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 asociate lor”, a devenit punctul 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 prezent 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 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.
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 persoane

afectate de o anumita boala, 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 internationale 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 asocieri 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 alele 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 programe computerizate care
ordoneaza, orienteaza si asambleaza secventele segmentelor mici,
 3) Adnotarea genomului, identificarea 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 relativ 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 initiala, 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 probleme etice-protectia datelor

individuale, aspecte sociale-inegalitatea de acces la aplicatiile testelor moleculare,

 Aspecte legale-patentarea datelor, metodelor,genelor.

“Nasterea si moartea genelor”

 Plasticitatea remarcabila a genomului uman, demonstrata 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 corelate
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 estimat la 12.600!(Ensembl, 2011).

 Studii recente in cadrul proiectului ENCODE au aratat ca unele pseudogene

procesate sunt transcrise activ 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 terminata 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, 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 persoane 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
celular, 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 modulata si de alti factori aditionali genelor.
 Proteomica investigheaza:
 -unde si cand proteinele sunt exprimate,
 -rata de producere/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 cronice.
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 alternativa promitatoare in
managementul bolii.
Nutrigenomica-cancer
 Mai mult anumiti nutrienti 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 nutrienti, 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 efective 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 choline 2
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!