GENOMICA

ASIST. UNIV DR FLORINA MIHAELA NEDELEA

GENOMICA

 1. CARTOGRAFIEREA CARACTERELOR MENDELIENE

 2. DEZECHILIBRU DE LINKAGE

 3. SECVENTIEREA GENOMULUI UMAN SI PROIECTUL GENOMULUI

UMAN

 4. NUTRIGENOMICA

 5. PROTEOMICA
 1. CARTOGRAFIEREA
CARACTERELOR MENDELIENE
 Cartografierea genica=determinarea localizarii unei gene pe un
anumit cromozom.

 Utilitate:
 -intelegerea mecanismelor bolilor genetice,
 -diagnosticul bolilor genetice,
 -stabilirea riscului de recurenta in familie,
 -eventual tratament.
CARTOGRAFIEREA CARACTERELOR
MENDELIENE
 Realizarea unei harti complete a genomului uman , o
“enciclopedie a tuturor genelor si bolilor genetice associate lor”, a
devenit punctual cheie al geneticii .

 Cartografierea genelor a fost o etapa prealabila necesara in

abordarea si finalizarea Genomului Uman.

 Cartografierea genica =localizarea unor gene care determina boli

monogenice sau susceptibilitate la boala,
Cartografierea genomului uman

 Cartografierea genelor pe cromozomii umani s-a realizat folosind

doua metode:

 -cartografierea genetica

 -cartografierea fizica.
Cartografierea genetica

 Cartografierea genetica reprezinta evaluarea tendintei a doua

segmente de ADN, o gena morbida si un marker, de a segrega
impreuna in meioza, si de a se transmite inlantuite de la parinti la
descendenti

 Prin studiul fenomenelor de inlantuire si recombinare genica

omoloaga (crossing over in meioza) se poate masura diastanta intre
locii genetici.
Cartografierea genetica

 Localizarea unei gene morbide incepe cu studiul familiilor in care se

manifesta boala.

 La membrii acestor familii se studiaza distributia bolii si a unor markeri

polimorfi , urmarind inlantuirea intre gene morbida si un anumit
marker. Pentru a fi utili in cartografiere, markerii trebuie sa fie inalt
polimorfi, si astfel creste probabilitatea ca familiile sa fie informative.

 Datorita marimii genomului uman trebuiesc analizati sute de marker

pentru a gasi o inlantuire.
Cartografierea genetica

 Daca markerul si gena morbida se afla pe loci foarte apropiati pe

acelasi cromozom, ele au tendinta de a se transmite impreuna=CO-
SEGREGARE.

 Daca distanta creste, exista posibilitatea de crossing over si iar

segmentele nealele segrega si se transmit separat, formand
combinatii noi (recombinanti).

 Cu cat distanta fizica intre gene este mai mare, cu atat creste
probabilitatea unui eveniment recombinant.
Cartografierea genetica

 Distanta intre loci se poate determina comparand genotipurile

urmasilor cu cele ale parintilor si evaluand frecventa (fractia) de
recombinare. Este definita ca scorul LOD(logarithm of
odds)=proportia descendentilor recombinanti/numarul total de
descendenti.
 Unitatea de masura intre doi loci=Morgan, in onoarea lui Thomas
Morgan care a descoperit 1910 fenomenul de crossing-over.
 Un centiMorgan=distanta genetica in care se produc recombinari
cu frecventa de 1%
 1cM echivalent cu o secventa ADN de 1Mb.
Analizele de inlantuire (linkage)

 Sunt bazate pe studiul familiilor, reprezinta o metoda valoroasa de

cartografiere deoarece permite stabilirea pozitiei unor gene (loci)
pe acelasi cromozom=SINTENIE, a ordinii si distantei intre ele.

 In present tehnicile noi bazate pe microretele permit testarea

rapida a sute de mii de SNPs-uri raspandite in genom pentru a
urmari CO-SEGREGAREA cu un anumit fenotip (boala).
Inlantuirea genica(linkage)

 Genele situate pe acelasi cromozom au tendinta de a se transmite

de la parinti la descendenti, prin gameti, impreuna “in bloc”.

 Fenomenul prin care genele nealele situate in immediate

proximitate pe acelasi cromozom nu segrega (nu se separa) in
meioza si au tendinta de a se transmite impreuna in succesiunea
generatiilor=inlantuire genica=linkage.

 Genele dintr-o regiune cromozomiala care se transmit impreuna

formeaza un grup de inlantuire=haplotip.
Gene alele
Linkage
Inlantuirea genica(linkage)

 Fenomenul de inlantuire genica nu este unul abasolut deoarece

numai genele situate foarte aproape una de alta se vor transmite
impreuna (inlantuite ex genele C,D,e ce determina grupul sangvin
Rh localizate pe cromozomul 1 se transmit totdeauna impreuna).

 Pentru genele situate mai la distanta una de alta pe acelasi

cromozom inlantuirea genica poate fi incomplete, ele putand fi
separate prin crossing over.
N Engl J Med. 2009 May

 Epilepsy, ataxia, sensorineural deafness, tubulopathy, and KCNJ10

mutations.
 Fahad Mahmood,1, Horia C. Stanescu,2,4 Jonathan Tobin,4 Philip L. Beales,4Robert
Kleta,2,3,4,‡ Detlef Bockenhauer,2,4,‡ and Claire Russell1,‡,§

 Recently, we and others elucidated the pathophysiological basis of

a multisystem disorder characterised by infantile-onset epilepsy,
debilitating ataxia, sensorineural deafness and a salt-wasting
tubulopathy, i.e. EAST syndrome (Bockenhauer et al., 2009; Scholl et
al., 2009).
Epilepsy, ataxia, sensorineural deafness,
tubulopathy, and KCNJ10 mutations.
 Five children from two consanguineous families presented with
epilepsy beginning in infancy and severe ataxia, moderate
sensorineural deafness, and a renal salt-losing tubulopathy with
normotensive hypokalemic metabolic alkalosis.

 We investigated the genetic basis of this autosomal recessive

disease, which we call the EAST syndrome (the presence of
epilepsy, ataxia, sensorineural deafness, and tubulopathy).
 Epilepsy, ataxia, sensorineural deafness, tubulopathy, and KCNJ10
mutations.

 Genotypes were examined with the use of a multipoint parametric

linkage analysis and haplotype reconstruction performed with
SimWalk (version 2.91) for an autosomal recessive model with
complete penetrance and a disease allele frequency of 0.001
(deCode SNP map with Asian allele frequencies).8
 The data were formatted with Mega2 (version 4.0) through
ALOHOMORA (version 0.30, Win32).9,10
 Mendelian inconsistencies were checked with the use of PedCheck
(version 1.1); unlikely genotypes were filtered with the use of Merlin
(version 1.1, alpha 3).11,12 The SimWalk haplotype output files were
visualized with HaploPainter.13
 Linkage Studies

 A haplotype reconstruction (Panel A) for the locus on chromosome

1 shows identical alleles (indicated by the same color) in the linked
region in all affected patients. The numbers (i.e., 1 or 2) next to the
alleles indicate the respective status of the single-nucleotide
polymorphisms used for genotyping.
 Recombinations in Patients 1-1 and 1-2 define this region.
 The parametric multipoint linkage analysis of the whole genome for
Family 1 (Panel B) has a single significant peak, with a maximum lod
score of almost 5 on chromosome 1. Genetic distance (in
centimorgans) and individual chromosomes (1 to 22) are indicated
on the lower and upper x axes, respectively.
 METHODS:
 Whole-genome linkage analysis was performed in the four affected children in
one of the families. Newly identified mutations in a potassium-channel gene
were evaluated with the use of a heterologous expression system. Protein
expression and function were further investigated in genetically modified mice.
 RESULTS:
 Linkage analysis identified a single significant locus on chromosome 1q23.2 with
a lod score of 4.98. This region contained the KCNJ10 gene, which encodes a
potassium channel expressed in the brain, inner ear, and kidney. Sequencing of
this candidate gene revealed homozygous missense mutations in affected
persons in both families. These mutations, when expressed heterologously in
xenopus oocytes, caused significant and specific decreases in potassium
currents. Mice with Kcnj10 deletions became dehydrated, with definitive
evidence of renal salt wasting.
 CONCLUSIONS:
 Mutations in KCNJ10 cause a specific disorder, consisting of epilepsy, ataxia,
sensorineural deafness, and tubulopathy. Our findings indicate that KCNJ10
plays a major role in renal salt handling and, hence, possibly also in blood-
pressure maintenance and its regulation.
 IDENTIFIED MUTATIONS

 Sequencing of the complete coding region of KCNJ10 revealed a

homozygous missense mutation, c.194G→C (p.R65P), in the four
affected patients in Family 1 and another homozygous missense
mutation, c.229G→C (p.G77R) for Patient 2-1.

 Parents were heterozygous for the respective mutations

 Supported by the Intramural Research Programs of the National

Human Genome Research Institute, National Institutes of Health, the
Special Trustees of the Great Ormond Street Hospital, St. Peter’s Trust
for Kidney, Bladder, and Prostate Research, the Grocers’ Charity,
the David and Elaine Potter Charitable Foundation, and Deutsche
Forschungsgemeinschaft (SFB699).
Generation and validation of a zebrafish model of EAST (epilepsy, ataxia,
sensorineural deafness and tubulopathy) syndrome
Fahad Mahmood,1,* Monika Mozere,2,* Anselm A. Zdebik,2,3,* Horia C. Stanescu,2,4
Jonathan Tobin,4 Philip L. Beales,4Robert Kleta,2,3,4,‡ Detlef Bockenhauer,2,4,‡
Generation and validation of a zebrafish model of EAST (epilepsy, ataxia,
sensorineural deafness and tubulopathy) syndrome
Fahad Mahmood,1,* Monika Mozere,2,* Anselm A. Zdebik,2,3,* Horia C. Stanescu,2,4
Jonathan Tobin,4 Philip L. Beales,4Robert Kleta,2,3,4,‡ Detlef Bockenhauer,2,4,‡

 To test potential therapeutics, suitable disease models are needed.

 Because the mouse Kcnj10 knockout has a much more severe

phenotype (including brain dysmorphology and neonatal death)
than humans with EAST syndrome, it is not an ideal model.

 Here, the authors set out to develop a model of EAST syndrome

using zebrafish, because zebrafish embryos and larvae are ideal
for in vivo, high-throughput drug discovery.
GWAS=genome wide association
studies
 Sunt analize de asociere, bazate pe studii populationale.

 In acest caz se studiaza frecventa unui “set de markeri” la un grup

de personae afectate de o anumita boala, comparative cu un
grup de persoane sanatoase.

 GWAS sunt utilizate pentru identificarea unor variante genetice

cauzatoare de boli complexe, multifactoriale.
GWAS=genome wide association
studies
 GWAS sunt studii bazate pe ipoteza ca variantele alelice ce
determina susceptibiltatea la o boala comuna se asociaza mai
frecvent decat ne asteptam cu anumiti markeri care definesc o
anumita regiune genomica (haplotip).
 Identificarea haplotipului asociat bolii permite definirea regiunii in
care este localizata varianta cauzala.
 In ultimii ani proiecte international cum sunt Hap Map si
1000Genomes au permis identificarea >18milioane SNPs si
caracterizarea blocurilor de inlantuire genetica=haplotipuri la
indivizi care apartin populatiilor diferite.
 Haplotip

 Sunt regiuni care se transmit in bloc si in interiorul carora

probabilitatea de recombinare este mica.
 Prin GWAS s-au identificat asocierei semnificative a aproximativ
800SNPs ce implica sute de loci in numeroase boli multifactorile.
 Astfel s-au identificat gene associate cu degenerescenta
maculara(CFH), boala coronariana (CDKN2A/2B), diabetul zaharat
(TCF7L2, SLC30A8), obezitatea (INSIG2,FTO).
Aplicatiile cartografierii genomului
uman

 Cunoasterea organizarii si functionarii aparatului genetic.

 Realizarea hartii genice =“anatomia”genomului uman.
 Elucidarea unor mecanisme patogenice in boli monogenice sau
multifactoriale.
 Dezvoltarea de metodologii noi de diagnostic cu ajutorul markerilor
ADN.
 Dezvoltarea strategiilor de terapie genica.
2. Dezechilibru de inlantuire

 Este o caracteristica populationala, si nu familiala, ce depinde de

distanta genetica intre loci si vechimea mutatiei.

 Frecventa teoretica cu care se gasesc anumite haplotipuri in

populatie se calculeaza prin frecventele individuale ale genelor
allele ce-l alcatuiesc. Daca se compara frecventa teoretica cu cea
reala, exista 2 situatii:
Dezechilibru de inlantuire

 1. Frecventa reala nu difera semnificativ de frecventa

teoretica=echilibru de inlantuire

 2. Daca frecventa reala in populatie a unui anumit haplotip este

mai mare decat frecventa teoretica=se produce o asociere alelica
preferentiala=dezechilibru de inlantuire (linkage disequilibrium).

Acest lucru se explica prin faptul ca bolnavii au un stramos comun

(efect de “fondator”).
3.Proiectul Genomului Uman

 20 Centre, 6 Tari, inceput 1990

Proiectul Genomului Uman

 Lansat in 1990 initial cu o durata de 15ani, Proiectul si-a propus

secventierea genomului uman haploid (22A+X+Y, 3,2Gb), constand
in identificarea si localizarea genelor ce alcatuiesc genomul.
 A implicat 3 etape majore:
 1) Secventierea unor fragmente mai mici,
 2) Asamblarea genomului cu ajutorul unor programme
computerizate care ordoneaza, orienteaza si asambleaza
secventele segmentelor mici,
 3) Adnotarea genomului, identificare elementelor structurale si
atasarea informatiei biologice (functie si expresie) la aceste
elemente =adnotare functionala.
Proiectul Genomului Uman

 O prima “schita”a genomului uman a fost gata in iunie 2000 si

publicata la 15 februarie 2001 in doua versiuni,
 Nature de catre IHGSC
 Science de compania privata Celera Genomics.

 Ambele versiuni raportau secventierea a 96% din eucromatina

(2,69Gb) si erau incomplete si imperfecte.
Nature on Feb. 15, 2001 (Lander et al., 2001) and Celera Genomics published its draft

sequence in Science on Feb. 16, 2001 (Venter et al., 2001)

Francis Sellers Collins (born April
14, 1950) is an American
physician-geneticist noted for his
discoveries of disease genes and
his leadership of the Human
Genome Project. He is director of
the National Institutes of Health
(NIH) in Bethesda, Maryland, USA.

Before being appointed director

of the NIH, Collins led the Human
Genome Project and other
genomics research initiatives as
director of the National Human
Genome Research Institute
(NHGRI), one of the 27 institutes
and centers at NIH
John Craig Venter (born October 14, 1946)
is an American biotechnologist, biochemist,
geneticist, and entrepreneur.
He is known for being one of the first to
sequence the human genome[1] and the
first to transfect a cell with a synthetic
genome.
Venter founded Celera Genomics, The
Institute for Genomic Research (TIGR) and
the J. Craig Venter Institute (JCVI), and is
now CEO of Human Longevity Inc.
 Efforts to bring Collins and Venter together to complete the
mapping of the human genome began in late 1999.

 In March 2000, US President Bill Clinton and British Prime Minister Tony
Blair made a joint declaration that all genome information should
be free to the public.

 This announcement led to cooperation between Collins and Venter,

and on June 26, 2000, Venter and Collins jointly announced that,
after nearly a decade of work, both the public Human Genome
Project headed by Collins and Celera Genomics headed by Venter
had deciphered essentially all the genes in human DNA.
Proiectul Genomului Uman

 Dintre datele obtinute la aceasta prima secventiere a genomului

uman mentionam:
 Secventele codante reprezinta <5% din genom, iar numarul
prognozat de gene era 30-35.000.
 Astfel genele sunt “insule” intr-un ocean de ADN necodant.
 Asadar genomul nu poate fi considerat ca o simpla succesiune de
gene pe cromozomi, ci o structura cu arhitectura complexa in care
genele sunt dispersate pe cromozomi si separate prin largi regiuni
intergenice, necodante!
Proiectul Genomului Uman

 Numarul genelor la om este relative mic!

 Ex 6000 gene-drojdie,
 13.000 gene drosofila,
 18.000 gene vierme,
 26.000 plante.

 Diferenta majora la om este reprezentata de complexitatea

proteinelor, structura lor modulara care permite combinatii noi!
Proiectul Genomului Uman

 Genomul a doua persoane neinrudite este identic 99,9% din

secventele nucleotidice.
 Astfel individualitatea este data de 0,1% (3milioane pb) care
determina variatii personalizate de secventa.

 Oamenii difera printr-o pereche de baze(SNPs) la aprox. 1000pb!

Proiectul Genomului Uman

 14 aprilie 2003, la 50ani de la descoperirea structurii ADN, a fost

anuntata versiunea “aproape” completa a genomului uman,
“inaugurandu-se era genomicii”.
 Genome browsers (site-uri de navigatie)

 www.ensemble.org
 www.ncbi.nlm.nih.gov/genome
 www.genome.ucsc.edu
Proiectul Genomului Uman

 Informatii aduse de versiunea finisata

 Contine aproximativ genele care codifica proteine, dar numarul lor
este mai mic decat in versiunea initial, fiind estimate la 20-25.000
 Cresterea numarului de gene ARN, al caror consecinte medicale
raman a fi elucidate.
 O parte majora a ADN-ului necodant , considerat inutil, pare sa
aiba functii importante, neelucidate complet.
 Rata mutatiilor la barbat >2x mai mare decat la femei.
Proiectul Genomului Uman

 S-a descoperit remarcabila plasticitate a genomului uman,

demonstrandu-se “nasterea si moartea “genelor umane si
evidentiind duplicatii segmentare.

 Prin proiectul ELSI au fost puse in discutie problem etice-protectia

datelor individuale, aspect sociale-inegalitatea de acces la
aplicatiile testelor moleculare,

 Aspecte legale-patentarea datelor, metodelor,genelor.

“Nasterea si moartea genelor”

 Plasticitatea remarcabila a genomului uman, demonstrate prin

studiul “nasterii si mortii”genelor umane.
 Nasterea genelor se face prin duplicatie, cele mai recente duplicatii
intereseaza aprox. 1200 gene, majoritatea fiind genele receptorilor
olfactivi, genele correlate cu imunitatea sau reproducerea.

 Moartea genelor se produce prin mutatii care transforma genele in

pseudogene non-procesate, nefunctionale.
 S-au identificat 37gene care au “murit” recent prin mutatii care le
fac gene nefunctionale!
“Nasterea si moartea genelor”

 Pseudogenele sunt secvente asemanatoare genelor, dar

nefunctionale datorita unor mutatii inactivatoare.

 Numarul lor estimate la 12.600!(Ensembl, 2011).

 Studii recente in cadrul proiectului ENCODE au aratat ca unele

pseudogene procesate sunt transcrise active si ar putea fi
“pseudogene reactivate”.
Proiectul Genomului Uman
 Totusi dupa publicarea versiunii finisate (2004) a
genomului uman, a urmat resecventierea cu noi
tehnici a fiecarui cromozom.
 2006 a fost re-secventiat cromozomul 1,
 2007 declarata terminate secventa intregului
genom (build 36).
 2009 Genome Reference Consortium(GRCh)
publica versiunea a 37-a a genomului uman,
structura sa este aprope complet descifrata.
Proiectul Genomului Uman-
componente
 1) ADN-ul genelor care codifica proteine si secvente inrudite
(pseudogene) -1/3
 2) ADN-ul extragenic, 2/3, reprezentat de genele ARN, duplicatii
segmentare si AND repetitiv.
 Secventele codante transcrise si translatate care corespund exonilor
genelor pentru proteine reprezinta doar 1,1% din genom.

 5% din secventele genomului uman sunt conservate in evolutie, si

sunt reprezentate de elemente functionale de baza-gene care
codifica proteine, ARN, regiuni de reglarea transcriptiei.
 Restul genomului =secvente ADN care au evoluat rapid si divergent.
Inca sunt lucruri de facut…

 Intelegerea-functiei
-expresiei
-reglarii genelor
-rolul AND-ului intergenic, sunt date ce
trebuiesc completate
-variatiile genetice intre indivizi si
populatii..
Informatii despre fiecare gena-
portaluri Entrez, Ensembl, Gene Wiki
 Gene: NF1 ENSG00000196712
 Description
 neurofibromin 1 [Source:HGNC Symbol;Acc:HGNC:7765]
 Synonyms
 VRNF, WSS, NFNS
 Location
 Chromosome 17: 31,094,927-31,382,116 forward strand.
 GRCh38:CM000679.2
 About this gene
 This gene has 23 transcripts (splice variants), 79 orthologues, is a
member of 1 Ensembl protein family and is associated with 88
phenotypes!
 NF1 (HGNC Symbol)
 CCDS
 This gene is a member of the Human CCDS set: CCDS11264.1, CCDS42292.1, CCDS45645.1
 UniProtKB
 This gene has proteins that correspond to the following UniProtKB identifiers: P21359
 RefSeq
 Overlapping RefSeq annotation not matched
 Overlapping RefSeq Gene ID 4763 matches and has similar biotype of protein_coding
 LRG
 LRG_214 provides a stable genomic reference framework for describing sequence variants for this
gene
 Ensembl version
 ENSG00000196712.16
 Other assemblies
 This gene maps to 29,421,945-29,709,134 in GRCh37 coordinates.
 View this locus in the GRCh37 archive: ENSG00000196712
 Gene type
 Known protein coding
Entrez

NEUROFIBROMIN 1; NF1

Alternative titles; symbols

NEUROFIBROMIN

HGNC Approved Gene Symbol: NF1

Cytogenetic location: 17q11.2 Genomic coordinates

(GRCh38): 17:31,094,926-31,377,676 (from NCBI)
 Phenotype Inheritance Phenotype
ocation Phenotype
MIM number (in progress) mapping key

Leukemia, juvenile
607785 SMu, AD 3
myelomonocytic

Neurofibromatosis,
162210 AD 3
familial spinal

17q11.2
Neurofibromatosis,
162200 AD 3
type 1

Neurofibromatosis-
601321 AD 3
Noonan syndrome

Watson syndrome 193520 AD 3

Procesul de adnotare structurala si functionala a
genomului uman a generat mai multe proiecte

 HapMap=proiect care isi propune realizarea unei harti haplotipice a

genomului uman, care cuprinde modele comune ale variatiei
genetice, in special SNPs, necesare pentru a stabili modul in care
aceste variante pot influenta sanatatea, predispozitia la boli si
raspunsul la factori de mediu si medicamente.
 ENCODE= (ENCyclopedia Of Dna Elements)= identificarea si
adnotarea elementelor functionale ale genomului.
 Genome 1000=catalog detaliat cu variatiile structurale ale
genomului uman, prin analiza genomurilor a cel putin 1000 persone
din grupuri entice diferite.
How We Use This Information?

 Better understanding of human disease-importance of right/wrong

diagnosis in life !!!
 Personalized medicine & Pharmacogenetics
 Greater insight into cognitive function
 Insight into human origins
 Identifying genetic susceptibility to disease
OMICA
 Studiul structurii, organizarii si functiei genomului uman se numeste
genomica.
 Proteomul reprezinta ansamblul de proteine sintetizate/exprimate
intr-un organit cellular, celula, tesut, organ care asigura functia
structurii respective.
 Proteomica=studiul functiei unor structuri pe baza expresiei globale
a proteinelor (cu ajutorul electroforezei bidimensionale,
cromatografiei, spectometriei de masa)
 Genomul este o structura fixa,
 Proteomul este dinamic, variaza temporal si spatial si in anumite
conditii de mediu.
Termenul proteome/proteomica
introdus de Mark Wilkins in 1994.
Provocari ale proteomicii/ versus
genomica
 1) o gena poate codifica mai mult de o proteina!
 Ex genomul uman are aprox 21.000 gene care codifica proteine,
dar numarul total de proteine > 250.000-1.000.000.
 2) Proteinele sunt dinamice, interactioneaza, sunt
sintetizate/degradate.
 3) Proteinele sufera modificari posttranslationale=pot varia de la o
persoana la alta, in conditii de mediu diferite, sau la aceeasi
persoana in functie de varsta sau medicamente administrate.
 4) concentratiile pot fi extreme de variabile. In cancer de exemplu
se crede ca cele mai importante proteine sunt cele in concentratii
foarte mici-dificil de evaluat!
Proteomica
 Cand vorbim de proteom ne putem referi la proteomul unei specii,
a unui organ (ex ficat). Proteomul nu este constant, difera de la
celula la celula si se schimba cu timpul.
 Mai mult, activitatea proteica este modulate si de alti factori
aditionali genelor.
 Proteomica investigheaza:
 -unde si cand proteinele sunt exprimate,
 -rata de producer/degradare a proteinelor,
 -cum sunt proteinele modificate,
Proteomica

 -miscarea proteinelor in compartimentele subcelulare,

 -implicarea proteinelor in caile metabolice,
 -interactiunea proteinelor.
Nature Reviews Cancer (September
2010)
 Proteomics-based techniques allow the identification of biomarkers
and protein expression signatures, which could be used to predict
responses to drugs and the clinical course of disease, and such
information could be used to individualize therapy.
 In addition, proteomic techniques are being used to gain an
understanding of how signalling pathways are altered in tumour
cells so that the underlying biology of a human tumour can be
understood.
 Moreover, proteomic platforms have been enlisted in drug
development to identify new drugs and to improve our
understanding of how to target various pathways.
Proteomica-medicina fetala

 Posibile aplicatii:

 -in evaluarea riscului de sarcini cu boli genetice,

 -predictia nasterii premature
 -preeclampsia
 -infectia intraamniotica.
Fetal Diagn Ther 2011

 Are Serum Protein Biomarkers Derived from Proteomic Analysis

Useful in Screening for Trisomy 21 at 11–13 Weeks? Anna Lucia Mastricci a, b
Ranjit Akolekar a Ramesh Kuppusamy a Mustafa Ahmed a Kypros H. Nicolaides a, b

 Conclusion:
 Proteins identified as potential biomarkers for trisomy 21 using
proteomic techniques have not been found to be useful in early
screening for this aneuploidy
Studiul PAPR-nasterea prematura

 Positive Clinical Validation Data for PreTRM® Test Presented at the

Society for Maternal-Fetal Medicine’s 36th Annual Pregnancy
Meeting 2016

 Results from the 5,501-patient Proteomic Assessment of Preterm Risk

(PAPR) study validate the newly available PreTRM® test, which
accurately and objectively predicts spontaneous preterm birth
(sPTB), in pregnant women whose blood is drawn for analysis as
early as 19 weeks of pregnancy.
PreTRM® Test

 PAPR study enrolled 5,501 pregnant women representative of the

United States population.

 By taking a novel proteomic approach, this study validated a

signature based on two proteins that are highly predictive of
preterm birth risk: IBP4, insulin-like growth factor binding protein 4,
and SHBG, sex-hormone binding globulin.

 Using proteomic technology, the PreTRM test measures and

analyzes proteins in the blood that are predictive of preterm birth.
International Society of Nutrigenetics / Nutrigenomics

The International Society of Nutrigenetics/Nutrigenomics (ISNN) was

established in 2005, under the Presidency of Artemis P. Simopoulos, (USA).
NUTRIGENOMICA
 Reprezinta aplicarea genomicii, proteomicii, metabolomicii in
cercetari nutritionale, pentru a stabili efectele alimentatiei asupra
functiei genomului precum si actiunile benefice/nocive ale
componentelor dietei la nivel individual sau populational.

 Substantele nutritive influenteaza raspunsuri fiziologice ce afecteaza

stabilitatea si expresia genomului sau amprentarea (imprinting).

 Intelegerea acestor mecanisme va ajuta la evaluarea

beneficiilor/riscurilor diferitelor recomandari dietetice, precum si
prevenirea instalarii unor boli, managemetul bolilor cornice.
Nutrigenomica

Principala provocare a cercetarilor din domeniul nutritiei este

complexitatea si dificultatea integrarii factorilor aditionali (stilul de
viata!), care afecteaza rezultatele si fac dificila interpretarea.
 Studiile pe termen lung in medicina sunt “gold standard”.
 Studiile nutritionale sunt influentate de complianta redusa pe
termen lung, modificari inevitabile ale stilului de viata.
 Dereglarile metabolice sunt recunoscute in multe afectiuni.
 Identificarea proceselor metabolice caracteristice bolilor si
dezvoltarea de strategii care blocheaza/corecteaza aceste cai pot
fi o alternative promitatoare in managementul bolii.
Nutrigenomica-cancer
 Mai mult anumiti nutrient nu servesc numai ca substrat sau produsi ai
reactiilor enzimatice, dar pot actiona ca si “reglatori”ai expresiei
genice si pot juca un rol in modularea cailor metabolice , fie in
domeniul preventiei sau al tratamentului.
 In cancer este cunoscuta dereglarea metabolica. Celulele
canceroase “prefera”sa utilizeze anumiti nutrient, ca glucoza si
glutamatul ca sursa de energie. De asemenea metabolismul lipidic
este crescut rezultand mediatori ca eicosanoizi, ce creeaza un
micromediu suportiv celulelor tumorale.
 Folosind nutrienti care pot modula aceste cai si sa interfere cu
particularitatile metabolice din cancer, interventiile nutritionale sunt
astfel capabile sa inhibe dezvoltatrea celulelor canceroase.
Nutrigenomica

 Mai mult fata de tratamentele conventionale, nutrientii pot fi

combinati sigur/sau pot exista in natura combinatii effective pentru
tinte multiple!
Effects of a High-Protein/Low-Carbohydrate Diet versus a Standard
Hypocaloric Diet on Weight and Cardiovascular Risk Factors: Role of a
Genetic Variation in the rs9939609 FTO Gene de Luis D.A, Romero E
J Nutrigenet Nutrigenomics 2015;8:128-136
(DOI:10.1159/000441142)
 The common polymorphism rs9939609 of the fat mass- and obesity-
associated gene (FTO) has been linked to obesity. Our aim was to
investigate its role in weight loss after the administration of a high-
protein/low-carbohydrate diet compared to a standard
hypocaloric diet (1,000 kcal/day)

 Weight loss was better in A allele carriers than noncarriers, and

metabolic improvement was better with the HP diet.
Nutrigenomica
 All humans have the same set of genes.
 Our differences come from the tiny variations in those genes.
 Those variations influence not only in how you look or behave
different to others… But in how your body reacts differently to
external factors.
 Especially how it reacts to the foods you eat and lifestyle you live.
 For example, some have great difficulty metabolising caffeine. For
others, it could be alcohol.
 Some have issues that increases their risk of Alzheimer’s
disease, known as APOE4.
Nutrigenomics: The Genome–Food Interface
M. Nathaniel Mead,2007

 Nutrigenomics therefore initially referred to the study of the effects

of nutrients on the expression of an individual’s genetic makeup.
More recently, this definition has been broadened to encompass
nutritional factors that protect the genome from damage.
Ultimately, nutrigenomics is concerned with the impact of dietary
components on the genome, the proteome (the sum total of all
proteins), and the metabolome (the sum of all metabolites).
 As in pharmacogenomics, where a drug will have diverse impacts
on different segments of the population, researchers recognize that
only a portion of the population will respond positively to specific
nutritional interventions, while others will be unresponsive, and still
other could even be adversely affected.
J Nutrigenet Nutrigenomics 2016;9:65-82
(DOI:10.1159/000445996)

 Bovine Mammary Nutrigenomics and Changes in the Milk

Composition due to Rapeseed or Sunflower Oil Supplementation of
High-Forage or High-Concentrate Diets
 Leroux C. · Bernard L. · Faulconnier Y. · Rouel J. · de la Foye
A. · Domagalski J. ·Chilliard Y.
 Fatty acid (FA) composition plays a crucial role in milk nutritional
quality. Despite the known nutritional regulation of ruminant milk
composition, the overall mammary mechanisms underlying this
regulation are far from being understood. The aim of our study was
to determine nutritional regulation of mammary transcriptomes in
relation to the cow milk composition
 Our results showed a higher amplitude of milk composition and
mammary transcriptome responses to lipid supplementation with
the LF-SO compared with the LF diet than with the HF-RS compared
with the HF diet. Forty-nine differentially expressed genes, including
genes involved in lipid metabolism, were identified with LF-SO versus
LF, whereas RS supplementation to the HF diet did not affect the
mammary transcriptome.

 Conclusions: This study highlights different responses to lipid

supplementation of milk production and composition and
mammary transcriptomes depending on the nature of lipid
supplementation and the percentage of dietary concentrate.
Nutrigenomics and metabolomics will change clinical nutrition and public
health practice: insights from studies on dietary requirements for choline2
Steven H Zeisel,
Am J Clin Nutr

 Investigators found longer survival and a 75% lower risk of diabetes

mellitus in humans whose paternal grandfathers experienced food
scarcity during the slow growth period just before puberty than in
those whose paternal grandfathers did not (30–32). Pembrey (32)
effectively argued that these effects of nutrition must occur via
epigenetic imprinting of paternal genes and pointed out that the
slow growth period before puberty occurs when the first viable pools
of spermatocytes emerge and when reprogramming of DNA
methylation imprinting begins. In a similar fashion, epi-genetic
events can modulate carcinogenesis in the adult;
NATURE REVIEWS ENDOCRINOLOGY | REVIEW
Personalized weight loss strategies—the role of macronutrient distribution
J. Alfredo Martinez
Nature Reviews Endocrinology 14 October 2014

The causes of variation in individual responses to various diets are currently

under debate, and some evidence suggests that differences are
associated with specific genotypes.

The initial findings of research into personalized nutrition, based on the

interactions of macronutrient intake and genetic background and its
potential influence on dietary intervention strategies.
http://www.dietvsdisease.org/
MTHFR Mutation

 So without the enzyme activity of MTHFR, methylation of folate and

folic acid cannot occur properly.
 The two main functional mutations (also known as polymorphisms)
of the gene are MTHFR C677T and MTHFR A1298C .
 Specifics aside, these genetic mutations are collectively known
as MTHFR mutations. They can be like a “defect” which limits
production of your MTHFR enzymes.
 It’s important that MTHFR mutation itself is not inherently
dangerous… but any form of genetic variance has the possibility to
affect health!
MTHFR Mutation

 Those with an MTHFR mutation are at risk for poor MTHFR enzyme
efficiency.
 Consequently, folate and folic acid cannot be efficiently converted
into their active form, known as 5-MTHF or L-methylfolate. Therefore
those nutrients can’t perform one of their key functions: breaking
down (recycling) Homocysteine.
 Homocysteine is an amino acid thought to damage the lining of
your arteries and other cells of the body. It is naturally formed in the
body, but gets broken down by 5-MTHF.
 Elevated homocysteine levels in the blood is an independent risk
factor for heart disease,
MTHFR Mutation

 Those with an MTHFR mutation may be predisposed to increased

levels of homocysteine, a strong risk factor for cardiovascular
disease.

 They are also more likely to develop a folate deficiency if their diet is
not rich in folate!
MTHFR Mutation
 Daily intake for folic acid is 400 μg.
 Folic acid is the conventional supplement for treating B-vitamin
deficiency, lowering homocysteine levels, and reducing the
incidence of Neural Tube Defects!
 It is so effective that the addition of folic acid back into to wheat
flour is now mandatory in Australia, USA, Canada and several other
countries.
 FDA and European Food Standards Agency have approved several
products containing 5-MTHF.
Va multumesc!