A multistate analysis of ulcerative colitis and colorectal cancer

Colorectal cancer (CRC) accounts for one in 10 new cancer cases worldwide. CRC risk is determined by a complex interplay of constitutional, behavioral, and environmental factors. Patients with ulcerative colitis (UC) are at increased risk of CRC, but effect estimates are heterogeneous, and many studies are limited by small numbers of events. Furthermore, it has been challenging to distinguish the effects of age at UC diagnosis and duration of UC. Multistate models provide a useful statistical framework for analyses of cancers and premalignant conditions. This thesis has three aims: to review the mathematical and statistical background of multistate models; to study maximum likelihood estimation in the illness-death model with piecewise constant hazards; and to apply the illness-death model to UC and CRC in a population-based cohort study in Finland in 2000–2017, considering UC as a premalignant state that may precede CRC. A likelihood function is derived for multistate models under noninformative censoring. The multistate process is considered as a multivariate counting process, and product integration is reviewed. The likelihood is constructed by partitioning the study time into subintervals and finding the limit as the number of subintervals tends to infinity. Two special cases of the illness-death model with piecewise constant hazards are studied: a simple Markov model and a non-Markov model with multiple time scales. In the latter case, the likelihood is factorized into terms proportional to Poisson likelihoods, which permits estimation with standard software for generalized linear models. The illness-death model was applied to study the relationship between UC and CRC in a population-based sample of 2.5 million individuals in Finland in 2000–2017. Dates of UC and CRC diagnoses were obtained from the Finnish Care Register for Health Care and the Finnish Cancer Registry, respectively. Individuals with prevalent CRC were excluded from the study cohort. Individuals in the study cohort were followed from January 1, 2000, to the date of first CRC diagnosis, death from other cause, emigration, or December 31, 2017, whichever came first. A total of 23,533 incident CRCs were diagnosed during 41 million person-years of follow-up. In addition to 8,630 patients with prevalent UC, there were 19,435 cases of incident UC. Of the 23,533 incident CRCs, 298 (1.3%) were diagnosed in patients with pre-existing UC. In the first year after UC diagnosis, the HR for incident CRC was 4.67 (95% CI: 3.07, 7.09) in females and 7.62 (95% CI: 5.65, 10.3) in males. In patients with UC diagnosed 1–3 or 4–9 years earlier, CRC incidence did not differ from persons without UC. When 10–19 years had passed from UC diagnosis, the HR for incident CRC was 1.63 (95% CI: 1.19, 2.24) in females and 1.29 (95% CI: 0.96, 1.75) in males, and after 20 years, the HR was 1.61 (95% CI: 1.13, 2.31) in females and 1.74 (95% CI: 1.31, 2.31) in males. Early-onset UC (age <40 years) was associated with a markedly increased long-term risk of CRC. The HR for CRC in early-onset UC was 4.13 (95% CI: 2.28, 7.47) between 4–9 years from UC diagnosis, 4.88 (95% CI: 3.46, 6.88) between 10–19 years, and 2.63 (95% CI: 2.01, 3.43) after 20 years. In this large population-based cohort study, we estimated CRC risk in persons with and without UC in Finland in 2000–2017, considering both the duration of UC and age at UC diagnosis. Patients with early-onset UC are at increased risk of CRC, but the risk is likely to depend on disease duration, extent of disease, attained age, and other risk factors. Increased CRC risk in the first year after UC diagnosis may be in part due to detection bias, whereas chronic inflammation may underlie the long-term excess risk of CRC in patients with UC

Genetic predisposition to colorectal cancer in young patients and in the general population

Colorectal cancer (CRC) is the third most common cancer worldwide and accounts for 10% of all new cancers. The purpose of this thesis was to provide new insights into the genetic architecture of CRC susceptibility, as well as the identification of individuals with substantial genetic risk. The first aim was to study the diagnostic approach to hereditary cancer syndromes in early-onset CRC patients. We investigated a series of 38 CRC patients diagnosed before age 40 years. To assess the practical feasibility and added value of whole-exome sequencing (WES) as a diagnostic test, we performed WES on 23 early-onset CRC patients with unknown etiology. Ten high-penetrance CRC predisposition genes (MLH1, MSH2, MSH6, PMS2, APC, MUTYH, SMAD4, BMPR1A, STK11 and PTEN) were analyzed for nonsynonymous variants, and family histories were acquired from national population registries. Hereditary CRC syndromes were diagnosed in 42% of the early-onset CRC patients (16/38; 95% CI, 26%-59%), but the diagnostic yield of WES was not superior to microsatellite instability testing and clinical assessment for gastrointestinal polyposis. The second aim was to study the contribution of rare germline variants to early-onset CRC. We analyzed WES data from 22 unexplained early-onset CRC patients and studied 95 familial CRC patients as a validation set. In this series of 22 early-onset CRC cases, we did not find any genes with recurrent loss-of-function (LoF) variants with minor allele frequency < 0.1%. This observation, together with negative family history in 86% (19/22) of the unexplained young patients, suggests that the genetic background of these patients may be complex. Rare LoF variants in three genes - ADAMTS4, CYTL1 and SYNE1 - were shared between early-onset and familial CRC cases. Both INTS5 and ACSL5 harbored rare missense variants in two of the 22 patients, whereas ARHGAP12, ATM, DONSON, MCTP2 and ROS1 showed rare homozygous variants in single early-onset CRC cases. Further studies are needed to determine whether the identified variants are associated with CRC risk. The third aim was to study the genetic basis of common, complex CRC. We conducted a genome-wide association study (GWAS) of CRC in 1,701 cases and 14,082 cancer-free controls from the Finnish population. A total of 9,068,015 single-nucleotide variants were imputed and analyzed, and most promising variants were studied in additional 11,647 cases and 12,356 controls of European ancestry. Thirteen previously published loci (2q35, 6p21.2, 8q23.3, 8q24.21, 10q22.3, 10q24.2, 11q13.4, 11q23.1, 14q22.2, 15q13.3, 18q21.1, 20p12.3 and 20q13.33) were associated with CRC in the Finnish population, but new risk loci were not found. These results replicate multiple CRC susceptibility loci and underscore similarities in the genetic architecture of CRC susceptibility between the Finnish population isolate and outbred populations, which informs the design of future GWASs.Paksu- ja peräsuolisyöpä on maailman kolmanneksi yleisin syöpätyyppi, jonka osuus kaikista uusista syövistä on noin 10%. Jos suolistosyöpä tai sen esiaste todetaan riittävän varhain, ovat hoitotulokset erinomaisia. Valtakunnallisilla seulontaohjelmilla voidaan vähentää suolistosyöpään liittyvää kuolleisuutta, mutta geneettisestä alttiudesta johtuen osa väestöstä hyötyy intensiivisemmästä seulonnasta ja muista syöpää ehkäisevistä toimenpiteistä. Tämän väitöskirjatyön tavoitteena oli tutkia suolistosyövän geneettisiä riskitekijöitä nuorilla potilailla ja yleisessä väestössä. Periytyvät syöpäalttiusoireyhtymät olivat yleisiä alle 40-vuotiaana suolistosyöpään sairastuneilla suomalaisilla potilailla (26-59% tässä aineistossa). Nämä oireyhtymät voitiin tunnistaa joko kasvaimissa todettujen DNA:n korjausvirheiden tai ruoansulatuskanavassa esiintyneiden hyvänlaatuisten kasvaimien perusteella. Laajamittaisen DNA:n sekvensoinnin käyttöä arvioitiin, mutta tässä aineistossa se ei tuonut diagnostista lisähyötyä edellä mainittujen piirteiden tunnistamisen jälkeen. Eräät harvinaiset geenimuutokset voivat aiheuttaa moninkertaisen syöpäriskin ja auttaa ymmärtämään syövän yleisiä syntymekanismeja. Suomen asutushistoriasta johtuen suomalaiseen väestöön on rikastunut harvinaisia geenivariantteja, joiden tutkiminen muissa väestöissä on haastavaa. Genominlaajuista sekvensointia käyttäen tutkimme harvinaisia geenimuutoksia 117:llä suomalaisella suolistosyöpäpotilaalla, joilla epäiltiin periytyvää syöpäalttiutta (sairastumisikä alle 40 vuotta tai lähisuvussa vähintään yksi toinen suolistosyöpätapaus; tunnetut oireyhtymät oli poissuljettu). Aineisto ei tarjonnut vahvaa näyttöä yhteisistä geneettisistä alttiustekijöistä tässä potilasryhmässä, mutta tunnistimme kymmenen ehdokasgeeniä, joiden vaikutusta suolistosyöpäalttiuteen voidaan arvioida laajemmissa tutkimuksissa. Aiemmissa tutkimuksissa on tunnistettu kymmeniä yleisiä geneettisiä variantteja, joista jokaisella on pieni vaikutus suolistosyövän yksilölliseen riskiin. Väestötasolla niiden vaikutukset ovat kuitenkin huomattavia, ja ne voivat summautuessaan aiheuttaa korkean sairastumisriskin. Tutkimme yli yhdeksää miljoonaa geneettistä varianttia 1 701:llä suomalaisella suolistosyöpäpotilaalla ja 14 082:lla verrokilla DNA-siruja käyttäen. Tutkimusta laajennettiin myös muihin eurooppalaisiin aineistoihin, jotka kattoivat yhteensä 11 647 suolistosyöpätapausta ja 12 356 verrokkia. Totesimme, että ainakin 13 aiemmin tunnistettua kromosomialuetta vaikuttivat suolistosyövän riskiin suomalaisessa väestössä. Uusia geneettisiä riskitekijöitä ei tunnistettu. Nämä tulokset vahvistavat aiempaa tietoa ja osoittavat geneettisiä yhtäläisyyksiä suomalaisten ja muiden eurooppalaisten välillä, mikä edistää tutkimusten suunnittelua tulevaisuudessa

Transformation and outcome of nodular lymphocyte predominant Hodgkin lymphoma : a Finnish Nationwide population-based study

Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) is a rare B-cell malignancy associated with excellent survival. However, some patients experience histological transformation into aggressive large B-cell lymphoma. Population-based data on transformation in patients with NLPHL is limited. We conducted a nationwide population-based study to estimate the risk of transformation and relative survival in patients diagnosed with NLPHL in Finland between 1995 and 2018. We identified a total of 453 patients (median age, 48 years; 76% males) with the incident NLPHL from the Finnish Cancer Registry. The cumulative incidence of transformation was 6.3% (95% CI, 4.2-9.6) at 10 years. After adjusting for sex, age and year of diagnosis, transformation was associated with a substantially increased risk of death (HR 8.55, 95% CI 4.49-16.3). Ten-year relative survival was 94% (95% CI, 89%-100%). The patients diagnosed at a later calendar year had lower excess risk of death (HR, 0.38 per 10-year increase; 95% CI, 0.15-0.98). We conclude that while the 10-year relative survival for the patients with NLPHL was excellent in this large population-based cohort for the entire study period, transformation resulted in a substantially increased mortality compared with the patients without transformation. Our results also suggest a reduction in excess mortality over time.Peer reviewe

Cancer Incidence and Mortality in the Oldest Old: a Nationwide Study in Finland

The world's population is aging rapidly. This study reports the burden of cancer in the oldest old (≥85 years) in Finland in 1953-2017 and estimates age-specific cancer rates in the old population (65-99 years) in 1988-2017. The Finnish Cancer Registry provided data on all cancer diagnoses, cancer deaths and other deaths in cancer patients in Finland in 1953-2017. Between 1953-1957 and 2013-2017, the proportion of incident cancers in those aged ≥85 years increased from 1.5% to 9.6% (597 to 15,360 new cases), and in 2013-2017, more new cancers were diagnosed at age ≥85 years than age <50 years. Cancer incidence and excess mortality attributable to cancer peaked at age 85-94 years and declined subsequently, whereas cancer-specific mortality continued to increase or plateaued. Due to demographic changes, the number of new cancers in the oldest old has increased substantially in Finland, and currently, nearly one in 10 cancers are diagnosed in this age group. The increasing cancer burden in the oldest old poses a major challenge for healthcare and needs to be addressed in designing clinical research and reporting of cancer registries. In old populations with competing risks of death, we propose excess cancer mortality as a measure of cancer-related mortality.Peer reviewe

Transformation and outcome of nodular lymphocyte predominant Hodgkin lymphoma: a Finnish Nationwide population-based study

Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) is a rare B-cell malignancy associated with excellent survival. However, some patients experience histological transformation into aggressive large B-cell lymphoma. Population-based data on transformation in patients with NLPHL is limited. We conducted a nationwide population-based study to estimate the risk of transformation and relative survival in patients diagnosed with NLPHL in Finland between 1995 and 2018. We identified a total of 453 patients (median age, 48 years; 76% males) with the incident NLPHL from the Finnish Cancer Registry. The cumulative incidence of transformation was 6.3% (95% CI, 4.2-9.6) at 10 years. After adjusting for sex, age and year of diagnosis, transformation was associated with a substantially increased risk of death (HR 8.55, 95% CI 4.49-16.3). Ten-year relative survival was 94% (95% CI, 89%-100%). The patients diagnosed at a later calendar year had lower excess risk of death (HR, 0.38 per 10-year increase; 95% CI, 0.15-0.98). We conclude that while the 10-year relative survival for the patients with NLPHL was excellent in this large population-based cohort for the entire study period, transformation resulted in a substantially increased mortality compared with the patients without transformation. Our results also suggest a reduction in excess mortality over time

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches. We developed a long-distance inverse PCR (LDI-PCR) based approach to monitor the mobility of active L1 elements based on their 3' transduction activity. LDI-PCR requires no prior knowledge of the insertion target region. By applying LDI-PCR in conjunction with Nanopore sequencing (Oxford Nanopore Technologies) on one L1 reported to be particularly active in human cancer genomes, we detected 14 out of 15 3' transductions previously identified by whole genome sequencing in two different colorectal tumour samples. In addition we discovered 25 novel highly subclonal insertions. Furthermore, the long sequencing reads produced by LDI-PCR/Nanopore sequencing enabled the identification of both the 5' and 3' junctions and revealed detailed insertion sequence information.Peer reviewe

Familial cancer risk in family members and spouses of patients with early-onset head and neck cancer

Background Reported patterns of familial aggregation of head and neck cancer (HNC) vary greatly, with many studies hampered by the limited number of subjects. Methods Altogether 923 early-onset ( Results Of all early-onset HNC families, only 21 (2.3%) had familial HNC cancers at any age and less than five familial early onset HNC cancers among first-degree relatives. The cumulative risk of HNC for siblings by age 60 (0.52%) was at population level (0.33%). No increased familial risk of early-onset HNC could be discerned in family members (SIR 2.68, 95% CI 0.32-9.68 for first-degree relatives). Conclusions Our study indicates that the cumulative and relative familial risk of early-onset HNC is modest in the Finnish population and, at most, only a minor proportion of early-onset HNCs are due solely to inherited genetic mutations.Peer reviewe

Multiple clinical characteristics separate MED12-mutation-positive and -negative uterine leiomyomas

Up to 86% of uterine leiomyomas harbour somatic mutations in mediator complex subunit 12 (MED12). These mutations have been associated with conventional histology, smaller tumour size, and larger number of tumours within the uterus. Prior studies, with limited sample sizes, have failed to detect associations between other clinical features and MED12 mutations. Here, we prospectively collected 763 uterine leiomyomas and the corresponding normal myometrial tissue from 244 hysterectomy patients, recorded tumour characteristics, collected clinical data from medical records, and screened the tissue samples for MED12 mutations to assess potential associations between clinical variables and mutation status. Out of 763 leiomyomas, 599 (79%) harboured a MED12 mutation. In the analysis of tumour characteristics, positive MED12-mutation status was significantly associated with smaller tumour size, conventional histology, and subserous location, relative to intramural. In the analysis of clinical variables, the number of MED12-mutation-positive tumours showed an inverse association with parity, and the number of mutation-negative tumours showed a positive association with a history of pelvic inflammatory disease. This study confirmed the previously reported differences and discovered novel differentiating features for MED12-mutation-positive and -negative leiomyomas. These findings emphasise the relevance of specific driver mutations in genesis and presentation of uterine leiomyomas.Peer reviewe

Genetic predisposition to uterine leiomyoma is determined by loci for genitourinary development and genome stability

Uterine leiomyomas (ULs) are benign tumors that are a major burden to women's health. A genome-wide association study on 15,453 UL cases and 392,628 controls was performed, followed by replication of the genomic risk in six cohorts. Effects of the risk alleles were evaluated in view of molecular and clinical characteristics. 22 loci displayed a genome-wide significant association. The likely predisposition genes could be grouped to two biological processes. Genes involved in genome stability were represented by TERT, TERC, OBFC1 - highlighting the role of telomere maintenance - TP53 and ATM. Genes involved in genitourinary development, WNT4, WT1, SALL1, MED12, ESR1, GREB1, FOXO1, DMRT1 and uterine stem cell marker antigen CD44, formed another strong subgroup. The combined risk contributed by the 22 loci was associated with MED12 mutation-positive tumors. The findings link genes for uterine development and genetic stability to leiomyomagenesis, and in part explain the more frequent occurrence of UL in women of African origin.Peer reviewe