45 research outputs found
GENE EXPRESSION SIGNATURES IN PRENATAL DIAGNOSIS OF ANEUPLOIDIES
Kromosomske bolezni predstavljajo pomemben zdravstveni problem, saj so v predrojstnem obdobju pogosto povezane z razvojnimi nepravilnostmi ali s spontano izgubo noseÄnosti. Å tevilÄne kromosomske nepravilnosti avtosomov niso združljive z življenjem, razen trisomije kromosoma 21, 18 in 13 (T21, T18, T13). Multiomski pristop omogoÄa sestavljeno raziskovanje genoma in transkriptoma ter poslediÄno prepoznavanje biooznaÄevalcev za razliÄna patoloÅ”ka stanja, pri Äemer nam kromosomski sindromi z dobro opredeljeno kliniÄno sliko lahko služijo kot model patoloÅ”kega stanja. Transkriptomske raziskave predrojstnih vzorcev s T21, T18 in T13 so pokazale spremembe v genskem izražanju, niso pa raziskovale diagnostiÄnih možnosti za napoved noseÄnosti z visokimi tveganji za trisomijo, niti niso ugotavljale skupnih znaÄilnosti v genskem izražanju pri trisomijah.
Postavili smo hipotezo, da obstajajo razlike v genskem izražanju, ki jih lahko uporabimo kot diagnostiÄni biooznaÄevalec za specifiÄno trisomijo in da je del razlik v genskem izražanju skupen pri razliÄnih trisomijah, kar lahko obravnavamo kot homeostatski odgovor.
Opravili smo ekspresijske mikromrežne ekperimente na predrojstnih vzorcih gojenih amniocitov s T21 in T18 ter gojenih celic horionskih resic s T13, ki smo jih primerjali z ujemajoÄimi vzorci z normalnim kariotipom. V prvem delu smo opravili diferencialno gensko ekspresijo (DGE) za vse trisomije in prepoznali podpise izražanja genov, ki so bili najbolj statistiÄno znaÄilni za T21, 18 in T13. Napovedno zanesljivost izbranih podpisov genskega izražanja smo preverili na dostopnih objavljenih transkriptomskih raziskavah in potrdili, da izbrani biooznaÄevalci z visoko zanesljivostjo napovedo status trisomije 21, 18 in 13.
V drugem delu raziskave smo primerjali podobnosti v DGE med vzorci s T21 in T18 ter ugotovili 6 genov s spremenjenim izražanjem, ki so skupni pri obeh trisomijah. Analiza obogatitve genskih setov in bioloÅ”kih procesov sta pokazali obogatitev genov povezanih s PI3K/AKT signalno potjo, G2/M kontrolno toÄko pri DNA okvari in predvideno inhibicijo regulatorja TP53 ter obogatitev genov povezanih s celiÄnim ciklom, celiÄno smrtjo in preživetjem, preživetjem organizma ter razvojem in delovanjem tkiv.
Z raziskavo smo ugotovili specifiÄne podpise izražanja genov, ki so za preiskovane trisomije znaÄilni in jih lahko uporabimo kot bioznaÄevalec. Zaznali smo tudi doloÄene skupne podobnosti v genskem izražanju pri T21 in T18, za katere menimo, da lahko odražajo genomski homeostatski odgovor na kromosomsko nepravilnost. NaÅ”i rezultati predstavljajo temelj za nadaljnje raziskave biooznaÄevalcev za noseÄnosti z visokimi tveganji in za razumevanje mehanizmov s katerimi se trisomiÄna celica upira kromosomski motnji.Chromosome diseases, associated with developmental abnormalities, represent an important health problem and often lead to pregnancy loss. Numerical autosome abnormalities are incompatible with life, with the exception of trisomy of chromosomes 21, 18 and 13 (T21, T18 and T13). A multiomics approach allows for combined genome and transcriptome analysis and the identification of biomarkers for various pathological conditions, where chromosome syndromes with a well-defined clinical presentation can serve as a model of the pathological condition. Reported transcriptomic studies on prenatal samples with T21, T18 and T13 showed changes in gene expression, but they did not investigate the diagnostic potential for predicting high-risk pregnancies, nor did they identify the common features in gene expression among trisomies.
We hypothesized that specific gene expression signature can be used as a diagnostic biomarker for certain trisomy and that there are some similarities in gene expression that are common in different trisomies and can be considered as a homeostatic genome response.
We performed gene-expression experiments on prenatal samples of cultivated amniocytes with T21 and T18, and cultivated cells of chorionic villi with T13 in comparison to matched prenatal samples with normal karyotype. In the first part of the study, we carried out differential gene expression (DGE) analyses and selected gene expression signatures as biomarkers specific for T21, 18 and T13. The classification performance of the selected gene subsets were verified on independent GEO datasets and confirmed that the selected biomarkers predict the T21, 18 or T13 with high reliability.
In the second part of the study, we compared the similarities in DGE for T21 and T18 and found 6 same-directionally dysregulated genes that are common in both data sets. The gene set enrichment and pathway analyses showed enrichment of genes associated with the PI3K / AKT signal pathway, the G2 / M check point in DNA defects and the predicted inhibition of the TP53 regulator and the enrichment of gene-related cell cycle, cell death and survival, the survival of the organism, and the development and function of tissues.
Our study found gene expression signature specific for the individual trisomy that can be used as a biomarker. In addition, we detected some similar differences in gene expression, that are common in T21 and T18, which may reflect the genomic homeostatic response to the chromosome change. Our results provide a basis for further investigations of biomarkers in high risk pregnancies and understanding of the mechanisms of trisomic cell resisting chromosomal perturbation
Genomic Testing for Prenatal Clinical Evaluation of Congenital Anomalies
Congenital anomalies occur in about 2ā3% of liveborn and 20% of stillborn infants. They constitute a serious public health and epidemiological problem. The etiology of congenital anomalies is complex; they can result from genetic factors, environmental factors, or a combination of both. It is estimated that genetic factors represent an important cause of congenital anomalies and may be due to different genetic mechanisms: aneuploidies, deletions and duplications of DNA segments, and single gene disorders. Due to the genetic complexity, the targeted prenatal genetic diagnostics of congenital anomalies is usually problematic and challenging. In recent years new diagnostic algorithms for prenatal genetic testing are being developed with the advent of new genomic technologies, like molecular karyotyping and next-generation sequencing. These technologies offer testing options that exceed conventional karyotyping and targeted molecular genetic testing with better diagnostic yield. In this chapter, an overview of the conventional genetic diagnostic approach and the use of new genomic technologies in the diagnostic algorithm of prenatally detected congenital anomalies are discussed
SadaÅ”njost i buduÄnost prenatalne dijagnostike u Sloveniji
Prenatal genetic testing is under the remit of the National Health Service in Slovenia and has been included in clinical routine since
the 1980s. Traditionally, prenatal services have consisted of karyotyping and rapid fetal aneuploidy screening to detect chromosome
abnormalities, whereas targeted mutation testing was used for single gene disorders. Development of array comparative genomic
hybridization and next generation sequencing allows for genome analysis at better resolution in a single experiment. While technological
advances in medicine continue to evolve, increasing diagnostic accuracy and broadening the spectrum of indications, all
these innovations require more investment along with more equipment and higher staffi ng rations trained to use it, placing burden
upon healthcare funding and expenditure. This prompts us to consider how to implement new techniques into the existing services
in order to update genetic services for the 21st century. Our aim is to develop a new approach to prenatal genetic services, which
would maximize diagnostic yield at an acceptable cost.Prenatalno genetiÄko testiranje u nadležnosti je Državne zdravstvene djelatnosti u Sloveniji i ukljuÄeno je u kliniÄku praksu od
1980.-ih godina. Prenatalne usluge tradicionalno obuhvaÄaju kariotipiziranje i brz probir na fetalne aneuploidije kako bi se otkrile
kromosomne anomalije, dok se za poremeÄaje jednog gena provodilo ciljano testiranje na mutacije . Razvoj komparativne genomske
hibridizacije na mikropostroju i sekvenciranje sljedeÄe generacije omoguÄava analizu genoma uz bolju rezoluciju u jednom
testu. Dok se tehnoloÅ”ki napredak u medicini nastavlja poboljÅ”avajuÄi tako dijagnostiÄku toÄnost i Å”ireÄi lepezu indikacija, ove inovacije
zahtijevaju sve veÄa ulaganja i sve viÅ”e opreme te dodatno osposobljeno osoblje koje Äe raditi s tom opremom, Å”to optereÄuje
zdravstvene fondove i poveÄava troÅ”kove. To nas potiÄe da razmotrimo kako uklopiti nove tehnike u postojeÄu službu kako bismo
genetiÄke usluge prilagodili potrebama 21. stoljeÄa. Cilj nam je razviti nov pristup prenatalnoj genetici kojim Äe se postiÄi najuÄinkovitiji
rezultati uz prihvatljive troŔkove
A critical update on endothelial nitric oxide synthase gene variations in women with idiopathic recurrent spontaneous abortion: genetic association study, systematic review and meta-analyse
A number of caseācontrol studies investigated the association between idiopathic recurrent spontaneous abortion (IRSA) and variations in the gene encoding endothelial nitric oxide synthase (NOS3), but yielded contradictory results. Our aim was to test the association of the NOS3 variable number of tandem repeats (VNTR) in intron 4 and +894 G/T single-nucleotide polymorphism (SNP) with IRSA in Slovenian women (148 IRSA and 149 control women), conduct a systematic review of literature on the association between NOS3 gene variations and IRSA, and perform meta-analyses of studies that met the inclusion criteria, defined by virtue of the European Society for Human Reproduction and Embryology evidence-based guidelines for recurrent spontaneous abortion. Genotyping was performed using PCR and restriction fragment length polymorphism methods. The systematic review of literature (English language) was conducted using PubMed and Scopus databases, to 1 November 2014. We determined no association of IRSA with the VNTR in intron 4 and +894 G/T SNP in Slovenian women. Furthermore, 16 caseācontrol studies were identified on the association between 15 NOS3 gene variations and IRSA. However, significant inconsistencies exist in the selection criteria of patients and controls between studies. The meta-analysis of VNTR in intron 4 was performed on five studies (894 patients, 944 controls), whereas the meta-analysis of +894 G/T SNP included six studies (1111 patients, 1121 controls). The association with IRSA was significant for the +894 G/T SNP under the dominant genetic model (GT+TT versus GG) based on fixed (odds ratio (OR) = 1.54, 95% confidence interval (CI) = 1.28ā1.86, P = <0.01) and random effects models (OR = 1.54, 95% CI = 1.03ā2.31, P = 0.03). In conclusion, the GT and TT genotypes of the +894 G/T SNP in women might contribute to a predisposition to IRSA. Additional genetic association and functional studies in different populations with larger numbers of participants and a uniformly defined IRSA are needed to clarify the contribution of NOS3 +894 G/T gene variation to IRSA
Insertion/deletion polymorphism in intron 16 of ACE gene in idiopathic recurrent spontaneous abortion: case-control study, systematic review and meta-analysis
Abstract
The insertion/deletion (I/D) polymorphism in intron 16 of the angiotensin I-converting enzyme gene (
ACE
) has been ex-
tensively studied as a predisposing factor for idiopathic recurrent spontaneous abortion (IRSA). A case-control study including 149
women with
ā„
3 spontaneous abortions and 149 controls was performed to test the association of
ACE
I/D polymorphism with IRSA. A
systematic review was conducted of previous case-control studies, with strict selection criteria for meta-analyses. We also aimed
to evaluate the potential differences in summary estimates between studies defining IRSA as
ā„
2 and
ā„
3 spontaneous abortions. Genotyping
was performed by PCR, and systematic review conducted using PubMed and Scopus. There was no association of the polymorphism
with IRSA in Slovenian women. Sixteen case-control studies, showing substantial differences regarding IRSA definition and selection
criteria for women were identified. Meta-analysis was performed and included four studies defining IRSA as
ā„
2 spontaneous abor-
tions and the current study, which defined IRSA as
ā„
3 spontaneous abortions. Based on random effects model, meta-analysis con-
ducted on 1192 patients and 736 controls showed no association with IRSA under dominant
(DD
+
IDvsII)
and recessive
(DDvsID
+
II)
genetic models.
Well-designed studies are needed to evaluate the role of
ACE
I/D polymorphism in IRSA defined as
ā„
3 spontaneous abortion
Y chromosome azoospermia factor region microdeletions are not associated with idiopathic recurrent spontaneous abortion in a Slovenian population: association study and literature review
Objective To investigate the potential association of Y chromosome microdeletions with idiopathic recurrent spontaneous abortion (IRSA) in a Slovenian population and compare our results with those of previously published studies in different populations, with the intention of clarifying the potential impact of Y chromosome microdeletions on IRSA. Design Caseācontrol and association study. Setting Departments of gynecology and obstetrics and university-based research laboratory. Patient(s) Male partners of 148 couples with at least three spontaneous pregnancy losses of unknown etiology, and 148 fertile men. Intervention(s) Multiplex polymerase chain reactions. Main Outcome Measure(s) Azoospermia factor (AZF) regions were tested for Y chromosome microdeletions according to European Academy of Andrology/European Molecular Genetics Quality Network guidelines. The PubMed database was searched to retrieve articles linking Y chromosome microdeletions and susceptibility to IRSA. Result(s) None of the IRSA or control men had microdeletions in the AZFa, AZFb, or AZFc regions. A total of nine previous studies examined the relationship between Y chromosome microdeletions and IRSA, yielding contradictory results, which we discuss in detail. Conclusion(s) On the basis of our comparisons, it is unlikely that Y chromosome microdeletions contribute to IRSA and are therefore currently not recommended for the routine evaluation of IRSA couples
Leberjeva hereditarna optiÄna nevropatija ā pregled bolezni z analizo prisotnosti v Sloveniji
Leberjeva hereditarna optiÄna nevropatija (LHON) je redka dedna mitohondrijska bolezen, ki povzroÄa slepoto najpogosteje pri mladih odraslih. Navadno se izrazi kot subakutna, neboleÄa izguba vida na eno oko, ki ji sledi poslabÅ”anje vida drugega oÄesa v nekaj tednih do mesecih. Bolezen veÄinoma puÅ”Äa trajne posledice, le pri nekaterih bolnikih lahko v redkih primerih pride do delnega spontanega izboljÅ”anja vida. Razmerje med moÅ”kimi in ženskimi bolniki se ocenjuje na 3 : 1. V zadnjih letih je z razvojem zdravilne uÄinkovine idebenone možno podporno farmakoloÅ”ko zdravljenje, ki lahko prispeva k delnemu izboljÅ”anju vidne funkcije. Bolezen zaradi svoje redkosti velikokrat ostane ne- ali napaÄno diagnosticirana. V Älanku predstavljamo Å”tiri kliniÄne primere bolnikov, pri katerih se je po obsežnem in dolgotrajnem diagnosticiranju izkazalo, da imajo LHON. Od leta 1996 se v Sloveniji vodi baza bolnikov z redkimi dednimi oÄesnimi boleznimi. Na tej podlagi je ocenjena prevalenca LHON 1/72.000. Ob sumu na bolezen so kljuÄni družinska anamneza slabovidnosti po materini strani, genetsko testiranje in napotitev na obravnavo ter zdravljenje v terciarno ustanovo