Jan Dumanski's projects in molecular oncology

Mosaic loss of chromosome Y (LOY) in blood cells is associated with smoking as well as shorter survival and higher risk of cancer in men

LOY and cancer

It is well known that men have an overall shorter life expectancy compared with women. However, it is less well recognized that incidence and mortality for sex-unspecific cancers are higher in men, a fact that is largely unexplained. Age-related loss of chromosome Y (LOY) is frequent in normal hematopoietic cells and it was first described more than 50 years ago, but the phenotypic consequences of LOY have been elusive. Our latest results suggest that LOY could be a key factor to explain the higher mortality of men.

Survival analyzes performed in the Swedish ULSAM-cohort (Uppsala Longitudinal Study of Adult Men) with >1100 participants indicated that LOY in peripheral blood could be associated with risks of all-cause mortality as well as non-hematological cancer mortality. Among the elderly men in this cohort, followed clinically for up to 20 years, at least 8.2 % of the subjects were affected by LOY in a significant fraction of blood cells.

The median survival time in men affected with LOY was half, i.e. 5.5 years shorter, compared to the men without mosaic LOY in blood cells. The association of LOY with risk of all-cause mortality was validated in the independent PIVUS-cohort (Prospective Investigation of the Vasculature in Uppsala Seniors) in which 20.5 % of men showed LOY. Our discovery of a correlation between LOY and all-cause mortality as well as non-hematological cancer mortality will be published in Nature Genetics.

These results illustrate the impact of post-zygotic mosaicism such as loss of chromosome Y (LOY) on disease risk and could explain why males have a higher mortality compared to females and are more frequently affected by cancer. They also suggest that chromosome Y is important in processes beyond sex determination and sperm production. LOY in blood could become a predictive biomarker of male carcinogenesis.

LOY and smoking as well as Alzheimer’s disease

Smoking is a major preventable environmental risk factor related to human health. Smoking killed about 100 million people during the 20th century and is projected to kill one billion people during this century, assuming that the current frequency of smoking is retained. Lung cancer is the prime cause of cancer associated death in relation to smoking. However, it is less well appreciated that smoking also causes tumours outside the respiratory tract, which is predominant in men and cumulatively roughly as common as lung cancer. Moreover, it is known that males have a higher incidence and mortality from most sex-unspecific cancers, disregarding smoking status, and this fact is largely unexplained by known risk factors.

We have published a paper in Science showing that smoking is associated with LOY in blood cells in three independent cohorts encompassing in total 6014 men. Our data also support a transient and dose-dependent mutagenic effect from smoking on LOY-status (Dumanski et al. 2015 Science, PMID: 25477213). Thus, smoking may induce LOY, linking the most common acquired human mutation with a severe preventable risk factor. Our results could explain the observed sex differences and why smoking seems a greater risk factor for cancer in men than women.

Furthermore, we have recently reported a strong association between LOY and Alzheimer’s Disease (AD) in males, which links LOY to another common disease responsible for morbidity/mortality in aging males. Thus, LOY in blood is associated with risks of both AD and cancer, suggesting a role of LOY in blood cells on disease processes in other tissues (published in American Journal of Human Genetics).

We explain the effect of LOY in blood cells on development of AD phenotype occurring in another tissue (the brain) by a hypothesis of defective immuno-surveillance; i.e. that LOY disturbs normal functions of immune system, vital for elimination of abnormal cells, such as cells forming amyloid plaques in the brain. We also hypothesize that LOY is present at various levels in different types of blood cells in AD patients versus controls.
 

Post-zygotic genetic variation: studies of human aging/longevity and age-associated aberrations

Monozygotic (MZ) twins represent an extraordinary resource in genetics; two individuals who can also be treated as a single subject genetically matched at conception and present in two copies. Therefore, it is a powerful model for analysis of de novo (post-zygotic or somatic) genetic variation. We have shown in 2008 that MZ twins frequently display disparate patterns of genomic copy number variation (CNV). We hypothesized that structural genetic rearrangements in human somatic cells also vary over time and these might represent a new mechanism contributing to the aging process in humans. 

Using age-stratified cohorts of 318 monozygotic (MZ) twins and 296 single-born subjects, we found age-related accumulation of copy-number variation in the nuclear genomes in vivo and frequency changes for both megabase- and kilobase-range variants. Megabase-range aberrations were found in 3.4 % (9 of 264) of subjects >60 years old; these subjects included 78 MZ twin pairs and 108 single-born individuals from Uppsala ULSAM-cohort. No such findings were observed in 81 MZ pairs or 180 single-born subjects who were <55 years old. Recurrent region- and gene-specific mutations, mostly deletions, were observed. Longitudinal analyses of 43 subjects whose data were collected 7–19 years apart suggest considerable variation in the rate of accumulation of clones carrying structural changes.

Furthermore, the longitudinal analysis of individuals with structural aberrations suggests that there is a natural self-removal of aberrant cell clones from peripheral blood. In three healthy subjects, we detected somatic aberrations characteristic of patients with myelodysplastic syndrome. The recurrent rearrangements uncovered here are candidates for common age-related defects in human blood cells. We anticipate that extension of these results will allow determination of the genetic age of different somatic-cell lineages and estimation of possible individual differences between genetic and chronological age. Our work might also help to explain the cause of an age-related reduction in the number of cell clones in the blood; such a reduction is one of the hallmarks of immunosenescence.
 

Novel biomarkers for breast cancer; disease prediction and progression

There exists a paradox in cancer research: although the high mortality from cancer is caused by metastatic spread of tumours, genetic research of metastases is underdeveloped. Contrary to the numerous transcriptome and genome analyses of primary tumours, there is a lack of comprehensive and high-resolution studies comparing genomic profiles of primary tumours and the metastases from the same patient.

We have recently completed pilot breast- and ovarian-cancer projects, testing the hypothesis that, upon high-resolution analysis, there are frequent genetic differences between matched primary tumours and lymph node metastases. We observed aberrations that can be linked to metastatic disease and many of the observed differences were previously linked to poor patient survival, based on extensive analyses of primary tumours. This provides a proof of concept that this approach towards finding new biomarkers for breast cancer progression and patient’s prognosis is viable.

The second part of this project deals with search for somatic genetic events in normal breast tissue predisposing to breast cancer. Our previous discoveries of genetic differences between differentiated tissues and in monozygotic twins indicate that the somatic mosaicism for CNVs, between normal cells in the same person is underestimated. This represents a paradigm shift in somatic cell genetics, which has implications for cancer research, as cancer is predominantly a genetic disorder of somatic cells. Hence, this gives an opportunity for analysis of de novo somatic aberrations that may predispose normal cells to cancer development, by comparisons of CNV/CpG methylome profiles between an uninvolved margin of histopathologically normal cells surrounding a primary tumour and blood of the same patient.

We compare genomes and epigenomes (CpG methylome) of primary tumours and metastases from patients with breast cancer. We also evaluate genetic and epigenetic (CpG methylation) profiles of normal margin of tissue surrounding primary tumour and blood DNA from the same patient. The objective is to identify patterns suggesting genomic global CNV/epigenetic instability, alternatively aberrations in specific genomic loci that might be coupled to breast cancer progression and predisposition/susceptibility.