Subcellular protein expression models for microsatellite instability in colorectal adenocarcinoma tissue images

Background New bioimaging techniques capable of visualising the co-location of numerous proteins within individual cells have been proposed to study tumour heterogeneity of neighbouring cells within the same tissue specimen. These techniques have highlighted the need to better understand the interplay between proteins in terms of their colocalisation. Results We recently proposed a cellular-level model of the healthy and cancerous colonic crypt microenvironments. Here, we extend the model to include detailed models of protein expression to generate synthetic multiplex fluorescence data. As a first step, we present models for various cell organelles learned from real immunofluorescence data from the Human Protein Atlas. Comparison between the distribution of various features obtained from the real and synthetic organelles has shown very good agreement. This has included both features that have been used as part of the model input and ones that have not been explicitly considered. We then develop models for six proteins which are important colorectal cancer biomarkers and are associated with microsatellite instability, namely MLH1, PMS2, MSH2, MSH6, P53 and PTEN. The protein models include their complex expression patterns and which cell phenotypes express them. The models have been validated by comparing distributions of real and synthesised parameters and by application of frameworks for analysing multiplex immunofluorescence image data. Conclusions The six proteins have been chosen as a case study to illustrate how the model can be used to generate synthetic multiplex immunofluorescence data. Further proteins could be included within the model in a similar manner to enable the study of a larger set of proteins of interest and their interactions. To the best of our knowledge, this is the first model for expression of multiple proteins in anatomically intact tissue, rather than within cells in culture.QNRF grant NPRP 5-1345-1-228. BBSRC and University of Warwick Institute of Advanced Study

On the suitability of baked clay for archaeomagnetic studies as deduced from detailed rock-magnetic studies

Extensive rock-magnetic investigations have been carried out on baked clays from four kilns (two from Bulgaria and two from Switzerland) found in archaeological sites of different age. Knowledge of the magnetic characteristics of the grains responsible for the archaeomagnetic signal enables us to determine which baked clays have the stablest magnetization and why this is so. This is important in directional studies, but even more so in painstaking palaeointensity studies that require a very careful evaluation of the suitability of the burnt clay material. The proposed rock-magnetic experiments enable the identification of the carriers responsible for the remanence and an adequate interpretation of the experimental results connected with the palaeointensity evaluation. The experimental methods employed are illustrated with the particular results obtained from each of the four kilns studied. The preliminary elucidation of the magnetic mineralogy of the archaeological samples helps first by obtaining a more reliable palaeointensity result, and secondly by explaining some of the discrepancies in the palaeodirectional results. Examples of successful and failed palaeointensity experiments are given in relation to the magnetic properties previously established for each oven. The burnt-clay materials in this present study satisfy the essential condition of carrying a thermoremanence. In spite of that, it is shown that there are many factors that can produce undesirable magnetic properties and thus restrict the suitability of these materials for archaeomagnetic analysis. The most important factors influencing the magnetic behaviour during magneto-diagnostic experiments are: the degree of heating in antiquity, the initial composition of the unbaked material and the burial conditions. The large difference in heating temperatures within a particular archaeological feature is a major cause of variation in magnetic behaviour amongst individual specimens, and so preventing a successful pre-selection of specimens for palaeointensity experiments. Nevertheless, the study has shown a very good coincidence between the determined rock-magnetic characteristics and the success rate in palaeointensity evaluatio

A model of the spatial tumour heterogeneity in colorectal adenocarcinoma tissue

Background There have been great advancements in the field of digital pathology. The surge in development of analytical methods for such data makes it crucial to develop benchmark synthetic datasets for objectively validating and comparing these methods. In addition, developing a spatial model of the tumour microenvironment can aid our understanding of the underpinning laws of tumour heterogeneity. Results We propose a model of the healthy and cancerous colonic crypt microenvironment. Our model is designed to generate synthetic histology image data with parameters that allow control over cancer grade, cellularity, cell overlap ratio, image resolution, and objective level. Conclusions To the best of our knowledge, ours is the first model to simulate histology image data at sub-cellular level for healthy and cancerous colon tissue, where the cells have different compartments and are organised to mimic the microenvironment of tissue in situ rather than dispersed cells in a cultured environment. Qualitative and quantitative validation has been performed on the model results demonstrating good similarity to the real data. The simulated data could be used to validate techniques such as image restoration, cell and crypt segmentation, and cancer grading.BBSRC and University of Warwick Institute of Advanced Study. QNRF grant NPRP 5-1345-1-228

Modelling and analysis of the tumour microenvironment of colorectal cancer

New bioimaging techniques have recently been proposed to visualise the colocation or interaction of several proteins within individual cells, displaying the heterogeneity of neighbouring cells within the same tissue specimen. Such techniques could hold the key to understanding complex biological systems such as the protein interactions involved in cancer. However, there is a need for new algorithmic approaches that analyse the large amounts of multi-tag bioimage data from cancerous and normal tissue specimens in order to begin to infer protein networks and unravel the cellular heterogeneity at a molecular level. In the firrst part of the thesis, we propose an approach to analyses cell phenotypes in normal and cancerous colon tissue imaged using the robotically controlled Toponome Imaging System (TIS) microscope. It involves segmenting the DAPI labelled image into cells and determining the cell phenotypes according to their protein-protein dependence profile. These were analysed using two new measures, Difference in Sums of Weighted cO-dependence/Anti-co-dependence profiles (DiSWOP and DiSWAP) for overall co-expression and anti-co-expression, respectively. This approach enables one to easily identify protein pairs which have significantly higher/lower co-dependence levels in cancerous tissue samples when compared to normal colon tissue. The proposed approach could identify potentially functional protein complexes active in cancer progression and cell differentiation. Due to the lack of ground truth data for bioimages, the objective evaluation of the methods developed for its analysis can be very challenging. To that end, in the second part of the thesis we propose a model of the healthy and cancerous colonic crypt microenvironments. Our model is designed to generate realistic synthetic fluorescence and histology image data with parameters that allow control over differentiation grade of cancer, crypt morphology, cellularity, cell overlap ratio, image resolution, and objective level. The model learns some of its parameters from real histology image data stained with standard Hematoxylin and Eosin (H&E) dyes in order to generate realistic chromatin texture, nuclei morphology, and crypt architecture. To the best of our knowledge, ours is the first model to simulate image data at subcellular level for healthy and cancerous colon tissue, where the cells are organised to mimic the microenvironment of tissue in situ rather than dispersed cells in a cultured environment. The simulated data could be used to validate techniques such as image restoration, cell segmentation, cell phenotyping, crypt segmentation, and differentiation grading, only to name a few. In addition, developing a detailed model of the tumour microenvironment can aid the understanding of the underpinning laws of tumour heterogeneity. In the third part of the thesis, we extend the model to include detailed models of protein expression to generate synthetic multi-tag fluorescence data. As a first step, we have developed models for various cell organelles that have been learned from real immunofluorescence data. We then develop models for five proteins associated with microsatellite instability, namely MLH1, PMS2, MSH2, MSH6 and p53. The protein models include subcellular location, which cells express the protein and under what conditions

Extended and revised archaeomagnetic database and secular variation curves from Bulgaria for the last eight millennia

International audienceThe efforts of geophysicists to describe geomagnetic field behaviour in the past lead to creation of different geomagnetic field models. On the other hand, the established regional palaeosecular variations of geomagnetic elements are increasingly used for dating purposes in archaeology. Both of these goals can be achieved if sufficient amounts of long archaeomagnetic data sets exist for different geographical regions. The accumulation of archaeomagnetic determinations began at the middle of the last century, parallel with the progressive development of experimental methodology and acceptance criteria. The presence of great number of old determinations requires their critical assessment. The important question about the reliability of the associated dating intervals should be also re-assessed. All this requires the continuous refinement and extension of the accumulated databases. This paper presents the last synthesis of Bulgarian archaeomagnetic database and the local palaeosecular variation curves obtained using a statistical treatment based on Bayesian approach (RenCurve software). The rock-magnetic characteristics of the newly included, non-published results are summarized

Further progress in the study of epsilon iron oxide in archaeological baked clays

[EN] The occurrence of ε-FeO in archaeological samples that have been subjected to high temperatures is gradually being detected by the use of micrometric structural characterization techniques. This work provides new information by revealing that the ε-FeO is formed as a response to temperature, the aggregation state and the position within the baked clay with respect to the nearest heat source. In addition, depending mainly on the atmospheric environment, the temperature reached by the combustion structure, the distance from the heating source and the particle aggregation, other iron oxide magnetic phases are produced. In the baked clay studied here, hematite is found over the whole range of samples studied but its magnetic contribution is negligible. Magnetite is observed at the sample surface, probably due to local atmospheric environment closest to the combustion source. Maghemite is found at all depths up to 6 cm below the sample surface. ε-FeO has a limited distribution, found within 2–3 cm of the sample surface. Furthermore, the viability of this compound as a palaeofield marker has been evaluated in both archaeological and synthetic samples. The results indicate that ε-FeO is able to register the direction of the magnetic field. Linear palaeointensity plots have been obtained in synthetic samples, although the value of the palaeofield could be, sometimes, overestimated.The authors also acknowledge the financial support from the Spanish Ministry of Science, Innovation and Universities under the projects RTI2018-095856-B-C21, CGL2017-87015-P, CGL2017-92285-EXP, CGL2017-92285-EXP/BTE, MAT2017-86540-C4-1-R, MAT2017-87072-C4-2-P and RTI2018-095303-A-C52, from Comunidad de Madrid NANOFRONTMAG S2013/MIT-2850 and NANOMAGCOST S2018/NMT-4321, and from the European Commission under H2020 frame by AMPHIBIAN Project ID: 720853. APO thanks the Ministry of Economy, Industry and Competitiveness (PTA Contract).Peer reviewe