Group Markkanen

Group Markkanen

Understanding the role of Base-Excision Repair in cellular physiology and pathology


Genetic instability and the accumulation of mutations in DNA, provoked by exogenous mutagens (such as UV irradiation or tobacco smoke), are well linked to processes like aging and a variety of disorders such as cancer [1, 2] and neurodegenerative diseases [3]. However, even without damage from exogenous sources, DNA is a very sensitive molecule and is known to be susceptible to spontaneous alterations like DNA base damage or single-strand DNA breaks. Indeed, this group of DNA damage is the most prevalent one to be found in the genome, and it has been estimated that at least 10’000 such lesions arise per cell per day even under ‘non-stressed’ conditions due to the intracellular milieu [4]. The major cellular pathway to safeguard the genome against these constantly arising DNA lesions is Base Excision Repair (BER, Figure 1). As a deficiency in BER activity results in the accumulation of endogenous DNA damage, it has been proposed that individual differences in BER capacity may underlie the propensity for diverse pathologies [5].

Our lab is interested in furthering understanding of the roles of BER on cellular homeostasis as well as its possible implications in cellular pathologies, and elucidating the mechanisms behind these processes. Within this framework, we are currently investigating the contributions of BER to tumour development as well as neurodevelopmental disorders, using both in vitro as well as in vivo approaches.

Figure 1

Figure taken from [6] Figure 1. Simplified scheme of base excision repair (BER). Modified after [7, 8]. (A) BER is initiated by damage-specific DNA glycosylases, which identify and release the corrupted base by hydrolysis of the N-glycosylic bond linking the DNA base to the sugar phosphate backbone (reviewed in [8, 9]). The arising abasic (AP) site is further processed by AP-endonuclease 1 (APE1), and depending on the mechanism by which the DNA base was removed, end processing of the modified 3′- and 5′-termini is performed by a variety of end-processing enzymes. This processing results in the generation of a 3′-OH and a 5′-P group adjacent to the DNA gap or break; (B) Single-strand breaks (SSBs) can also arise from direct disintegration of oxidised deoxyribose. This process usually leads to damaged or modified termini, which are processed by a variety of enzymes to 3′-OH and 5′-P groups. SSBs are then handled identically to the BER intermediates from this point onward; (C) Further processing of the SSB containing intermediate stemming from either source is carried out by the core BER complex that includes DNA polymerase β (Pol β), XRCC1 (X-ray repair cross-complementation group 1) and DNA ligase IIIa (Lig III). Pol β possesses a dRP-lyase activity that removes the 5′-sugar phosphate and also, functioning as a DNA polymerase, adds one nucleotide to the 3′-end of the arising single-nucleotide gap. Finally, the XRCC1-Lig III complex seals the DNA ends, therefore accomplishing complete DNA repair [10-13].

Analysis of Gene Expression Signatures in Cancer-Associated Stroma from Canine Mammary Tumours


Most cancers are of epithelial origin, and derive from the emergence of a corrupted epithelial cell population that gives rise to aggressively growing tumour cells. Yet, these tumour cells are not living in an isolated environment, and – far from being self-sufficient - heavily depend on their microenvironment for growth and survival (reviewed in [14]). While the vast majority of research over the past half a century has focused on the cancer cells themselves, progress over the last decade has started to unveil the importance of the tumour microenvironment in cancer formation and progression. The so-called cancer stroma consists of extracellular matrix as well as a variety of cells, including endothelial cells, immune cells and fibroblasts (reviewed in [15]). Under physiological conditions, stroma serves as an important barrier to prevent epithelial transformation. However, in response to emerging epithelial cancerous lesions, the stromal compartment undergoes a reprogramming towards a tumour-supportive function – termed cancer-associated stroma (CAS) - and plays a key role in cancer initiation and progression [14]. The pivotal role of CAS in many human carcinomas (such as breast, lung, prostate and colorectal carcinomas) has been widely documented [16]. It has even been suggested, that components of CAS serve as actual drivers initiating the development of a tumour from precancerous cells (e.g. [15]). Importantly, due to their central role for tumour cell survival and the much higher genetic stability of stromal cells compared to cancer cells themselves, targeting CAS is evolving as promising strategy for therapeutic approaches with lower risk to develop therapeutic resistance through mutations [17]. Recent progress shows that CAS directly supports the growth of tumour, e.g. through cytokines, growth factors, nutrients and proteases (e.g. reviewed in [14, 16]). Studies performed in human clinical tumour samples have begun to shed light on mechanisms driving the formation of CAS, as well as the molecular dialogue between CAS and tumour cells (e.g. [18-21]. Nevertheless, the underlying reprogramming mechanisms driving the change from normal stroma into CAS remain far from being completely understood.

Canine mammary tumours are highly relevant in the veterinary clinical setting, due to their incidence (the most frequent cancer in intact female dogs) and the difficulties of therapeutic intervention associated with all current cancer treatments [22]. Interestingly, due to the closely related pathophysiology, the study of cancer in domestic dogs is lately emerging as valuable tool to better understand the biology behind tumour development and find novel anti-cancer treatments [23, 24]. Particularly canine mammary tumours are viewed as excellent model of human breast cancer, due to strong clinical and molecular similarities and availability of specimens [25, 26].

Nevertheless, high-quality studies specifically assessing the mechanisms involved in formation of canine cancer are sparse. Moreover, in order to provide better therapeutic options to canine patients suffering from cancer, it is important to understand canine cancer biology itself, and not only extrapolate data from the human situation. Taking into account the importance of CAS for human cancer development, it is likely that CAS also plays a pivotal role in the development of canine tumours. So far however, there is no data regarding the role of CAS in the biology and development of canine tumours. Therefore it is completely unclear whether CAS has a role in growth of canine tumours, what mechanisms are involved in its formation, and if canine CAS is comparable to human CAS.

The aim of the project is to analyse the gene-expression changes in the stroma of canine mammary carcinomas, to support the discovery of potential new predictive biomarkers or novel targets for cancer treatment in dogs. Furthermore, we aim at understanding how these changes compare to human cancers. 



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