Data report on gene expression after hepatic portal vein ligation (PVL) in rats

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Due to the increasing life expectancy and life style, the incidence of primary liver cancer is steadily rising. Worldwide, it is the fourth leading reason of cancer-associated death [29,33]. The etiology of liver cancer is highly diverse including besides others viral, toxic, nutritional, etc. risk factors that render treatment options as complex as different pathogenic pathways are involved [22,13,12]. Besides novel pharmacological and cell therapy approaches, surgical interventions are the only potentially curative strategies [3]. Among these, hepatic resection intends to remove the solid tumor taking into account tumor location and size as well as vascular supply of the parts of the liver to be removed and of the remaining liver. Since the lobar organisation of the liver is mirrored by separate venous blood drainage of the lobes, liver resection in general means removal of the tumor bearing lobe(s). The loss of even more than 60 % of the liver mass may be tolerated given that the future liver remnant provides sufficient post-surgery regenerative and metabolic function. To enhance the function of the future liver remnant, the technique of portal vein embolisation is used clinically. This procedure aims at increasing the future liver volume anticipating that volume equals function, i.e., volume growth of the non-ligated lobe(s) compensates for the surgical liver mass loss. However, volume does not necessarily reflect function. Therefore, in order to assess post-surgery hepatic metabolic and regenerative capacities, it is necessary to characterise changes in gene expression in the atrophic and hypertrophic lobes, respectively, and to correlate these changes with the prospective functional efficiency of the liver remnant after resection of the tumor bearing ligated liver lobe(s).Experimentally, portal vein ligation is comparable with portal vein embolisation applied in clinical settings. For the data collection presented here, we applied a model of 60% portal vein ligation in the rat, i.e., the left median and the lateral left lobes as well as the right superior and inferior lobes were deprived by ligation of the portal vein, while the right median and the left superior and inferior lobes remained unaffected (see Fig. 1), accordingly modified as described [31,25].Although non-coding RNAs (ncRNAs) such as microRNA (miRNA) or long ncRNA (lncRNA) have been shown to be deeply involved in the pathophysiology of almost all acute and chronic liver diseases, many of the especially liver-specific ncRNAs, have been not even annotated yet [24]. Our group developed new transcriptome assembly pipelines by combining existing tools to identify the different isoforms of mRNAs and lncRNAs [16,11].Non-coding RNAs in human genome. From the pilot project of ENCODE we know that less than 3 % of the human genome code for proteins [10,9]. The remaining genome is divided into 45 % repetitive elements (SINEs, LINEs, transposons), 26 % introns and other unique non-coding DNA [15]. The question of their meaning has raised and is only being answered slowly. By now, we know that at least 80% of the human genome has a function [9]. Some ncRNAs are known to be located within introns, in 5' and 3' untranslated regions (UTRs), antisense to protein-coding sequences or just close to them. However, the in silico identification of the ncRNAs is still a huge challenge. Due to their diverse and fast evolving sequence they are identified most efficiently by a combined in silico/ex vivo approach, that is sequencing the transcriptome and establishing tissue/organ/organism-specific bioinformatical tools. During the last decade, miRNAs, as regulators of various cell processes, received major attention. However, currently there are 3016 ncRNA families described (Rfam v.14.1 [17]), of which 800 are associated to human, covering more than 16.000 genomic regions 1 . Additionally, the existence of long non-coding RNAs (>200 nt) containing introns themselves is estimated in humans by GENCODE v.33 to 17952 loci2 . Our knowledge about lncRNAs is limited and no general computer program for their identification including secondary structure information and protein interactions is developed, yet.Non-coding RNAs in liver. Although only a fraction of liver-specific ncRNAs are known, here we summarize important examples of ncRNA participating in the pathogenesis of different forms of liver disease and how they can be used as therapeutic tools or targets for novel treatment paradigms, following the suggestions of Roy et al. [24], see Tab. 1. A large number of ncRNA genes being involved in metabolic processes, inflammation and immune response are differentially expressed during aging and other biological processess. We therefore expect to see ncRNAs and especially miRNAs to play a role in senescence and inflammation in rat liver when comparing PVL with healthy liver [5].MicroRNAs in liver. MicroRNAs (miRNAs) are a class of small, non-protein coding RNAs that play a crucial role in mediating post-transcriptional gene silencing [6]. These molecules, typically 18 to 25 nucleotides in length, act as regulators of gene expression by binding to the 3' untranslated region of target genes [4]. Interestingly, the intricate machinery governing miRNAs holds significant importance not only in the context of liver diseases [30], but also in processes related to portal vein ligation [27].In the realm of liver biology, miRNAs exert profound effects on various aspects of liver function and pathology. They participate in regulating processes such as hepatocyte proliferation [27], differentiation, apoptosis, and lipid metabolism [1]. Dysregulation of miRNAs has been implicated in the pathogenesis of liver diseases ranging from viral hepatitis [26] to hepatocellular carcinoma [23]. Moreover, the role of miRNAs in portal vein ligation, a surgical procedure often used in experimental models to study liver regeneration, underscores their significance beyond disease states [28]. MiRNAs are intricately involved in the molecular pathways underlying the response to portal vein ligation, influencing the regeneration capacity of the liver and impacting overall hepatic function [8]. Overall, the multifaceted involvement of miRNAs in liver biology and portal vein ligation highlights their versatility and potential as therapeutic targets in the context of liver diseases and surgical interventions.Experiments were conducted from March 1 until April 13, 2022. Male Sprague-Dawley rats (Charles river, 320-440 g) were housed under a 12 h dark/light cycle at ambient temperature with free access to food and water. The experiments were run with four different groups including four animals each for the PVL and the sham operation at two different time points (2 and 5 days) after surgery (16 animals). An additional weight-matched two animals without any treatment were run along as control in order to identify potential surgery-induced differences as compared with the sham-operated animals. The two time points were chosen following the rational that post-surgery regeneration after PVL might follow similar kinetics as regeneration after partial hepatecomy featuring a maximum regenerative response after 2 days and returning to starting conditions again after 5 days [2,14]. The PVL operation was a modified procedure as described previously [32] by ligating in addition to the left median and left lateral portal vein before the bifurcation, the right superior and inferior portal veins before the bifurcation. In sham-treated animals, the abdominal cavity was opened by a midline incision and closed again thereafter. After the sham or the PVL operation, the animals were left under housing conditions. At 2 and 5 days after surgery, respectively, the animals were euthanized under 2,% isoflurane anesthesia and livers explanted. The weight-matched control animals without any treatment were run along. Tissue pieces (ca. 50 mg) from the left (LML, ligated)and the

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