Review on the immunogenicity of decellularized xenogeneic scaffolds published in Material Science and Engineering C(July 2021)
Publication of the Laboratory of Pharmacogenomics and the Laboratory of Cancer Treatment "Non-coding RNAs as Biomarkers of Tumor Progression and Metastatic Spread in Epithelial Ovarian Cancer"(April 2021)
Results of development and experimental use of nanofibrous materials for healing support of intestinal anastomoses published in Biomedicines(February 2021)
Automatic segmentation of histological images for quality evaluation in tissue engineering(January 2021)
M. Jirik, I. Gruber, V. Moulisova, V. Liska et al.
M. Jirik, I. Gruber, V. Moulisova, V. Liska et al.
Oncological and surgical treatment of malignant focal processes of the liver reaches its limits in cases where the amount of affected parenchyma is too large or where the hilar structures are involved – stages at which a complete removal of the tumor tissue equals a total loss of the organ. In such patients, restoration of the liver function by means of conventional liver transplantation is generally out of the question, as it requires the administration of drugs to suppress the immune system’s response. Since the immune system fights not only pathogens but also cancerous cells, immunosuppression can lead to a rapid recurrence of the disease originating from the remnants of the malignant cells left in the body. The hope for a change lies in tissue engineering research, which promises to create an artificial replacement organ using the patient's own cells, thereby reducing the need for immunosuppression. Our Laboratory of Cancer Treatment and Tissue Regeneration, headed by Professor Václav Liška, located at the Biomedical Center of the Faculty of Medicine in Pilsen, is engaged in such research.
An important step in our approach to the production of an artificial organ is the preparation of an inanimate skeleton of the liver (scaffold), which is obtained from the liver of a domestic pig and is intended for subsequent colonization by living cells. To evaluate the quality of this scaffold, it is necessary to distinguish the areas of the liver lobules and their surroundings (septa). To follow our previously described quality assessment methodology, it has hitherto been necessary to manually label parts of the scaffold samples in histological slides stained with hematoxylin and eosin. In cooperation with colleagues from the Department of Cybernetics of the Faculty of Applied Sciences at the University of West Bohemia in Pilsen and Universitätsklinikum Jena, we designed an algorithm that produces the label automatically. The algorithm, which is based on convolutional neural networks, was published in the Sensors journal (Q1, IF=3.275).
RIGHT: Liver scaffold in the final stage of preparation
Compared to classical methods of computer vision, convolutional neural networks usually offer better results, but require a considerable amount of training data. Therefore, we designed a two-phase training procedure. In the first phase, we use the methods of classical computer vision for semi-automatic segmentation using texture features. In this phase, we use training datasets where less than 5% of the image area is annotated. The output data are then used in the second phase for training a neural network. The architecture of the neural network is inspired by the U-Net network. After the training, full segmentation is produced automatically.
LEFT: Hematoxylin-and-eosin-stained liver scaffold
Automatic histological image processing allows extensive skeletal quality measurements to be made. An important benefit of this method is the repeatability of measurements and their independence from the human factor, once the network is trained. In the follow-up research, our team is going to integrate the proposed method into a freely available application, which will make it possible to compare the results of laboratories from all over the world.
RIGHT: Two-phase training procedure
Identifying novel susceptibility genes for colorectal cancer risk from a transcriptome-wide association study of 125,478 subjects(October 2020)
Team of Laboratory of Cancer Treatment and Tissue Regeneration participates on research of GECCO (The Genetics and Epidemiology of Colorecal Cancer Consortium) in Seattle, USA. The new outcome appeared in last days. Scientific article: „Identifying novel susceptibility genes for colorectal cancer risk from a transcriptome-wide association study of 125,478 subjects“ is published in Gastroenterology (IF 17.373, Q1) and reveals that five genes in four novel loci are associated with CRC risk in individuals of European descent, along with an additional nine genes in known GWAS loci that have not been previously reported. Identification of CRC risk loci and susceptibility genes can help identify individuals at high risk. These findings have significant implications for genetic screening.
More information find here.
A Double Edged Sword role of Interleukin-22 in Wound Healing and Tissue Regeneration(September 2020)
Recently, we published a review article entitled “A Double Edged Sword role of Interleukin-22 in Wound Healing and Tissue Regeneration” in prestigious journal ‘Frontiers in Immunology’. Frontiers in Immunology is the official Journal of the International Union of Immunological Societies (IUIS). It is a leading journal in its field, publishing rigorously peer-reviewed research across basic, translational and clinical immunology. The Frontiers in Immunology journal is 5th most cited Immunology journal in the world and ranks in the top Impact Factor and Cite Score percentiles with Impact factor: 5.5. Cite score, 5.62. In this article we reviewed the detailed role of Interleukin -22 in inflammation, mucous production, protective role against pathogens, wound healing and tissue regeneration. Article describes the pivotal role of IL-22 in instigation of various cancers due to its pro-inflammatory and tissue repairing activity. Overall, article, summarize how healing effects of IL-22, when executed in an uncontrollable fashion can lead to carcinogenesis.
Sobia Manzoor joined research group (Cancer treatment and Tissue Regeneration labs) of Professor Vaclav Liska at Biomedical Centre, Faculty of Medicine in Plzen, Charles University, Prague, Czech Republic as a senior postdoctoral researcher in December 2019. In her postdoctoral research, she is investigating the role of IL22 in persuading, development, and metastasis of hepatocellular carcinoma. Published article is a part of her postdoctoral research project „Regeneration of liver parenchyma and its relation to carcinogenesis of primary liver tumors“.
Fig. 1. Scheme of ScaffAn analysis of decellularized liver scaffold
Quantitative evaluation of the quality of decellularized liver scaffolds(June 2020)
Last week, our group published a paper focusing on research related to preparation of scaffolds for liver tissue engineering purposes in the Journal of Tissue Engineering (Q2, IF = 4.1).
The research article “Novel morphological multi-scale evaluation system for quality assessment of decellularized liver scaffolds” addresses the lack of consistence in the scaffold quality assessment; a consistence that would enable to select only high quality scaffolds for cell repopulation experiments. Apart from conventional histological and microscopy techniques, we employed computer analysis enabling quantitative evaluation of morphological scaffold preservation. We designed a new open source software ScaffAn (Fig. 1) allowing to distinguish fine differences in scaffold quality, and thus to predict the interaction of the scaffold with the cells it is being repopulated with. ScaffAn can be further developed by wide scientific community for analysis of liver scaffolds from other species or even of other decellularized organs. The research was led by Dr. Vladimira Moulisova and performed in close collaboration with Prof. Uta Dahmen from the University Hospital in Jena.
Full paper is freely available on journal website (doi: 10.1177/2041731420921121)
Two small steps ahead in mapping individual susceptibility towards colorectal cancer(April 2020)
We would like to introduce two major works of co-authors of Pavel Vodička, Ludmila Vodičková and Veronika Vymetálková from the team of the Laboratory of Cancer Treatment and Tissue Regeneration. These two publications published in Q1 journal Gastroenterology (IF 19.809) are based on the research they were working on.
Murphy N.; Carreras-Torres R.; …; Vodička P.; Vodičková L.; Vymetálková V.: Circulating Levels of Insulin-like Growth Factor 1 and Insulin-like Growth Factor Binding Protein 3 Associate With Risk of Colorectal Cancer Based on Serologic and Mendelian Randomization Analyses. Gastroenterology. 2020 Apr;158(5):1274-1286.e12. doi: 10.1053/j.gastro.2019.12.012. See more.
In this analysis of blood samples from almost 400 000 participants from the UK Biobank, they found the association between circulating level of Insulin-like growth factor 1 (IGF1) and colorectal cancer. They used genetic data from 52 865 cases with colorectal cancer. Higher level of IGF1, determined by genetic factors, was associated with icreased risk of colorectal cancer. Further studies are needed to determine how this signaling pathway might contribute to colorectal carcinogenesis.
Archambault A. N; Su Yu-Ru; Jeon J.; Thomas M.; Lin Yi; Conti D. V; ...; Vodičková L.; Vodička P....: Cumulative Burden of Colorectal Cancer-Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer. Gastroenterology. 2020 Apr;158(5):1274-1286.e12. doi: 10.1053/j.gastro.2019.12.012. See more.
In this analysis of associations with colorectal carcinoma (CRC) per standard deviation of polygenic risks score (PRS), they found the cumulative burden of CRC-associated common genetic variants to more strongly associate with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive examinations.
Congratulation to authors!
Work of the Laboratory of Cancer Treatment and Tissue Regeneration and the Laboratory of Pharmacogenomics published in Scientific Reports(January 2020)
The result of a successful cooperation of scientific and clinical teams of the Biomedical Center of the Faculty of Medicine in Pilsen, Charles University, is the publication of the article Protein expression of ABCC2 and SLC22A3 associates with prognosis of pancreatic adenocarcinoma in the journal Scientific Reports (Q1, IF2018: 4.1).
The article addresses associations between immunohistochemically assessed localization of drug transporters in pancreatic adenocarcinoma tumor cells and the prognosis of this tumor in patients.
The paper is a result of a common effort of the teams of the Laboratory of Cancer Treatment and Tissue Regeneration and the Laboratory of Pharmacogenomics of the Biomedical Center of the Faculty of Medicine in Pilsen, Charles University, of the Department of Surgery and Department of Pathology, University Hospital Pilsen, and of the Department of Oncology, Faculty Hospital Olomouc.
Lenka Červenková and Václav Liška participated in the work for the Laboratory of Cancer Treatment and Tissue Regeneration, and Pavel Souček for the Laboratory of Pharmacogenomics.
Our Recent Clinical Study: Beta-Blockers Increase the Effect of Bevacizumab-Based Treatment of Colorectal Cancer(Decmber 2019)
In November 2019, the paper „Incidental Use of Beta-Blockers Is Associated with Outcome of Metastatic Colorectal Cancer Patients Treated with Bevacizumab-Based Therapy: A Single-Institution Retrospective Analysis of 514 Patients“ was published in Cancers (Q1, IF2019: 6.162). This is an extensive retrospective study involving a total of 514 patients with metastatic colorectal cancer who were treated between 2005 and 2019 at the Department of Oncology and Radiotherapy, Faculty of Medicine and University Hospital in Pilsen, Charles University. The work, led by doc. Ondřej Fiala (in the photo to the right), is based on the systematic cooperation of the Department of Oncology and Radiotherapy, the Department of Surgery and the Faculty of Medicine in Pilsen, Charles University. This collaboration is carried out under the auspices of the Laboratory of Tumor Treatment and Tissue Regeneration of the Medical Faculty’s Biomedical Center, which has long been involved in various clinical and experimental aspects of colorectal cancer and primary liver tumours.
Beta-adrenergic signalling plays an essential role in several processes that are important for the development and progression of various cancers. These processes include angiogenesis. The effect of the use of beta-blockers on the prognosis of cancer patients treated with anti-angiogenic agents is unclear and has been scarcely studied clinically. The aim of this study was to evaluate the association between the use of beta-blockers and the effect of treatment with a combination of chemotherapy and bevacizumab (a monoclonal antibody against vascular endothelial growth factor), which blocks angiogenesis. The association between progression-free survival (PFS) and overall survival (OS) with the use of beta-blockers and other common antihypertensive agents was evaluated. Of the commonly used antihypertensive agents, only beta-blockers had a significant impact on survival. The medians of PFS and OS in patients using beta-blockers prolonged to 11.4 and 26.8 months compared to the baseline values of 8.3 and 21.0 months in patients not using beta-blockers (p = 0.006 and p = 0.009, respectively). In the Cox multivariate model, the use of beta-blockers was a significant factor predicting both PFS (HR = 0.763, p = 0.021) and OS (HR = 0.730, p = 0.020). The results of this study show a significant association between the use of beta-blockers and the effect of treatment based on a combination of chemotherapy and bevacizumab. This is the first study of this kind conducted in a clinically relevant group of patients suggesting that beta-blockers might be the preferred type of antihypertensive in patients with metastatic colorectal cancer treated with this type of targeted therapy.
“From a clinical point of view, comedication is an extremely interesting topic in cancer patients. Although the results of this study are interesting, they need to be interpreted with caution, mainly because of its non-randomized retrospective design. We will stay focused on this topic with respect to other malignancies where anti-angiogenic targeted treatment is used,” adds doc. Fiala.
Lisa - Computer Vision Algorithms for Liver Research(September 2019)
Liver perfusion influences many important liver functions and it is therefore crucial to describe and understand it at both the macroscopic and microscopic level. To achieve that in the whole organ, it is necessary to analyse the geometric model of its main anatomical structures. This means to obtain the shape of the parenchyma and the shape of the vascular tree. These data are extracted from volumetric data using computer vision methods implemented in our application Lisa.
In our research, we work with two scales. To extract the shape of the liver parenchyma and the macroscopic model of the vascular system, we use clinical computed tomography (CT) with a resolution of 0.65–5.0 mm (Mik et al., 2018). The extraction of the vascular bed geometry is performed using data from high-resolution computed tomography (Micro-CT) with a resolution of 1.9–4.7 μm (Jirik et al., 2016).
The segmentation of the liver parenchyma in the macro CT is performed interactively by the modified Graph-Cut algorithm (Boykov et al., 2001) available in the Lisa (Mik et al., 2018, LISA website) application. First, the user interactively selects sample voxels (seeds) representing the subject of interest (liver parenchyma) and background (other tissues). An intense Gaussian Mixture Model with three foreground and background components is then created. Segmentation of the vascular bed is performed by a modified connected threshold algorithm. Binary morphological operations are applied in the post-processing step.
For flow modelling and quantitative analysis, the Quantan application (Jirik et al., 2016) identifies individual segments of the vascular tree, whose structure is thus quantitatively described and represented in a machine-readable way. For each segment its radius, length, tortuosity, and branching angles are determined. Further, it is possible to evaluate the volume fraction, surface density and length density of the vessels. This information can be subsequently used to model liver perfusion (Rohan et al., 2018).
References:Boykov, Y. Y., & Jolly, M. P. (2001). Interactive graph cuts for optimal boundary & region segmentation of objects in N-D images. Computer Vision, 2001. ICCV 2001. Proceedings. Eighth IEEE International Conference On, 1, 105–112. Retrieved from http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=937505
Jirik, M., Tonar, Z., Králíčková, A., Eberlová, L., Mírka, H., Kochová, P., … Liška, V. (2016). Stereological quantification of microvessels using semiautomated evaluation of X-ray microtomography of hepatic vascular corrosion casts. International Journal of Computer Assisted Radiology and Surgery, 11(10), 1803–1819. https://doi.org/10.1007/s11548-016-1378-3
Mik, P., Tonar, Z., Malečková, A., Eberlová, L., Liška, V., Pálek, R., … Witter, K. (2018). Distribution of Connective Tissue in the Male and Female Porcine Liver: Histological Mapping and Recommendations for Sampling. Journal of Comparative Pathology, 162, 1–13. https://doi.org/10.1016/j.jcpa.2018.05.004
Rohan, E., Lukeš, V., Turjanicová, J., & Jiřík, M. (2018). Towards image-based analysis of the liver perfusion using a hierarchical flow model. Lecture Notes in Computational Vision and Biomechanics, 27. https://doi.org/10.1007/978-3-319-68195-5_64
Liver transplants on the go(August 2018)
We are establishing a model of liver transplantation in domestic pig. So far, we have managed to get several long-time surviving transplantees and we are working to get more to evaluate the project. Perfecting the methodology and skills to perform experimental liver transplants on a routine basis is crucial for the goal of developing re-cellularized engineered liver grafts and testing them in vivo.
Highlights from the 6th International Symposium Interface Biology of Implants (IBI) 2019 in Warnemünde(May 2019)
A great interdisciplinary meeting Interface Biology of Implants took place in Warnemünde (Germany) between 8 and 10 May 2019.
This conference bringing together scientists interested in different aspects of biomaterial development was organized by the University of Rostock under the lead of prof. Joachim Rychly already for the sixth time. Although it was a rather small conference (only a single lecture hall with no more than 200 participants), the organizers managed to invite a number of speakers who are the world leaders in their field. Many researchers and students from around the world from Los Angeles to Hanoi attended the meeting and created an amazing collaborative environment. The Biomedical Center was represented by Dr. Vladimira Moulisova from the Laboratory of Tumor Treatment and Tissue Regeneration; her poster showed results from the study of decellularized tissue scaffolds (PDF) that is ongoing in the team lead by Assoc. Prof. Vaclav Liska.