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 markeri 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.

 Analiza de linkage se foloseste in mod direct de cunoasterea

pedigree-ului familiei pentru a identifica modul de transmitere a
unei patologii si de a testa transmiterea bolii impreuna cu o
anumita regiune genomica sau o varianta alelica specifica.
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 imediata 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 incompleta, ele putand fi
separate prin crossing over.
Analiza de linkage
 Depinde de determinarea frecventei de recombinare ca masura a
apropierii a doi loci pe un cromozom. Notatia pentru frecventa de
recombinare (in proportie, nu procent) este litera greaca THETA =
poate varia de la 0-0,5

 Daca 2 loci sunt apropiati astfel incat theta=0 =LINKAGE

COMPLET.

 Daca 2 loci sunt departati astfel incat theta=0,5=linkage-ul NU este

prezent, iar locii se asorteaza independent.
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,4
Robert 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. 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.
 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.
 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 analiza populationala.

 In acest caz se studiaza frecventa unui “set de markeri” la un grup de personae afectate
de o anumita boala, ce vor avea o frecventa crescuta, comparativ 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 asociate 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”).
Cauzele dezechilibrului de linkage

 Cand o alela a unei afectiuni apare pentru prima data intr-o

populatie, prin mutatie sau migrarea unui fondator care poarta alela,
ansamblul particular de alele de pe locii polimorfici linkati de
locusul afectiunii constituie un HAPLOTIP in care este localizata
alela afectiunii.

 Vitezacu care recombinarea va muta alela bolii intr-un nou haplotip

depinde de m.m factori:
 1)numarul generatiilor de la aparitia mutatiei in populatie (numarul
oportunitatilor de recombinare),

 2)Frecventa generationala a recombinarii intre loci. Cu cat valoarea

THETA MAI MICA, cu atat este mai mare sansa ca haplotipul care
contine boala sa persiste intact,

 3) Procesele de selectie naturala.

 Daca o combinatie haplotipica sufera o selectie pozitiva si se transmite
preferential sau o selectie negativa, si prin urmare este mai putin
transmisa, aceste vor fi supra respectiv subreprezentate in acea
populatie.
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 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).

 Studiirecente in cadrul proiectului ENCODE au aratat ca unele

pseudogene procesate sunt transcrise active si ar putea fi
“pseudogene reactivate”.
Proiectul Genomului Uman
 Totusidupa 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.
 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, type
162200 AD 3
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?

 Betterunderstanding 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.
 Proteomica / 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 

 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)

 Weightloss 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.
 1) identification of genes, gene regulation, gene expression, and genetic variants
related to nutrition, metabolism, energy utilization, activity, and feeding behaviors;

2) characterization of epigenetic changes caused by diet, or effects of epigenetic

changes on nutrition, metabolism, energy utilization, activity, and feeding behaviors; 

3) bioinformatic approaches relevant to nutrigenomics; 

4) studies on the gut microbiota’s metagenome, as well as gene regulation or gene

expression within the microbiome that influences an organism’s nutrition,
metabolism, energy utilization, activity, and feeding behaviors; 
Nutrigenomics: The Genome–Food Interface
M. Nathaniel Mead,2007

 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.
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
 Thosewith 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.
 Nutrigenomics approaches are being applied to a wide range of
conditions:

 Risk of developing metabolic syndrome based on genetic variants and

contingent on diet/lifestyle

 Links between gut microbiota, obesity and mental health!

 Correlation between a specific nutrient intake and disease, such as 

coffee and cardiac irregularities.
It’s early days – and nutrigenomics is complicated

Significant, limitations:

•Research is ongoing to examine new and existing nutrigenomic biomarkers (for example, 
miRNAs); however, the interactions between multiple biomarkers in one individual is
hugely complex.
•For ‘omics’ assays, basic issues such as which tissues should be analysed are not yet
resolved!
•We may have confirmed correlations (for example, between nutrient intake and gene
expression), but the underlying causal relationships are still largely a mystery.
•Food and behavioural diaries, which rely on recall and effort, are unreliable.
Va multumesc!