Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease–Associated Colorectal Cancer

doi: 10.1053/j.gastro.2021.04.042Background & Aims Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. Methods Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. Results Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNT-induced epithelial–mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4α binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 5′untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. Conclusions Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.BACKGROUND & AIMS: Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. METHODS: Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. RESULTS: Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNTinduced epithelial-mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4 alpha binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 50 untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. CONCLUSIONS: Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.Peer reviewe

MASTL promotes cell contractility and motility through kinase-independent signaling

Microtubule-associated serine/threonine-protein kinase-like (MASTL) is a mitosis-accelerating kinase with emerging roles in cancer progression. However, possible cell cycle-independent mechanisms behind its oncogenicity remain ambiguous. Here, we identify MASTL as an activator of cell contractility and MRTF-A/SRF (myocardin-related transcription factor A/serum response factor) signaling. Depletion of MASTL increased cell spreading while reducing contractile actin stress fibers in normal and breast cancer cells and strongly impairing breast cancer cell motility and invasion. Transcriptome and proteome profiling revealed MASTL-regulated genes implicated in cell movement and actomyosin contraction, including Rho guanine nucleotide exchange factor 2 (GEF-H1, ARHGEF2) and MRTF-A target genes tropomyosin 4.2 (TPM4), vinculin (VCL), and nonmuscle myosin IIB (NM-2B, MYH10). Mechanistically, MASTL associated with MRTF-A and increased its nuclear retention and transcriptional activity. Importantly, MASTL kinase activity was not required for regulation of cell spreading or MRTF-A/SRF transcriptional activity. Taken together, we present a previously unknown kinase-independent role for MASTL as a regulator of cell adhesion, contractility, and MRTF-A/SRF activity. [Abstract copyright: © 2020 Taskinen et al.

Maksan transkriptomin ja sen geneettisen säätelyn karakterisointi

The FinnGen study is a unique, large-scale research project combining human genetics with digital health care data from the Finnish population in order to to provide new insights to various diseases. FinnGen performs genome-wide association studies (GWASs) to identify associations between genetic variants and diseases, such as intrahepatic cholestasis of pregnancy (ICP), with a perspective on Finnish-enriched variants. Although GWASs have provided various important findings on their own, follow-up analyses are often needed to understand the causal genes and molecular mechanisms behind the association signals. As the majority of GWAS variants lie in non-coding regions, they are thought regulate gene expression, i.e., act as an expression quantitative trait locus (eQTL). Therefore, the integration of GWAS results with transcriptomic data has become a key downstream analysis in GWAS. A commonly used method is colocalization analysis between eQTL and GWAS data. By testing for shared causal variants between the two traits, the analysis can pinpoint plausible causal genes underlying the disease associations. These approaches, however, may not work perfectly if the two data come from different populations. Given the unique genetic structure of Finns and the emerging findings from FinnGen, there is a growing interest to generate and analyse Finnish transcriptomic data. This thesis aims to characterize a Finnish liver transcriptome and its genetic regulation as well as to integrate the Finnish liver eQTLs with Finnish GWAS results via colocalization analysis in order to facilitate functional genomics follow up on Finnish-specific GWAS discoveries. To this end, an RNA sequencing (RNA-seq) analysis pipeline was designed and implemented to process a new collection of 136 Finnish liver (FinnLiver) RNA-seq samples. The primary analyses elucidated that the liver RNA-seq data generated and processed is of high quality and, as expected, reflective of liver tissue’s transcriptome. EQTL analysis identified that expression levels of 16.3% of the genes were associated with nearby common genetic variants. Comparison of the FinnLiver eQTLs with an international liver eQTL resource from the GTEx project showed that the majority (77.7%) of the eQTLs were concordant between the two data, indicating globally shared patterns of gene expression regulation, yet identified also a number of data set-specific signals. Integration of the eQTLs with the FinnGen ICP GWAS results revealed seven colocalizing genes. Four of these showed also significant colocalization in GTEx liver highlighting these as possible causal genes for ICP. The other three genes were specific in colocalization to FinnLiver, potentially pointing to the relevance of having population-specific transcriptomic data for GWAS follow-ups.Suomalaisen väestön ainutlaatuista geneettistä rakennetta hyödynnetään FinnGen-tutkimuhankkeessa, joka yhdistää suomalaista terveysrekisteri- ja genomitietoa tavoitteenaan lisätä ymmärrystä sairauksien syistä. FinnGen-tutkimuksessa suoritetaan genomin laajuisia assosiaatioanalyyseja (GWAS), joiden tarkoituksena on löytää yhteyksiä perimän variaation ja tautien, kuten raskaushepatoosi, välille. Suuri osa GWAS-tuloksien varianteista sijoittuvat ei-koodaavalle alueille genomissa, minkä takia jatkoanalyyseja tarvitaan kausaalisten geenien havaitsemiseen. Ei-koodaavat variantit voivat reguloida geeniekspressiota ekspressio-kvantitatiivisen ominaisuuden lokuksena (eQTL), pikemminkin kuin vaikuttaa suoraan proteiinirakenteeseen. Nämä GWAS- ja eQTL-tulokset voidaan integroida GWAS jatkoanalyysina, jotta voidaan ja selvittää mikä geeni välittää geneettisen variaation vaikutuksen tautiin. Tähän käytetään kolokalisaatioanalyysia, joka etsii jaettuja kausaalisia variantteja GWAS- ja eQTL-tulosten välillä. Tämän diplomityön tavoitteena on karakterisoida suomalaisen maksan transkriptomi ja sen geneettistä säätelyä sekä integroida suomalaisen maksan eQTL-tulokset suomalaisten GWAS-tuloksien kanssa kolokalisaatioanalyysin avulla. Työn tarkoituksena on jatkoanalysoida toiminnallisen genetiikan avulla Suomeen rikastuneita GWAS-löydöksiä. Diplomityössä suunniteltiin ja rakennettiin pipeline RNA-sekvensointitiedon analysointiin, jolla prosessoitiin 136 suomalaisen maksan (FinnLiver) RNA-sekvensoitinäytettä. Maksanäytteiden geeniekspressioprofiileista, solutyyppikompositiosta sekä vertailusta kansainvälisen GTEx-aineiston maksan kanssa voitiin päätellä, että maksanäytteet todella olivat hyvälaatuista maksakudosta, mikä oli oletettavissa. EQTL-analyysi määritti 16,3 % geenin olevan assosioitunut lähellä olevan geneettisen variantin kanssa. Näistä 77,7 % oli yhteneväisiä kansainvälisen eQTL maksa-aineiston, GTEx:n kanssa, osoittaen globaalisti yhteisiä geeni ekspression regulaatiota. Tuloksissa havaittiin myös pelkästään toisessa datassa olevia merkitseviä signaaleja. EQTL ja FinnGen raskaushepatoosi GWAS tuloksien integroiminen toi ilmi seitsemän kolokalisoivaa geeniä, joista neljä olivat merkitseviä myös GTEx:n maksan kolokalisaatioanalyysissa, ja voisivat täten olla mahdollisia kausaalisia geenejä raskaushepatoosille. Kolme muuta geeniä näkyvät vain Finn-Liverissa, mahdollisesti osoittaen populaatio-spesifisyyden merkityksen GWAS-jatkotutkimuksissa

RYHDISTÄYDY! : Opetusvideo ryhdistä ja ergonomiasta 5.-luokkalaisille

Ryhdillä on merkittävä rooli ihmisen kokonaisvaltaisessa hyvinvoinnissa. Koska lapsuudessa opitut toimintamallit usein jatkuvat aikuisuudessa on tärkeää, että jo alakouluikäinen tietää millainen on hyvä ryhti ja mitkä kaikki tekijät siihen voivat vaikuttaa. Pitkään kestävä huono istuma-asento niin koulussa kuin vapaa-ajalla voi aiheuttaa tuki- ja liikuntaelinvaivoja. Nämä tekijät olivat yhtenä perustana opinnäytetyöllemme. Opinnäytetyön toimeksiantajana toimi Kempeleen terveyskeskuksen fysioterapiaosasto. Opinnäytetyömme tulostavoitteena oli valmistaa opetusvideo ryhdistä ja ergonomiasta Kempeleen alakoulujen 5.-luokkalaisille sekä siihen liittyvä oppilaiden vanhemmille suunnattu kirjallinen ryhtiopas. Välittömänä toiminnallisena tavoitteena oli antaa tietoa ryhdistä ja ryhtiin vaikuttavista tekijöistä. Pitkän ajan toiminnallisena tavoitteena oli, että oppilaat motivoituvat kiinnittämään huomiota ryhtiinsä sekä korjaamaan työskentelyasentojaan. Tuotteiden laatukriteereiksi asetettiin mielenkiintoisuus, informatiivisuus, selkeys ja ymmärrettävyys. Tuotteissa käytetty aineisto perustuu opinnäytetyön tietoperustaan. Tietoperustaan koottiin laajasti tietoa ryhdistä, ergonomiasta sekä ryhtiin liittyvästä anatomiasta kansainvälisistä ja kotimaisista tutkimuksista sekä kirjallisuudesta. Ryhdistäydy! -opetusvideo sisältää tietoa hyvästä seisoma- ja istuma-asennosta, ryhtiin liittyvästä anatomiasta, repusta, kengistä sekä lasten liikuntasuosituksista ja ruutuajasta. Opetusvideo koostuu erilaisista osioista: faktoista, pohdinnoista, toiminnallisista testaa itse -tehtävistä sekä tietovisasta. Lasten vanhemmille suunnatussa ryhtioppaassa käsitellään samoja aihealueita sekä keinoja, joilla vaikuttaa lapsen ryhtiin ja ergonomiaan. Projektin tuloksena Kempeleen peruskoulujen opettajat saavat käyttöönsä Ryhdistäydy! -opetusvideon, jota he voivat hyödyntää oppimateriaalina tuki- ja liikuntaelinoireiden ennaltaehkäisyssä. Lisäksi alakouluikäiset ja heidän vanhempansa saavat tietoa mm. hyvästä ryhdistä ja ergonomiasta. Lisäksi projektin tekijät voivat hyödyntää valmistettuja tuotteita ohjausmateriaalina työelämässä. Jatkossa alakouluikäisille voisi suunnitella taukoliikuntahetken esim. välitunnille sekä kirjallisen oppaan tai mobiilisovelluksen liikkuvuudesta ja ryhtilihasten harjoittamisesta.Good posture has a major role in wholesome well-being. Behavior patterns are learned as a child through examples, so it is important to know what good posture is like and what kind of factors affect the posture. Long-term bad sitting position both at school and during spare time can cause problems in the musculoskeletal system. Our bachelor thesis is based on these factors. This project was commissioned by the department of physiotherapy in Kempele Health Care Center. The profit target of our bachelor thesis was to make an interesting and informative educational video about good posture and ergonomics for the 5th grade pupils of Kempele elementary schools and a written guide about good posture for the pupils’ parents. The immediate functional goal was to give information about good posture and the factors which affect the posture. The long-term functional goal was to motivate pupils to take interest in their posture and alter their working positions. The data used in the end products is based on the frame of reference of the bachelor thesis. Information about posture, ergonomics and the anatomy of posture was gathered to the frame of reference. Information was also collected from international and domestic researches and literature. The Ryhdistäydy! –educational video contains information of good sitting and standing posture, the anatomy of posture, a good backpack, shoes, exercise recommendations for children and screen time. The educational video consists of different parts: facts, ponderings, test yourself and quiz. The written guide handles the same subjects and ways to affect a child’s posture and ergonomics. As a result of the project the teachers in Ylikylä school get to use the Ryhdistäydy! –educational video, which they can utilize in teaching. Furthermore pupils and their parents gain knowledge about good posture and ergonomics among other things. As a further development idea for this thesis there could be an exercise program or a mobile application about body mobility and training of the posture muscles for pupils in elementary schools

MANF protects human pancreatic beta cells against stress-induced cell death

There is a great need to identify factors that could protect pancreatic beta cells against apoptosis or stimulate their replication and thus prevent or reverse the development of diabetes. One potential candidate is mesencephalic astrocyte-derived neurotrophic factor (MANF), an endoplasmic reticulum (ER) stress inducible protein. Manf knockout mice used as a model of diabetes develop the condition because of increased apoptosis and reduced proliferation of beta cells, apparently related to ER stress. Given this novel association between MANF and beta cell death, we studied the potential of MANF to protect human beta cells against experimentally induced ER stress. Primary human islets were challenged with proinflammatory cytokines, with or without MANF. Cell viability was analysed and global transcriptomic analysis performed. Results were further validated using the human beta cell line EndoC-beta H1. There was increased expression and secretion of MANF in human beta cells in response to cytokines. Addition of recombinant human MANF reduced cytokine-induced cell death by 38% in human islets (p <0.05). MANF knockdown in EndoC-beta H1 cells led to increased ER stress after cytokine challenge. Mechanistic studies showed that the protective effect of MANF was associated with repression of the NF-kappa B signalling pathway and amelioration of ER stress. MANF also increased the proliferation of primary human beta cells twofold when TGF-beta signalling was inhibited (p <0.01). Our studies show that exogenous MANF protein can provide protection to human beta cells against death induced by inflammatory stress. The antiapoptotic and mitogenic properties of MANF make it a potential therapeutic agent for beta cell protection.Peer reviewe