Browsing by Subject "genetics"

Uterine leiomyoma (also known as myoma) is the most common neoplasia in women during reproductive age and it represents a burden for public health care. Approximately 70% of Caucasian women develop myomas, although only 25% of cases are symptomatic. The genetic background of myomas varies significantly and the most common genetic causes are mutations in genes Mediator complex subunit 12 (MED12), Fumarate hydratase (FH) or YEATS Domain containing 4 (YEATS4) , rearrangements affecting the High Mobility Group AT-hook 2 (HMGA2), and deletions in COL4A5/6 locus. MED12 mutations represent the most common genetic alteration in myomas, being present in approximately 70% of cases. Genome organization comprises different levels of complexity, spanning from regulation of individual genes to changes in the architecture of large portions of chromosomes. Literature offers massive evidence of changes in genome organization among different cell types and between several tumor and related healthy cells, but information about these changes in myoma is lacking. The aim of this study is to determine the main features of genome organization in myomas belonging to the aforementioned five genetic subclasses, in order to identify which are the underlying common pathways that are dysregulated in the neoplasia. This is achieved by mapping regions of open chromatin in myomas and related my-ometrium samples with ATAC-seq. Sample’s clustering seems not to be individual-dependent, while tumors belonging to FH, YEATS4 and COL4A5/6 subclasses form distinct clusters, unlike MED12 and HMGA2 subclasses. Six open chromatin regions located within genes were identified in 19/25 tumors and not in myometrium. Seven myometrium-specific open chromatin regions were identified in 21/25 myometria and in less than 10 tumors. As expected, Gene Ontology enrichment analysis revealed that myomas belonging to FH subclass are characterized by deregulation of metabolic pathways. Many of the identified genes in the open chromatin regions have been linked to other tumors in previous studies. Tumor-specific open chromatin regions locate within oncogenes, while myometrium-specific ones are found in proximity of tumor suppressor genes, suggesting a biological role in myomagenesis for these genes. Further investigation on the identified genes (e.g. transcriptional regulation, gene expression and protein level) and addi-tional studies on chromatin architecture are needed to fully unravel the mechanism of myomagenesis.

DBH-geeni koodaa dopamiinia hajottavaa entsyymiä, joka on liitetty palkkiojärjestelmään vaikuttamisen kautta erilaisiin riippuvuuksiin. DBH:n variaatioiden on todistettu liittyvän tupakointikäytänteisiin ja –tapoihin monessa tutkimuksessa. Viimeisimpänä rs3025343 liitettiin tupakoinnin lopettamiseen suuressa GWAS meta-analyysissa. Tutkimuksemme tavoitteena olikin replikoida kyseinen löydös suuressa väestötutkimusnäytteessämme. Lisäksi halusimme tutkia, vaikuttaisiko rs3025343 jonkin muun ympäristötekijän kautta vai itsenäisesti tupakoinnin lopettamiseen. Tutkimusnäytteemme on peräisin suomalaisesta väestönäytteestä, FINRISK-tutkimuksesta. Siihen lukeutuu 26,582 genotyypattua henkilöä tupakointistatuksineen. Analyysit rajasimme 11,926 yksilöön, jotka olivat joko nykyisiä tupakoitsijoita (n=6,578) tai vähintään 6kk sitten tupakoinnin lopettaneita (n=5,348). Henkilöistä oli saatavilla myös kattavasti muita tietoja mukaan lukien sosioekonominen status, terveyteen liittyviä tapoja ja terveydentila, joita käytimme analyyseissä hyväksi. Yhteys rs3025343 ja tupakoinnin lopettamisen välillä (OR=1.12, p=0.094, 95%CI=0.98-1.30) osoittautui tutkimuksessamme identtiseksi GWAS-tutkimuksen kanssa (OR=1.12, 95%CI=1.08-1.18). Mikään testatuista fenotyypeistämme ei vaikuttanut tuohon yhteyteen merkitsevästi. Siviilisääty, koulutustaso, masennus, alkoholin käyttö, itseraportoitu terveys sekä COPD assosioituivat fenotyyppitekijöistä tupakoinnin lopettamiseen, mutta mikään edellämainituista assosiaatioista ei riippunut tutkimastamme genotyypistä. Vaikka tutkimustuloksemme ei ole tilastollisesti merkitsevä, efektikoko viittaa vahvasti siihen, että tutkimallamme polymorfismilla on jonkinasteinen yhteys tupakoinnin lopettamiseen. Merkitevyyden esiinsaamiseksi riittävällä voimalla (80%) otoskoon tulisi olla niinkin suuri kuin 36,092 tapausta ja 29,343 kontrollia, koska harvinaisemman alleelin kantajia on suhteellisen vähän (7,1%). DBH-geenin variaatiot ovat osoittautuneet monessa tutkimuksessa olevan yhteydessä nikotiiniriippuvuuteen tai tupakoinnin lopettamiseen. Jos näitä yhteyksiä saadaan tutkittua lisää, on mahdollista että tietoja voitaisiin käyttää hyväksi tulevaisuudessa esim. yksilöllisesti räätälöidyssä tupakoinnin lopettamisen hoidossa.

Background and objectives: Autism spectrum disorders (ASD) are developmental neuropsychiatric disorders in which core symptoms are problems in communication and interaction as well as restrictive and repetitive behaviour and interests. ASD is 2-5 times more common in males than in females. In recent years, researchers have found, that there are differences between females and males in ASD symptoms, neuropsychological characteristics, comorbid problems, neurobiology and etiology. The purpose of this systematic review is to give a comprehensive picture about the role of female sex/gender in ASD. To establish this, the review covers symptoms of autism, neuropsychology, neurobiology, comorbidity, neurogenetics and neuroendocrinology. Research questions were the following: 1) Is there evidence of sex/gender differences in ASD symptoms and comorbidity disorders? 2) Are there sex/gender differences to be found in ASD etiology? 3) What kind of support different explanations about sex/gender bias have gotten in various research areas? The purpose of the study is also to integrate the existing theories into one model that takes account to different aspects of sex/gender differences in ASD. Methods: The protocol of this systematic review follows "The Preferred Reporting Items for Systematic Reviews and Meta-Analyses" (PRISMA) when applicable. Eligibly criteria and search terms were selected in a way that would offer the widest range of articles covering the subjects of this study. Literature search was conducted using the Medline and PsychINFO as search engines. The final sample consisted of a total of 129 articles. Data was extracted on all relevant variables of the study, that were the number of participants, age of participants, specific diagnoses, methods and results. Results: Sex/gender differences in ASD were found in all areas that were included in this systematic review. Females with high function ASD (HFASD) were found to have less problems in social communication and interaction and less repetitive and restricted behavior and interests than males with HFASD. In addition, HFASD were found to have better language skills than males with HFASD. However, females with ASD were found to have more sensory processing problems, mental health problems and epilepsy than males with ASD. Females with ASD were also found to have lower full-scale intelligence quotient than males with ASD. In the context of etiology, it has been found that there are sex/gender differences in neuroanatomy, susceptibility genes and hormone levels. Conclusions: Results from this systematic review suggest that females with HFASD are underdiagnosed. This results from etiological sex/gender differences that cause partially different clinical presentation of ASD between females and males. ASD research has also concentrated mostly on males with ASD while ignoring females with ASD. Underdiagnosing can have many unfavorable consequences for females with HFASD since if they do not have a diagnosis, they do not get support. In the future, it is crucial to pay attention to females with ASD in the clinical work and scientific research.

Endometrial polyps are one of the most common benign uterine lesions, affecting approximately 10% of all adult women. While endometrial polyps have a high prevalence, their molecular pathogenesis and genetic background are largely undefined. Accordingly, the aim of this thesis was to characterize the somatic mutational landscape of endometrial polyps – to identify mutations in cancer-associated genes, and to identify mutational signatures contributing towards the somatic mutational spectrum. The present study was conducted using whole exome sequencing of 23 endometrial polyps and 18 matching normal blood samples. Mutational signature analysis was conducted using MutationalPatterns and SigProfiler. Endometrial polyps were found to carry varying number of somatic mutations in their exomes, most of them present at a low allelic fraction. Moreover, 43% (10/23) of the polyps were identified to carry one to four cancer-associated mutations, including mutations in genes such as PIK3CA 17% (4/23), KRAS 13% (3/23) and ERBB1 9% (2/23), which are well-established cancer driver genes. Cancer-associated mutational signatures do not have a notable contribution towards the somatic mutational spectrum of endometrial polyps. However, a novel signature, ‘signature B’, characterized by T>G mutations, was found to affect a subset of polyp samples. To conclude, the whole exome sequencing of endometrial polyps revealed several mutations in cancer-associated genes and a novel mutational signature, which may contribute to the development of these benign tumours. However, further research is required to confirm and validate the novel signature, and to define the genetic alterations leading to the polyp pathogenesis.

The field of gene technology, which falls under the umbrella of biotechnology, presents challenges in business development and commercialisation. Understanding the field characteristics is crucial for successful commercialisation, as it can significantly impact the available strategies for bringing products or services to market, ultimately shaping the business model. This study aims to investigate and understand the challenges associated with commercializing gene technology, including identifying any typical challenge profiles specific to the field and possibly arising from the biological material. The research involves semi-structured interviews with multiple companies, venture capitals, and experts in the field to gain a comprehensive understanding of the challenges. The collected data is then analysed to identify common characteristics and business practices against a commercialisation model frame. The motivation behind this study is to provide researchers and other stakeholders with insights into the challenges they may face while commercializing gene technologies, with the aim of lowering the threshold for business creation. The findings reveal that there are two major groups of companies, each with their specific challenges. The challenges for the major group revolve around business know-how, HR, and sales, while the minor group faces challenges related to technology and regulation. However, a common theme is the limited market awareness among customers, which requires significant efforts in sales, marketing, and communications. The study provides guidance to company founders on the different challenges they should be prepared for and offers insights to society on how to harness the value of gene technologies.

Uterine leiomyomas are benign smooth muscle tumors arising in myometrium. They are very common, and the incidence in women is up to 70% by the age of 50. Usually, leiomyomas are asymptomatic, but some patients suffer from various symptoms, including abnormal uterine bleeding, pelvic pain, urinary frequency, and constipation. Uterine leiomyomas may also cause subfertility. Genetic alterations in the known driver genes MED12, HMGA2, FH, and COL4A5-6 account for about 90 % of all leiomyomas. These initiator mutations result in distinct molecular subtypes of leiomyomas. The majority of whole-genome sequencing (WGS) studies analyzing chromosomal rearrangements have been performed using fresh frozen tissues. One aim of this study was to examine the feasibility of detecting chromosomal rearrangements from WGS data of formalin-fixed paraffin embedded (FFPE) tissue samples. Previous results from 3’RNA-sequencing data revealed a subset of uterine leiomyoma samples that displayed similar gene expression patterns with HMGA2-positive leiomyomas but were previously classified as HMGA2-negative by immunohistochemistry. According to 3’RNA-sequencing, all these tumors overexpressed PLAG1, and some of them overexpressed HMGA2 or HMGA1. Thus, the second aim of this study was to identify driver mutations in these leiomyoma samples using WGS. In this study, WGS was performed for 16 leiomyoma and 4 normal myometrium FFPE samples. The following bioinformatic tools were used to detect somatic alterations at multiple levels: Delly for chromosomal rearrangements, CNVkit for copy-number alterations, and Mutect for point mutations and small insertions and deletions. Sanger sequencing was used to validate findings. The quality of WGS data obtained from FFPE samples was sufficient for detecting chromosomal rearrangements, although the number of calls were quite high. We identified recurrent chromosomal rearrangements affecting HMGA2, HMGA1, and PLAG1, mutually exclusively. One sample did not harbor any of these rearrangements, but a deletion in COL4A5-6 was found. Biallelic loss of DEPDC5 was seen in one sample with an HMGA2 rearrangement and in another sample with an HMGA1 rearrangement. HMGA2 and HMGA1 encode architectural chromatin proteins regulating several transcription factors. It is well-known that HMGA2 upregulates PLAG1 expression. The structure and functionality of HMGA2 and HMGA1 are very similar and conserved, so it might be that HMGA1 may also regulate PLAG1 expression. The results of this study suggest that HMGA2 and HMGA1 drive tumorigenesis by regulating PLAG1, and thus, PLAG1 rearrangements resulting in PLAG1 overexpression can also drive tumorigenesis. A few samples, previously classified as HMGA2-negative by immunohistochemistry, revealed to harbor HMGA2 rearrangements, suggesting that the proportion of HMGA2-positive leiomyomas might be underestimated in previous studies using immunohistochemistry. Only one study has previously reported biallelic inactivation of DEPDC5 in leiomyomas, and the results of this study support the idea that biallelic loss of DEPDC5 is a secondary driver event in uterine leiomyomas.

Preeclampsia is a vascular pregnancy disorder characterized by new-onset hypertension and proteinuria and/or new-onset preeclampsia associated symptoms during the second half of pregnancy. The pathophysiology of the disorder is not fully understood, but incomplete placentation and maternal tolerance towards fetal tissue are known to play a part in the disease pathogenesis. Predisposing factors include nulliparity, obesity, diabetes, chronic hypertension and autoimmune diseases. Furthermore, women who have experienced preeclampsia are more susceptible to cardiovascular disease later in life. One established biomarker for preeclampsia is the increased concentration of the soluble Fms-like tyrosine kinase 1 (sFlt1) in the maternal serum. sFlt1 is frequently overexpressed in preeclampsia and it is linked with angiogenic imbalance and endothelial dysfunction, although its role in the disorder is not completely clear. Preeclampsia has a genetic background. There are protective and predisposing variants in and near the Fms related tyrosine kinase 1 gene (FLT1; coding for sFlt1) that have been associated with preeclampsia either in the mother or in the fetus. In this study, five genetic polymorphisms over a 2.3 kb region in the 3’ untranslated region of FLT1 were genotyped by Sanger sequencing and fragment analysis in altogether 1200 individuals consisting of case and control mother–child pairs of the Finnish Genetics of Pre-eclampsia Consortium (FINNPEC) cohort. These polymorphisms were tested for association with various preeclampsia-related phenotypes by Fisher’s exact test. In the maternal genome, the minor alleles of rs17086497 and rs57760154 were associated with extreme hypertension (systolic blood pressure >180 mmHg) (p=0.004, OR=1.77) and obesity (p=0.023, OR=1.63). Homozygosity for these minor alleles was associated with pregnancy complications in general (p=0.026, OR=2.53) and the early-onset form of preeclampsia (p=0.004, OR=3.34). Additionally, the minor alleles of rs9554314, rs3138582 and rs149279513 were associated with extreme hypertension (p=0.045, OR=1.63) and obesity (p=0.023, OR=1.78). Moreover, a suggestive association to severe proteinuria (> 5 g/24h) was found in the maternal genome. In the fetal genome, significant negative associations were reached for rs17086497 and rs57760154 in terms of the serum concentration of sFlt1 in the preeclampsia group (p=0.008, OR=0.23). Overall, the results seem to link the studied region in the maternal genome to preeclampsia with severe features. This supports the idea of preeclampsia as a heterogeneous disorder with varying etiology and mechanisms and thus highlights the importance of differentiating between the various sub-phenotypes. For example, the association of the same allele in the fetal genome with lower maternal sFlt1 levels and in the maternal genome with severe symptoms of preeclampsia suggests that the sFlt1 level might not be a good measure in all patients. Additionally, the observed associations with extreme hypertension and obesity point to the possibility that this region might be relevant for the endothelial damage that is thought to be a central factor in creating the later-in-life disease susceptibility.

Biallelic germline mutations in ERCC6L2 cause bone marrow failure (BMF) and predisposition to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). The patients often develop varying cytopenias, and underlying hypoplasia in the bone marrow is usually evident. The aim of this thesis was to characterize the transcriptome of patient -derived fibroblasts with biallelic germline ERCC6L2 mutation. Moreover, the aim was to study changes on the gene expression at the RNA level in fibroblasts in different media conditions, ROS levels in ERCC6L2 -mutated fibroblasts, and whether addition of glutamine impacts the ROS levels. Fibroblasts from 16 skin biopsies were cultured; eight samples were from healthy controls and eight samples from patients with known mutations in ERCC6L2. Fibroblasts were cultured in different media conditions, followed by RNA extraction and RNA sequencing. We observed downregulation in base excision repair, nucleotide excision repair, mismatch repair, DNA replication, homologous recombination, and cell cycle in ERCC6L2 -mutated cells. MAPK signaling pathway, p53 signaling pathway, apoptosis, AMPK signaling pathway, and TGF-beta signaling pathway were in turn upregulated in ERCC6L2 -mutated cells. The medium did not affect the gene expression significantly across samples. We suspect that the effect of medium was not detected at the RNA level, but it might affect post-translational modifications. We also detected increased ROS levels in ERCC6L2 samples compared to control and observed decreased ROS levels in ERCC6L2 and control samples with excess glutamine. This study shows that biallelic mutations in ERCC6L2 do not only affect the bone marrow but can also affect tissues outside of the hematopoietic system. The transcriptomic analysis identified important biological processes, which could be studied with more detail in the future to further explore the pathology of the ERCC6L2 disease.

Canine uveal melanoma (UM) usually manifests as a slowly developing, darker pigmented and well distinguishable mass in the iris. Less than a third of them are considered malignant, which is much less than with other melanocytic cancers. In contrast, in humans, 90% of UM occurs in the choroid and half of the patients eventually develop aggressive and often lethal metastases. Understanding the disease process and genetic background in dogs might also help us further the knowledge and improve the treatment options of humans. There is a hereditary component to the oncogenesis of the UM: the disease is more common in a Caucasian race and is also found in certain families. It is also more prevalent in certain dog breeds; Labrador Retrievers seem to be overrepresented. Several susceptibility genes have been identified in humans. One with the strongest association with UM is a tumor suppressor gene BAP1, which is dysfunctional or missing in nearly half of the human uveal melanomas. This gene is a so-called secondary driver of the UM and mutations in it spark the metastasizing process. There is a germline mutation of BAP1 in fourth of Finnish UM families and these mutations are also connected to various other cancers. Moreover, BAP1 shows over 98% protein product homology and almost 80% mRNA homology between dogs and humans, making it an appealing study target also for canines. Should a single variant account for high UM risk, a DNA test could be developed to be used in breeding and veterinary diagnostics. In this work, I mapped the BAP1 germline mutations of seven Labrador Retrievers with diagnosed uveal melanomas or melanocytomas. It was found that four dogs shared the same set of five heterozygous single nucleotide variants (SNV). One of the SNVs within exon 17 was synonymous, g.37,363,076G>A, p.(Ser721Ser), while the other four SNVs were intronic, residing close to exons 4, 10, 11 and 14. In the future, variant comparisons with healthy Labradors are needed to study the role of the identified variants for the development of UM, as the SNVs now found could also just be a part of a common variation in the Labrador Retriever gene pool. To grasp a bigger picture of the UM tumor development, the tumors themselves should also be analyzed for somatic mutations. Moreover, when we know that the disease is likely affected by over a hundred genes, studying just one gene is unnecessarily self-restricting. Modern full genome sequencing techniques should be used for catching all the predisposing genes simultaneously.

Melatonin is a circadian regulatory hormone with neuroprotective properties. We have previously demonstrated the association of genetic variant rs12506228 near the melatonin receptor 1A gene (MTNR1A) with intolerance to shift work. Furthermore, this variant has been connected to Alzheimer’s disease. Because of the previously suggested role of melatonin signalling in foetal neurocognitive and sleep development, we studied here the association of rs12506228 with early development. The study sample comprised 8-month-old infants from the Finnish CHILD-SLEEP birth cohort (n=1301). Parental questionnaires assessed socioemotional, communication and motor development, as well as sleep length and night awakenings. The A allele of rs12506228 showed an association with slower socioemotional (P=0.025) and communication (P=0.0098) development but no direct association with sleep. However, the association of the Finnish seasons with infant sleep length interacted with rs12506228. Taken together, rs12506228 near MTNR1A, which has been previously linked to adult and elderly traits, is shown here to associate with slower early cognitive development. In addition, these results suggest that the darker seasons associate with longer infant sleep time, but only in the absence of the rs12506228 AA genotype. Since the risk allele has been connected to fewer brain MT1 melatonin receptors, these associations may reflect the influence of decreased melatonin signalling in early development.