Computational morphogenesis – Embryogenesis, cancer research and digital pathology

Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance

Information for organismal patterning can come from a variety of sources. We investigate the possibility that instructive influences for normal embryonic development are provided not only at the level of cells within the embryo, but also via interactions between embryos. To explore this, we challenge groups of embryos with disruptors of normal development while varying group size. Here, we show that Xenopus laevis embryos are much more sensitive to a diverse set of chemical and molecular-biological perturbations when allowed to develop alone or in small groups, than in large groups. Keeping per-embryo exposure constant, we find that increasing the number of exposed embryos in a cohort increases the rate of survival while incidence of defects decreases. This inter-embryo assistance effect is mediated by short-range diffusible signals and involves the P2 ATP receptor. Our data and computational model emphasize that morphogenesis is a collective phenomenon not only at the level of cells, but also of whole bodies, and that cohort size is a crucial variable in studies of ecotoxicology, teratogenesis, and developmental plasticity.

A Polymeric Nanobeacon for Monitoring the Fluctuation of Hydrogen Polysulfides during Fertilization and Embryonic Development

Fertilization and early embryonic development as the beginning of a new life are key biological events. Hydrogen polysulfide (H₂ S_n ) plays important roles during physiological regulation, such as antioxidation-protection. However, no report has studied in situ H₂ S_n fluctuation during early embryonic development because of the low abundance of H₂ S_n and inadequate sensitivity of probes. We herein construct a polymeric nanobeacon from a H₂ S_n -responsive polymer and fluorophores, which is capable of detecting H₂ S_n selectively and of signal amplification. Taking the zebrafish as a model, the polymeric nanobeacon revealed that the H₂ S_n level was significantly elevated after fertilization due to the activation of cell multiplication, suppressed partially during embryonic development, and finally kept steady up to zebrafish emergence. This strategy is generally accessible for biomarkers by altering the responsive unit and significant for facilitating biological analysis during life development.

Endometriosis, infertility and MicroRNA's: A review

The review aims to explore circulating small non- coding regulatory Ribonucleic Acids (miRNA) as biomarkers of endometriosis; a reproductive age group disorder. miRNA are linked with genetic, epigenetic and angiogenic factors, hormones, cytokines, chemokines, oxidative stress (OS) markers, mediators of inflammation, hypoxia, angiogenesis and altered immune system contributing to the pathogenesis of endometriosis. Hormonal imbalance occurs by decreased levels of miRNAs -23a and miRNAs -23b and increase in miRNAs -:135a, 135b, 29c and 194-3p. Angiogenesis by vascular endothelial growth factor is attributed to increased miRNAs -126, miRNAs -210, miRNAs -21, miRNAs -199a-5p and miRNAs 20A. OS upregulates miRNAs -302a by increased levels of Tumor Necrosis factor (TNF)-α, TNF- β and Interleukin -1β. Upregulation of miRNAs -199a and miRNAs -16 promotes inflammation and cell proliferation in the endometriotic lesions. The gold standard to diagnose endometriosis is laparoscopy, yet miRNA can be validated as diagnostic tool for detection, progression and prevention of endometriosis in large, independent cohorts of women, with and without endometriosis.

Experimental Assessment of Color Deconvolution and Color Normalization for Automated Classification of Histology Images Stained with Hematoxylin and Eosin

Histological evaluation plays a major role in cancer diagnosis and treatment. The appearance of H&E-stained images can vary significantly as a consequence of differences in several factors, such as reagents, staining conditions, preparation procedure and image acquisition system. Such potential sources of noise can all have negative effects on computer-assisted classification. To minimize such artefacts and their potentially negative effects several color pre-processing methods have been proposed in the literature-for instance, color augmentation, color constancy, color deconvolution and color transfer. Still, little work has been done to investigate the efficacy of these methods on a quantitative basis. In this paper, we evaluated the effects of color constancy, deconvolution and transfer on automated classification of H&E-stained images representing different types of cancers-specifically breast, prostate, colorectal cancer and malignant lymphoma. Our results indicate that in most cases color pre-processing does not improve the classification accuracy, especially when coupled with color-based image descriptors. Some pre-processing methods, however, can be beneficial when used with some texture-based methods like Gabor filters and Local Binary Patterns.

Cytokine profiles in maternal serum are candidates for predicting an optimal timing for the delivery in early-onset fetal growth restriction

OBJECTIVE

We examined whether maternal serum cytokine profiles of mothers with early-onset fetal growth restriction (FGR) were associated with delivery within 2 weeks after sampling during the third trimester.

STUDY DESIGN

This exploratory prospective cross-sectional study included a total of 20 singleton fetuses with early-onset FGR and 31 healthy controls. Maternal serum samples during the early third trimester were analyzed for 23 cytokines.

RESULTS

Of 20 fetuses with early-onset FGR, 14 had delivery within 2 weeks after sampling. Multivariate analysis revealed that maternal serum concentrations of soluble vascular endothelial growth factor receptor-1 (sVEGFR-1) and soluble CD40 ligand (sCD40L) were independently associated with delivery within 2 weeks in early-onset FGR. Among cases of early-onset FGR, concentrations of almost all maternal serum cytokines were similar. Maternal serum sVEGFR-1 concentrations were high when delivery occurred within 2 weeks. Maternal serum sCD40L concentrations were elicited only in cases in which delivery within 2 weeks occurred due to fetal deterioration.

CONCLUSION

We identified two biomarkers, one specific for FGR and the other dependent on severity, that were significant components of angiogenic activities and inflammation factors. Imbalances in serum protein expression may have a substantial effect on the pathogenesis of FGR.

Novel insights into breast cancer progression and metastasis: A multidisciplinary opportunity to transition from biology to clinical oncology

According to the most recent epidemiological studies, breast cancer shows the highest incidence and the second leading cause of death in women. Cancer progression and metastasis are the main events related to poor survival of breast cancer patients. This can be explained by the presence of highly resistant to chemo- and radiotherapy stem cells in many breast tumor tissues. In this context, numerous studies highlighted the possible involvement of epithelial to mesenchymal transition phenomenon as biological program to generate cancer stem cells, and thus participate to both metastatic and drug resistance process. Therefore, the comprehension of mechanisms (both cellular and molecular) involved in breast cancer occurrence and progression can lay the foundation for the development of new diagnostic and therapeutical protocols. In this review, we reported the most important findings in the field of breast cancer highlighting the most recent data concerning breast tumor biology, diagnosis and therapy.

A general framework dedicated to computational morphogenesis Part II - Knowledge representation and architecture

In our previous paper we introduced morphogenesis and post-embryonic life as arising from cells interacting via coupled chemical, electrical and mechanical processes occurring across multiple organization levels. We reviewed these processes from the perspectives of developmental biology and how they relate to physics-based constitutive equations that are well suited to model intercellular interactions' fields. In this paper we will describe a knowledge representation and architectural design strategy that can organize and encode the biochemical, biological and biophysical data necessary to represent and model the highly specialized and diversified cells that constitute living tissues. Since there are about 200 different types of cells in mammalian tissues, a huge amount of molecular, cellular and tissue data must be accounted for. This data cannot be incorporated in an ad hoc manner but, on the contrary, must be organized according to some sound principles. We give an overview of these principles and describe how they can be incorporated as proper features of a Knowledge Base System (KBS) dedicated to computational morphogenesis (CM).

A general framework dedicated to computational morphogenesis Part I - Constitutive equations

In order to understand living organisms, considerable experimental efforts and resources have been devoted to correlate genes and their expressions with cell, tissue, organ and whole organisms' phenotypes. This data driven approach to knowledge discovery has led to many breakthrough in our understanding of healthy and diseased states, and is paving the way to improve the diagnosis and treatment of diseases. Complementary to this data-driven approach, computational models of biological systems based on first principles have been developed in order to deepen our understanding of the multi-scale dynamics that drives normal and pathological biological functions. In this paper we describe the biological, physical and mathematical concepts that led to the design of a Computational Morphogenesis (CM) platform baptized Generic Modeling and Simulating Platform (GMSP). Its role is to generate realistic 3D multi-scale biological tissues from virtual stem cells and the intended target applications include in virtuo studies of normal and abnormal tissue (re)generation as well as the development of complex diseases such as carcinogenesis. At all space-scales of interest, biological agents interact with each other via biochemical, bioelectrical, and mechanical fields that operate in concert during embryogenesis, growth and adult life. The spatio-temporal dependencies of these fields can be modeled by physics-based constitutive equations that we propose to examine in relation to the landmark biological events that occur during embryogenesis.