology. Transcriptome analysis from astrocytes derived from the wt or the mutant mice confirm that these astrocytes lack exons 3 and 4 like in the human mutations of PA. However, no other genes/exons were statistically significant with regards to differential expression between astrocytes derived from KO or from WT animals, suggesting that astrocytes in culture may be able to compensate the PCC deficiency. Histological analysis of neuronal and glial markers during brain development (TUJ1, MAP2 for neurons; nestin and Iba1 for glia) do not show significant alterations neither in distribution nor numbers of cells in the developing brain of the PCCA-/- mice. Analysis in the adult brain of mutant mice shows some variable degree of microgliosis but no indication of reactive astrocytes. No gross abnormalities were observed in cortex, hippocampus, striatum or cerebellum of adult brains of PCCA-/- mice, either. In summary, astrocytes from PCCA deficient mice show surprisingly little alterations both in vitro and in vivo. Our results evidence the need to further understand the effects of PA in brain cells to help develop potential new therapies that can preserve brain function in children affected by this devastating disease. HIGHLIGHTSO_LIAstrocytes detoxify ammonia in brain and may be affected by propionic acidemia, a disorder that causes hyperammonemia in brain. C_LIO_LIRNA seq of astrocytes in culture derived from PCCA mutant mice does not show effect in these cells. C_LIO_LIIn vivo analysis of glial and neuronal cells also shows no difference in development or adult mutant mice C_LIO_LIAstrocytes may not be an adequate target of clinical therapies in this disorder C_LI

neuroscience

Brain-scale emergence of slow-wave synchrony and highly responsive asynchronous states based on biologically realistic population models simulated in The Virtual Brain

Understanding the many facets of the organization of brain dynamics at large scales remains largely unexplored. Here, we construct a brain-wide model based on recent progress in biologically-realistic population models obtained using mean-field techniques. We use The Virtual Brain (TVB) as a simulation platform and incorporate mean-field models of networks of Adaptive Exponential (AdEx) integrate-and-fire neurons. Such models can capture the main intrinsic firing properties of central neurons, such as adaptation, and also include the typical kinetics of postsynaptic conductances. We hypothesize that such features are important to a biologically realistic simulation of brain dynamics. The resulting "TVB-AdEx" model is shown here to generate two fundamental dynamical states, asynchronous-irregular (AI) and Up-Down states, which correspond to the asynchronous and synchronized dynamics of wakefulness and slow-wave sleep, respectively. The synchrony of slow waves appear as an emergent property at large scales, and reproduce the very different patterns of functional connectivity found in slow-waves compared to asynchronous states. Next, we simulated experiments with transcranial magnetic stimulation (TMS) during asynchronous and slow-wave states, and show that, like in experimental data, the effect of the stimulation greatly depends on the activity state. During slow waves, the response is strong but remains local, in contrast with asynchronous states, where the response is weaker but propagates across brain areas. To compare more quantitatively with wake and slow-wave sleep states, we compute the perturbational complexity index and show that it matches the value estimated from TMS experiments. We conclude that the TVB-AdEx model replicates some of the properties of synchrony and responsiveness seen in the human brain, and is a promising tool to study spontaneous and evoked large-scale dynamics in the normal, anesthetized or pathological brain.

neuroscience