Jan Dumanski's projects in molecular oncology

Mosaic loss of chromosome Y (LOY) in blood cells is associated with more severe COVID-19, as well as higher mortality, risk for cancer and Alzheimer’s disease in men

Loss of chromosome Y as a possible factor associated with COVID-19 infection severity

The COVID-19 pandemic has revealed a large disparity in the severity and mortality of the disease in men. Understanding male bias in COVID-19 is an aspect that is still being explored from a genetic and epidemiological point of view. Therefore, in our recent project, we decided to investigate whether LOY could be a male-specific risk factor predisposing men to the life-threatening course of COVID-19 disease.

Our study cohort consisted of 211 COVID-19 patients treated in intensive care units (ICU). Of these, 139 patients were subject to cell sorting for LOY analysis in granulocytes, low-density neutrophils (LDNs), monocytes, and PBMCs. We showed that the highest levels of LOY are found in cells of the myeloid lineage, crucial for the development of severe disease, especially in LDN, pathological cells present in large numbers in the peripheral blood of critically ill COVID-19 patients. In addition, we demonstrated that LOY was associated with multiple clinical variables, most importantly severity of the disease according to WHO score and mortality during ICU treatment.

An interesting aspect of this project was also the analysis of LOY in patients who recovered from the disease. Cell clones with LOY were transient and dynamic when samples that were taken from the same patients during ICU stay and 3–6 months later are compared.

As the pandemic continues, we focus on expanding the research cohort to learn more about LOY's functional impact on the development of severe COVID-19. One of the approaches we use for this purpose is innovative plasma proteome analysis and single-cell RNA sequencing technology.

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.

Thanks to our and others' studies LOY is now a well-recognized factor increasing the risk of Alzheimer's disease and cancer in males, however, our recent results shed light on molecular mechanisms linking LOY with aberrations of immune functions in males.

Prostate cancer patients have a high percentage of LOY cells in peripheral blood mononuclear cells. In particular, LOY is the most pronounced in CD4+ T cells which encompass regulatory T cells playing one of the key roles in forming an immunosuppressive environment in cancers.

Our analyses of gene expression in whole blood and single cells isolated from cancer patients showed a LOY-associated widespread dysregulation of gene expression which we termed LATE (LOY-associated transcriptional effect). It affects approximately 500 autosomal genes, among which are genes involved in the direct regulation of immune functions as well as genes associated with general regulation of gene expression, splicing or cell signalling.

Our findings highlight a surprisingly broad role for chromosome Y, challenging the view of it as a "genetic wasteland", and support the hypothesis that altered immune function in leukocytes could be a mechanism linking LOY to increased risk for disease.

LOY and Alzheimer’s disease

Our results revealed 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. Additionally, recent DNA analysis of sorted peripheral blood cells showed that men with AD were primarily affected by LOY in NK cells (Cellular and Molecular Life Sciences).

Smoking as a risk factor of LOY

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.

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.

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 immuno-senescence.

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.

Somatic genetic events in normal breast tissue

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.