L’intestino nella L’intestino nella prospettiva dell’epigeneticaprospettiva dell’epigenetica

Domenico MastrangeloDomenico Mastrangelo

Senior Scientist (research)Senior Scientist (research)Dipartimento di Scienze MedicheDipartimento di Scienze Mediche

Chirurgiche e NeurologicheChirurgiche e Neurologiche

Università degli Studi di SienaUniversità degli Studi di Siena

LA GENETICA MENDELIANALA GENETICA MENDELIANA

GENE = porzione discreta di DNA che sintetizza una proteina

Espressione genica = sintesi di una proteina da parte di un gene

REGOLAZIONE GENETICA DELL’ESPRESSIONE GENICA

Human Genome Project (HGP)Human Genome Project (HGP)

- 3,6 miliardi di paia di basi 3,6 miliardi di paia di basi nel DNA genomiconel DNA genomico- costo dell’HGP – 2,7 miliardi dollaricosto dell’HGP – 2,7 miliardi dollari- numero di geni umani previsto > 100.000numero di geni umani previsto > 100.000- Drosophila 14.000 geni, pollo 23.000 geni; mais 59.000 geni; Drosophila 14.000 geni, pollo 23.000 geni; mais 59.000 geni; uomo 25.000 geniuomo 25.000 geni

Geni che codificano proteine

Pseudogeni

DNA non codificanteSequenze uniche

DNA non codificanteSequenze ripetitive

IL “MICROCOSMO” (DNA)IL “MICROCOSMO” (DNA)

Spazzatura??? Spazzatura???

Spazzatura???

MateriaMateriaOscuraOscura

73%73%

EnergiaEnergiaOscuraOscura

23%23%

Atomi6%

IL “MACROCOSMO” (Universo)IL “MACROCOSMO” (Universo)

… last fall, scientists with the international ENCODE (the Encyclopedia OfDNA Elements) consortium, launched by the National Genome Research Institute in 2003, announced what the authors said was a breakthrough in identifying all the functional elements in the human genome sequence. Published across 30 papers in Nature, the consortium claimed that long stretches of DNA, previously dismissed as “junk”, are in fact crucial to the way our genome works …

THE MYTH OF “JUNK” DNATHE MYTH OF “JUNK” DNA

98% of human chromosomes98% of human chromosomesare “junk” DNA between genes.are “junk” DNA between genes.Large sections are remnants ofLarge sections are remnants ofviral and bacterial infectionsviral and bacterial infections

Collectively, the papers describe 1,640 data sets generated across 147 different cell types. Among the many important results there is one that stands out above them all: more than 80% of the human genome's components have now been assigned at least one biochemical function.

LA GENETICA MENDELIANA NON SPIEGA …LA GENETICA MENDELIANA NON SPIEGA …

… … come si possa generare tanta diversità fenotipica e complessitàcome si possa generare tanta diversità fenotipica e complessitàfunzionale a partire da uno stesso (ed unico) DNA! … funzionale a partire da uno stesso (ed unico) DNA! …

MUTAZIONIMUTAZIONIalterazioni della alterazioni della strutturastruttura del DNA … del DNA …

… … o dei cromosomi di cuio dei cromosomi di cuiil DNA rappresenta l’ossatura …il DNA rappresenta l’ossatura …

EPIGENETICAEPIGENETICA

… … il termine fu coniato nel 1942 da Conrad Hal il termine fu coniato nel 1942 da Conrad Hal Waddington, per definire: Waddington, per definire: ““ … lo studio delle … lo studio delle modificazioni ereditabili dell’ espressione genica modificazioni ereditabili dell’ espressione genica o del fenotipo cellulare, non legate a o del fenotipo cellulare, non legate a cambiamenti della struttura del DNA.cambiamenti della struttura del DNA.” ”

MECCANISMI DI REGOLAZIONE EPIGENETICA MECCANISMI DI REGOLAZIONE EPIGENETICA DELL’ESPRESSIONE GENICADELL’ESPRESSIONE GENICA

MECCANISMI DI REGOLAZIONE EPIGENETICA MECCANISMI DI REGOLAZIONE EPIGENETICA DELL’ESPRESSIONE GENICADELL’ESPRESSIONE GENICA

MECCANISMI DI REGOLAZIONE EPIGENETICA MECCANISMI DI REGOLAZIONE EPIGENETICA DELL’ESPRESSIONE GENICADELL’ESPRESSIONE GENICA

MECCANISMI DI REGOLAZIONE EPIGENETICA MECCANISMI DI REGOLAZIONE EPIGENETICA DELL’ESPRESSIONE GENICADELL’ESPRESSIONE GENICA

Una sola cellula… un solo DNA e … migliaia di fenotipi cellulari …Una sola cellula… un solo DNA e … migliaia di fenotipi cellulari …

Il DNA delle cellule germinali presenta numerosi “tags” epigenetici inquanto tutte le cellule di un individuo adulto sono “specializzate” per svolgere compiti definiti. Con la fecondazione questi “tags” vengono

rimossi e l’oocita può trasformarsi in qualsiasi tipo di cellula …

… … come si possa generare tanta diversità fenotipica e complessitàcome si possa generare tanta diversità fenotipica e complessitàfunzionale a partire da una singola cellula! … funzionale a partire da una singola cellula! …

L’EPIGENETICA (non la genetica mendeliana!) SPIEGA …L’EPIGENETICA (non la genetica mendeliana!) SPIEGA …

Principi:Principi:

1.1.L’espressione genica non dipende (solo) da L’espressione genica non dipende (solo) da cambiamenti (mutazioni) nella struttura del DNAcambiamenti (mutazioni) nella struttura del DNA2.2.Il “fenotipo” cellulare” (l’aspetto e le caratteristiche Il “fenotipo” cellulare” (l’aspetto e le caratteristiche di una cellula) non è dovuto (solo) a cambiamenti di una cellula) non è dovuto (solo) a cambiamenti (mutazioni) della struttura del DNA(mutazioni) della struttura del DNA3.3.Un “fenotipo” cellulare può essere ereditato Un “fenotipo” cellulare può essere ereditato indipendentemente da cambiamenti (mutazioni) nella indipendentemente da cambiamenti (mutazioni) nella struttura del DNAstruttura del DNA

EPIGENETICAEPIGENETICA

Epigenetics, or why the question isn't "Environment OR Genetics"

ENVIRONMENT = The combination of external physical conditions that affect and influence the growth, development, and survival of organisms

… environmental factors may exert neurobiological and behavioral effects through epigenetic changes. “Environment” in this context can be used in the very broad sense and include hormonal, social, nutritional, and toxicological exposures occurring prenatally, postnatally, or in adulthood. During prenatal development, adverse experiences are associated with a heightened risk of physical and psychiatric dysfunction … (Champagne FA, Risman EF: Behavioral epigenetics: A new frontier in the study of hormones and

behavior. Hormones and Behavior 59 (2011) 277–278)

Beta-adrenergic signaling from the sympathetic nervous system has been found to up-regulated a diverse array of genes that contribute to tumor progression and metastasis, whereas glucocorticoid-regulated genes can inhibit DNA repair and promote cancer cell survival and resistance to chemotherapy… (Cole SW: Nervous system regulation

of the cancer genome. Brain, Behavior, and Immunity 30 (2013) S10–S18)

Jean-Baptiste Lamarck (1744-1829) is best remembered for a discredited theory of heredity, the "inheritance of acquired traits." He proposed that environment changes caused changes in behavior which in turn led to the increase or decrease of particular structures. Lamarck had a colorful and distinguished career: in turns soldier, bank clerk, Professor of "insects and worms" he died a poor man and was buried in a rented grave.

It is increasingly recognized that environmental exposure to chemical, nutritional and behavioral factors alters gene expression and affects health and disease by not only mutating promoter and coding regions of genes, but also by modifying the epigenome. Faulk C, Dolinoy DC: Timing is everything: The when and how of environmentally induced changes in the epigenome of animals Epigenetics 6:7, 791-797; July 2011;

CANCER EPIGENETICS

L’ereditarietà dei caratteri acquisiti …L’ereditarietà dei caratteri acquisiti …J.B. LamarckJ.B. Lamarck

?

a) Dietary supplementation of female mice during pregnancy. The diets of female a/a mice are supplemented with methyl-donating substances (that is, folic acid, choline, vitamin B12 and betaine) or the phytoestrogen genistein 2 weeks before mating with male Avy/a agouti mice, and throughout pregnancy and lactation

b) Maternal dietary supplementation and coat-colour distribution in Avy/a offspring. The coat colour is primarily yellow in the offspring that are born to unsupplemented mothers, whereas it is mainly brown in the offspring from mothers that were supplemented with methyl-donating compounds or genistein. 

?

L’intestino è la sede principale del sistema immunitario …

During the differentiation of T and B cells, immune-receptor loci in the genome must be made sterically accessible so that they can undergo rearrangement. Here, we discuss how this is carried out by the stepwise removal of epigenetic repression mechanisms — such as later-replication timing, heterochromatization, histone hypo-acetylation and DNA methylation — in a manner that initially favours one allele in each cell. We propose that this mechanism of allelic exclusion might also be the basis for the generation of gene diversity in other systems.

L’epigenetica e’ alla base del funzionamento del sistema immunitario

L’epigenetica e’ alla base del funzionamento del sistema immunitario

L’epigenetica e’ alla base del funzionamento del sistema immunitario

L’epigenetica e’ alla base del funzionamento del sistema immunitario

THE HUMAN MICROBIOME

The human microbiome refers to all of the microbial organisms that reside in the body including bacteria, fungi, and archaea.  Notably, the human body contains over 10 times more microbial cells than human cells!

… il rapporto cellule/batteri, nell’organismonormale, è 1/10 (per ogni cellula, 10 batteri! …)

Through live-birth, mammals have important opportunities for mother-to-child microbial transmission through direct surface contact. However, many modern practices can reduce organism and gene flow; several examples are illustrated. After initial introductions, there is strong selection by hosts for microbes with specific phenotypes, consistent with the extensive conservation shown in Fig. 1. Acquisition is modified by differences in offspring genetics and epigenetics (with respect to both maternal and paternal genes) that inform the competition for host resources by the vertically transmitted or environmentally acquired microbes. Ancestral organisms that have particular tissue-specific and niche-specific adaptations facilitate tissue tropisms and are selected for, thus explaining the conserved niche-specificity compositions.

THE GUT MICROBIOTA

… is part of the human microbiome …

THE GUT MICROBIOTA… time to get a little dirty? …

… is part of the human microbiome …

Composition and luminal concentrations of dominant microbial species in various regions of the gastrointestinal tract.

Gut microbiota is an assortment of microorganisms inhabiting the length and width of the mammalian gastrointestinal tract. The composition of this microbial community is host specific, evolving throughout an individual's lifetime and susceptible to both exogenous and endogenous modifications.

THE GUT MICROBIOTA

THE GUT MICROBIOTA

THE GUT MICROBIOTA

… and the epigenetic regulation of the immune system …

THE GUT MICROBIOTA

… and the “environment” ……

… the multiple low-molecular-weight substances of indigenous gut microbiota origin should be considered one of the main endogenous factors actively participating in epigenomic mechanisms that are responsible for the mammalian genome reprograming and post-translated modifications. Gut microecological imbalance caused by various biogenic and abiogenic agents and factors can produce different epigenetic abnormalities and the onset and progression of metabolic diseases associated …

Shenderov BA et al: Gut indigenous microbiota and

Epigenetics. Microbial Ecology in Health & Disease 2012, 23: 17195 - DOI: 10.3402/mehd.v23i0.17195

THE GUT MICROBIOTATHE GUT MICROBIOTA

The complex web of gut microbiota contributions to host physiology. Different gut microbiota components can affect many aspects of normal host development, while the microbiota as a whole often exhibits functional redundancy. In gray are shown members of the microbiota, with their components or products of their metabolism. In white are shown their effects on the host at the cellular or organ level. Black ellipses represent the affected host phenotypes. Only some examples of microbial members/components contributing to any given phenotype are shown. AMP, antimicrobial peptides; DC, dendritic cells; Gm−, Gram negative; HPA, hypothalamus-pituitary-adrenal; Iap, intestinal alkaline phosphatase; PG, peptidoglycan; PSA, polysaccharide A.

THE GUT MICROBIOTATHE GUT MICROBIOTA

Gut microbiota now appears to influence the host at nearly every level and in every organ system, highlighting our interdependence and coevolution. Its adaptation to our changing life-styles (such as diet- and ethnicity-associated differences in gut microbiota composition) is astounding, highlighting that the consequences of our behaviors affect not only the environment without, but also that within us.

Inna Sekirov, Shannon L. Russell, L. Caetano M. Antunes, and B. Brett Finlay: Gut Microbiota in Health and Disease Physiol Rev 90: 859–904, 2010; doi:10.1152/physrev.00045.2009.

THE GUT MICROBIOTATHE GUT MICROBIOTA… … and health …and health …

THE BRAIN-GUT AXISTHE BRAIN-GUT AXIS… … health … and epigenetics …health … and epigenetics …

THE BRAIN-GUT AXISTHE BRAIN-GUT AXIS… … health … and epigenetics …health … and epigenetics …

THE BRAIN-GUT-MICROBIOTA AXISTHE BRAIN-GUT-MICROBIOTA AXIS… … health … and epigenetics …health … and epigenetics …

The novel conceptual model “Brain-Gut-Microbiota Axis” has received emerging attention recently

THE BRAIN-GUT-MICROBIOTA AXISTHE BRAIN-GUT-MICROBIOTA AXIS… … health … and epigenetics …health … and epigenetics …

Gut microbes produce substance such as tryptophan-related metabolites kynurenic acid, short chain fatty acids, and neurometabolites GABA, noradrenalin, and dopamine that potentially target to and influence functions of our central nervous systems.

… Mind altering microorganisms …

In the process of neurodevelopment, they modulate the expression level of many critical genes, such as brain-derived neurotropic factor (BDNF), NMDA receptors or 5-HT receptors and communicate with brain regions like striatum, hippocampus, amygdale, hypothalamus, and cingulated gyrus.

… and microbiota altering brain …

It has long been known that the colonization of gut flora is related to the stress response of the hosts, changing their states of anxiety and exploratory behavior.

Colorectal Cancer Epigenetics: Complex Simplicity