Polyploid cells show great among-species and among-tissues diversity and relation to developmenta... more Polyploid cells show great among-species and among-tissues diversity and relation to developmental mode, suggesting their importance in adaptive evolution and developmental programming. At the same time, excessive polyploidization is a hallmark of functional impairment, aging, growth disorders, and numerous pathologies including cancer and cardiac diseases. To shed light on this paradox and to find out how polyploidy contributes to organ functions, we review here the ploidy-associated shifts in activity of narrowly expressed (tissue specific) genes in human and mouse heart and liver, which have the reciprocal pattern of polyploidization. For this purpose, we use the modular biology approach and genome-scale crossspecies comparison. It is evident from this review that heart and liver show similar traits in response to polyploidization. In both organs, polyploidy protects vitality (mainly due to the activation of sirtuin-mediated pathways), triggers the reserve adenosine-5′-triphosphate (ATP) production, and sustains tissue-specific functions by switching them to energy saving mode. In heart, the strongest effects consisted in the concerted up-regulation of contractile proteins and substitution of energy intensive proteins with energy economic ones. As a striking example, the energy intensive alpha myosin heavy chain (providing fast contraction) decreased its expression by a factor of 10, allowing a 270-fold increase of expression of beta myosin heavy chain (providing slow contraction), which has approximately threefold lower ATP-hydrolyzing activity. The liver showed the enhancement of immunity, reactive oxygen species and xenobiotic detoxication, and numerous metabolic adaptations to long-term energy depletion. Thus, somatic polyploidy may be an ingenious evolutionary instrument for fast adaptation to stress and new environments allowing tradeoffs between high functional demand, stress, and energy depletion.
Diseases of the human cardiovascular system are the main cause of death in developed countries. T... more Diseases of the human cardiovascular system are the main cause of death in developed countries. Therefore, searching for new risk factors thereof is of particular interest. Upon comparing epidemiological data with data of transcriptome of cardiomyocytes and comparative physiology of vertebrate ontogenesis, we have come to the conclusion that one such factor may be gastroenteritis. This disease includes at once several stimuli able to cause functional and metabolic alterations in the heart: tachycardia, hormonal and ionic mis balance, and outflow of resources from the cardiovascular system. Using the model of rat neonatal gastroen teritis caused by the widespread human and animal enteropathogen Cryptosporidium parvum (Apicomplexa, Sporozoa), we studied the change of expression of α and β myosin heavy chains after the developed cryptosporidiosis. Online data obtained by methods of immunocytochemistry, quantitative morphometry, and polymerase chain reaction not only have confirmed our suggestion, but also have shown that moderate 4 day long cryptosporidiosis is sufficient for producing a significant (1.7 to 4.5 fold) shift in the ratio of myosin isoforms toward the β isoform beta at the level of mRNA and at the level of protein (2.5-6 times). The reciprocity of the changes, as well as their clear similarity at the level of mRNA and of protein, indicates that the cryptosporidial gastroenteritis involves all the main chains of a complex network of regulation of expression of the myosin heavy chains. A shift of the ratio of myosin isoforms toward the β isoform that has an ATPase activity several times lower than the α isoform is the commonly accepted indicator of human heart failure; therefore, the cryptosporidial gastroenteritis can be considered a novel risk factor for decrease of the heart's contractile ability. Our data may be of interest for clinical and preventive medicine.
Changes in gene expression play an important role in evolution and can be relevant to evolutionar... more Changes in gene expression play an important role in evolution and can be relevant to evolutionary medicine. In this work, a strong relationship was found between the statistical significance of evolutionary changes in the expression of orthologous genes in the five or six homologous mammalian tissues and the across-tissues unidirectionality of changes (i.e., they occur in the same direction in different tissues -- all upward or all downward). In the area of highly significant changes, the fraction of unidirectionally changed genes (UCG) was above 0.9 (random expectation is 0.03). This observation indicates that the most pronounced evolutionary changes in mammalian gene expression are systemic (i.e., they operate at the whole-organism level). The UCG are strongly enriched in the housekeeping genes. More specifically, in the human-chimpanzee comparison, the UCG are enriched in the pathways belonging to gene expression (translation is prominent), cell cycle control, ubiquitin-dependent protein degradation (mostly related to cell cycle control), apoptosis, and Parkinson's disease. In the human-macaque comparison, the two other neurodegenerative diseases (Alzheimer's and Huntington's) are added to the enriched pathways. The consolidation of gene expression changes at the level of pathways indicates that they are not neutral but functional. The systemic expression changes probably maintain the across-tissues balance of basic physiological processes in the course of evolution (e.g., during the movement along the fast-slow life axis). These results can be useful for understanding the variation in longevity and susceptibility to cancer and widespread neurodegenerative diseases. This approach can also guide the choice of prospective genes for studies aiming to decipher cis-regulatory code (the gene list is provided).
International Journal of Molecular Sciences, Nov 19, 2020
Tumours were recently revealed to undergo a phylostratic and phenotypic shift to unicellularity. ... more Tumours were recently revealed to undergo a phylostratic and phenotypic shift to unicellularity. As well, aggressive tumours are characterized by an increased proportion of polyploid cells. In order to investigate a possible shared causation of these two features, we performed a comparative phylostratigraphic analysis of ploidy-related genes, obtained from transcriptomic data for polyploid and diploid human and mouse tissues using pairwise cross-species transcriptome comparison and principal component analysis. Our results indicate that polyploidy shifts the evolutionary age balance of the expressed genes from the late metazoan phylostrata towards the upregulation of unicellular and early metazoan phylostrata. The up-regulation of unicellular metabolic and drug-resistance pathways and the downregulation of pathways related to circadian clock were identified. This evolutionary shift was associated with the enrichment of ploidy with bivalent genes (p < 10 −16). The protein interactome of activated bivalent genes revealed the increase of the connectivity of unicellulars and (early) multicellulars, while circadian regulators were depressed. The mutual polyploidy-c-MYC-bivalent genes-associated protein network was organized by gene-hubs engaged in both embryonic development and metastatic cancer including driver (proto)-oncogenes of viral origin. Our data suggest that, in cancer, the atavistic shift goes hand-in-hand with polyploidy and is driven by epigenetic mechanisms impinging on development-related bivalent genes.
Design and development of highly sensitive method bioinformatics are important for investigation ... more Design and development of highly sensitive method bioinformatics are important for investigation of casual relationships between epigenetic changes and gene activity. Cell polyploidy may trigger such changes. However, maintaining the balance of gene dosage, polyploidy may provide only a rather weak effect on their expression. Currently, there is no comprehensive and concordant data in regard to ploidy-associated transcriptomic changes. To find out how polypoidy affects gene activity, we have developed an integrative bioinformatic method of pairwise cross-species transcriptome analysis of mammalian tissues with various polyploidy degrees. The main benefit of this approach is its ability to separate species- and tissue-specific noises of evolutionary conserved effects. We demonstrat the application of the method for the analysis of gene modules and protein interactions networks coordinating programs of development, differentiation and pluripotency. The analysis was performed with transcriptomes of polyploid and diploid organs (human and mouse heart and liver). Our data indicate that ploidy-induced genes enrich Gene Ontology (GO) biological processes and KEGG pathways related to development, morphogenesis and stem cells biology (including Hippo, Pi3K, WNT, Hedgehog and TGF-β pathways) with higher degree than ploidy-inhibited genes. Thas, our data are the first to show that polyploidy may induce and coordinate developmental modules.
Journal of Evolutionary Biochemistry and Physiology, Sep 1, 2013
Disturbances at the childhood age increase risk of the appearance of cardiovascular diseases deca... more Disturbances at the childhood age increase risk of the appearance of cardiovascular diseases decades later. The nature of this interconnection called ontogenetic programming is not completely understood. Valuable sources of knowledge about mechanisms of ontogenetic programming are data of interspecies study of biology of the body life cycles and of heart physiological capabilities. Taken into account the interspecies differences, these data allow finding the correct direction of experimental investigations. Results of studies of almost 100 homoiothermal species have shown the slow growth and a high loading on the heart at postnatal development to decrease its aerobic capability in adults. Basing on these data, we suggested that the neonatal gastroenteritis causing tachyarrhythmia, malabsorption, and the growth deceleration might lead to pathological changes in the heart. Our task was to evaluate the effect of cryptosporidial gastroenteritis of different degrees of severity on heart of the neonatal rats. By using methods of Real-Time PCR, immunocytochemistry, image analysis, and study of interatrial septum, we have established that a gradual increase of intensity of infestation with Cryptosporidium parvum oocytes causes sharp changes corresponding to the &quot;all or nothing&quot; response. At a weak infestation the interatrial septum was close (like in control), while significant changes in expression of isoforms of heavy chains of alpha- and beta-myosin were absent. At the intermediate and severe infestation, in the interatrial septum the foramen ovale was visualized and there were observed cardiac atrophy and a strong shift of ration of expression of myosin heavy chains toward the low-velocity beta chain. Thus, by disturbing the frequency-strength ratios and causing outflow of resources from the formed heart, the neonatal gastroenteritis produces pathological changes of the organ molecular and anatomical structures. Our results can be interest to evolutionary biologists and physicians, as they show importance of knowledge of evolutionary-comparative investigations for the search for novel risk factors of heart diseases and demonstrate interconnection between gastroenteritis, pathology of interatrial septum, and a change of composition of the main contractile proteins in cardiomyocytes.
Inflammation, malnutrition and growth retardation during critical time-windows of development pla... more Inflammation, malnutrition and growth retardation during critical time-windows of development play a powerful role in ontogenetic programming of the lifelong risk to many adult diseases (including metabolic syndrome, obesity and diabetes). Cellular mechanisms and the accurate timing and duration of critical periods for the liver remain obscure. To resolve this problem, we developed a postnatal suckling-weanling rat model of mild, moderate, and acute gastroenteritis challenged by a protozoan parasitic spread throughout the whole world, namely Cryptosporidium parvum. The physiological state of the liver was evaluated by hepatocyte ploidy and protein content that were measured by cytophotometry and image analysis on isolated cells. Hepatocyte ploidy is known to irreversibly increase after stress and is associated with the decrease in liver physiological capacity. Hepatocyte hypertrophy reflects cell functional loading. From our results, cryptosporidiosis is able to provoke a burst in premature hepatocyte polyploidization and hypertrophy (in proportion to parasitic load), and thus plays an important role in epigenetic programming of hepatocyte structure and function. We revealed two sensitive periods in liver growth. The first period (the less sensitive) covers the time before the establishment of homoiothermy, i.e. 6e9 days after birth. The second period (the more sensitive) covers the time of weaning when the change of type of nutrition and the peak of hepatocyte polyploidization and differentiation occurs. Thus, our data provide direct evidence that phenomenon of ontogenetic programming is reflected at the cellular level.
Background: The aim of our study was to find out, whether cardiomyocyte genome duplication partic... more Background: The aim of our study was to find out, whether cardiomyocyte genome duplication participates in developmental programming of adult hypertension and impaired heart aerobic capacity, and if it does, whether ploidy-related programming is reversible and what are the timeframes of the most critical window. For this propose we studied the effect of the well-known factors of programming, including growth retardation, infection, and cardiac overload on the level of neonatal cardiomyocyte ploidy, protein content and shape. Methods: Using the model of rat cryptosporidial gastroenteritis, we shifted the time point of infection day by day through the neonatal period and traced the immediate and postponed effects of disease on isolated cardiomyocyte ploidy, phenotype, and protein content. Results: We found that gastroenteritis caused cardiac atrophy and a burst-like premature genome accumulation, elongation, narrowing and protein loss in the cardiomyocytes. These changes resulted in sharp increase of DNA content at the expense of contractile proteins. We also revealed clear indications of critical window of heart development during the peak of cardiomyocyte transition from proliferation to hypertrophy. After the rehabilitation, the atrophy of heart and cardiomyocyte remodelling showed a conspicuous restoration, whereas the hyperpolyploidization did not regress. An irreversible manner of excessive genome duplication and its well-known ability to alter gene expression confirm our suggestion that it is implicated in the ontogenetic programming of heart development. Conclusion: We provided the first evidence that developmental programming can operate through cardiomyocyte genome duplication and that the critical window coincides with cell transition from proliferation to hypertrophy. Our data help determine the timing of critical window for human heart and would allow successful prevention of human cardiac abnormalities even before they become tangible.
Cytofluorimetric study of ploidy levels in ventricular cardiomyocytes was carried out on 36 adult... more Cytofluorimetric study of ploidy levels in ventricular cardiomyocytes was carried out on 36 adult bird species belonging to 10 orders as well as on the quail Coturnix coturnix, of different ages. It was shown that polyploidization of quail cardiomyocytes occurs during the first 40 days after hatching and ends by the time growth is completed. In adult birds, the cardiomyocyte ploidy hardly changed at all. Interspecies comparison revealed that in the adult bird myocardium 2cx2 myocytes are predominant, accounting for at least 50% of the cell population. Multinuclear cells with three to eight diploid nuclei were widespread. The percentage of such cells was five to six times higher in precocial species than in altricial birds of the same weight. Myocytes with polyploid nuclei were rare. A significant interspecies variability of cardiomyocyte ploidy levels was observed. The most prominent differences were found between the precocial and the altricial birds. The mean number of genomes in cells correlated both with the body mass and with the growth rate of the birds. The differences between the precocial and altricial birds disappeared when a statistical method was used to eliminate the effect of the growth rate, but did not when the effect of body mass was eliminated. Among the altricial birds, which are generally immobile during growth, the cardiomyocyte ploidy levels also correlated more closely with growth rate than with body mass. The opposite was observed in the precocial birds, which are highly mobile from the first minutes of life. We conclude that the interspecies variability of bird cardiomyocyte ploidy levels is a result of changes in the balance between the cardiac functional load and the growth rate; this is manifested at the cellular level as a competition between the proliferation and differentiation of cardiomyocytes.
International Journal of Molecular Sciences, Sep 29, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cryptosporidiosis causes persistent diarrhea in infants, immunocompromised patients and elderly p... more Cryptosporidiosis causes persistent diarrhea in infants, immunocompromised patients and elderly persons. Long-term consequences of the disease include increased risk of malignancy, cardiomyopathy and gastrointestinal inflammation. This study aimed to investigate prolonged effects of cryptosporidiosis on innate immunity and growth in neonatal C3HA mice. The disease was challenged by Cryptosporidium parvum oocyst inoculation into 7-days old animals. The mice whose intestine smears contained 3-5 or 6 and more oocysts per microscopic field at the day 5 after infection were considered as mildly or Accepted Article This article is protected by copyright. All rights reserved. severely infected, correspondingly. To determine natural killer cell (NK) activity, we applied 3 H-uridine cytotoxic assay to the animals at 5-68 days after infection using K562 cells as targets. At severe infection, there was a statistically significant 1.5-2.0 fold decline of body mass, spleen mass and spleen cellularity that persisted in animals of all ages. Accordingly, NK cytotoxicity showed even more drastic drop reaching 2.7-3.0 folds that was statistically significant in all animals. At mild infection, the discovered effects were less pronounced and reached significance only in some age groups. Thus, our study provides evidence that NK cells show long-term cytotoxic activity decrease following Cryptosporidium infection in neonatal mice, particularly in severe disease.
Whole-genome duplication (WGD), or polyploidy, increases the amount of genetic information in the... more Whole-genome duplication (WGD), or polyploidy, increases the amount of genetic information in the cell. WGDs of whole organisms are found in all branches of eukaryotes and act as a driving force of speciation, complication, and adaptations. Somatic-cell WGDs are observed in all types of tissues and can result from normal or altered ontogenetic programs, regeneration, pathological conditions, aging, malignancy, and metastasis. Despite the versatility of WGDs, their functional significance, general properties, and causes of their higher adaptive potential are unclear. Comparisons of whole-transcriptome data and information from various fields of molecular biology, genomics, and molecular medicine showed several common features for polyploidy of organisms and somatic and cancer cells, making it possible to understand what WGD properties lead to the emergence of an adaptive phenotype. The adaptation potential of WGDs may be associated with an increase in the complexity of the regulation of networks and signaling systems; a higher resistance to stress; and activation of ancient evolutionary programs of unicellularity and pathways of morphogenesis, survival, and life extension. A balance between the cell and organismal levels in controlling gene regulation may shift in stress towards the priority of cell survival, and the shift can lead to cardiovascular diseases and carcinogenesis. The presented information helps to understand how polyploidy creates new phenotypes and why it acts as a driving force of evolution and an important regulator of biological processes in somatic cells during ontogeny, pathogenesis, regeneration, and transformation.
The prevalence of purifying selection in the nature suggests that larger organisms bear a higher ... more The prevalence of purifying selection in the nature suggests that larger organisms bear a higher number of slightly deleterious mutations because of smaller populations and therefore weaker selection. In this work redistribution of purifying selection in favor of information genes, pathways and processes was found in primates compared with treeshrew and rodents on the ground of genome-wide analysis. The genes which are more favored in primates belong mainly to regulation of gene expression and development, in treeshrew and rodents, to metabolism, transport, energetics, reproduction and olfaction. The former occur predominantly in the nucleus, the latter, in the cytoplasm and membranes. Thus, although purifying selection is on average weaker in the primates, it is stronger concentrated on the 'information technology' of life (regulation of gene expression and development). Increased accuracy of information processes probably allows escaping 'error catastrophes' in spite of more complex organization, larger body size and higher longevity.
International Journal of Molecular Sciences, Oct 28, 2021
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Temperature is an important exogenous factor capable of leading to irreversible processes in the ... more Temperature is an important exogenous factor capable of leading to irreversible processes in the vital activity of cells. However, the long-term effects of heat shock (HS) on mesenchymal stromal cells (MSC) remain unstudied. We investigated the karyotype and DNA repair drivers and pathways in the human endometrium MSC (eMSC) survived progeny at passage 6 after sublethal heat stress (sublethal heat stress survived progeny (SHS-SP)). G-banding revealed an outbreak of random karyotype instability caused by chromosome breakages and aneuploidy. Molecular karyotyping confirmed the random nature of this instability. Transcriptome analysis found homologous recombination (HR) deficiency that most likely originated from the low thermostability of the AT-rich HR driving genes. SHS-SP protection from transformation is provided presumably by low oncogene expression maintained by tight co-regulation between thermosensitive HR drivers BRCA, ATM, ATR, and RAD51 (decreasing expression after SHS), and oncogenes mTOR, MDM2, KRAS, and EGFR. The cancer-related transcriptomic features previously identified in hTERT transformed MSC in culture were not found in SHS-SP, suggesting no traits of malignancy in them. The entrance of SHS-SP into replicative senescence after 25 passages confirms their mortality and absence of transformation features. Overall, our data indicate that SHS may trigger non-tumorigenic karyotypic instability due to HR deficiency and decrease of oncogene expression in progeny of SHS-survived MSC. These data can be helpful for the development of new therapeutic approaches in personalized medicine.
Whole-genome duplications are important for the growth of genome complexity. We investigated vari... more Whole-genome duplications are important for the growth of genome complexity. We investigated various factors involved in the evolution of yeast whole-genome duplicates (ohnologs) making emphasis on the analysis of protein interactions. We found that ohnologs have a lower number of protein interactions compared with small-scale duplicates and singletons (by about − 40%). The loss of interactions was proportional to their initial number and independent of ohnolog position in the protein interaction network. A faster evolving member of an ohnolog pair has a lower number of interactions compared to its counterpart. The Gene Ontology mapping of non-overlapping and overlapping interactants of paired ohnologs reveals a sharp asymmetry in GO terms related to regulation. The fraction of these terms is much higher in nonoverlapping interactants (compared to overlapping interactants and total dataset). Network clustering coefficient is lower in ohnologs, yet they show an increased density of protein interactions restricted within the whole ohnologs set. These facts suggest that subfunctionalization (or subneofunctionalization) reflected in the loss of protein interactions was a prevailing process in the divergence of ohnologs, which distinguishes them from small-scale duplicates. The loss of protein interactions was associated with the regulatory divergence between the members of an ohnolog pair. A small-scale modularity (reflected in clustering coefficient) probably was not important for ohnologs retention, yet a larger-scale modularity could be involved in their evolution.
Polyploid cells show great among-species and among-tissues diversity and relation to developmenta... more Polyploid cells show great among-species and among-tissues diversity and relation to developmental mode, suggesting their importance in adaptive evolution and developmental programming. At the same time, excessive polyploidization is a hallmark of functional impairment, aging, growth disorders, and numerous pathologies including cancer and cardiac diseases. To shed light on this paradox and to find out how polyploidy contributes to organ functions, we review here the ploidy-associated shifts in activity of narrowly expressed (tissue specific) genes in human and mouse heart and liver, which have the reciprocal pattern of polyploidization. For this purpose, we use the modular biology approach and genome-scale crossspecies comparison. It is evident from this review that heart and liver show similar traits in response to polyploidization. In both organs, polyploidy protects vitality (mainly due to the activation of sirtuin-mediated pathways), triggers the reserve adenosine-5′-triphosphate (ATP) production, and sustains tissue-specific functions by switching them to energy saving mode. In heart, the strongest effects consisted in the concerted up-regulation of contractile proteins and substitution of energy intensive proteins with energy economic ones. As a striking example, the energy intensive alpha myosin heavy chain (providing fast contraction) decreased its expression by a factor of 10, allowing a 270-fold increase of expression of beta myosin heavy chain (providing slow contraction), which has approximately threefold lower ATP-hydrolyzing activity. The liver showed the enhancement of immunity, reactive oxygen species and xenobiotic detoxication, and numerous metabolic adaptations to long-term energy depletion. Thus, somatic polyploidy may be an ingenious evolutionary instrument for fast adaptation to stress and new environments allowing tradeoffs between high functional demand, stress, and energy depletion.
Diseases of the human cardiovascular system are the main cause of death in developed countries. T... more Diseases of the human cardiovascular system are the main cause of death in developed countries. Therefore, searching for new risk factors thereof is of particular interest. Upon comparing epidemiological data with data of transcriptome of cardiomyocytes and comparative physiology of vertebrate ontogenesis, we have come to the conclusion that one such factor may be gastroenteritis. This disease includes at once several stimuli able to cause functional and metabolic alterations in the heart: tachycardia, hormonal and ionic mis balance, and outflow of resources from the cardiovascular system. Using the model of rat neonatal gastroen teritis caused by the widespread human and animal enteropathogen Cryptosporidium parvum (Apicomplexa, Sporozoa), we studied the change of expression of α and β myosin heavy chains after the developed cryptosporidiosis. Online data obtained by methods of immunocytochemistry, quantitative morphometry, and polymerase chain reaction not only have confirmed our suggestion, but also have shown that moderate 4 day long cryptosporidiosis is sufficient for producing a significant (1.7 to 4.5 fold) shift in the ratio of myosin isoforms toward the β isoform beta at the level of mRNA and at the level of protein (2.5-6 times). The reciprocity of the changes, as well as their clear similarity at the level of mRNA and of protein, indicates that the cryptosporidial gastroenteritis involves all the main chains of a complex network of regulation of expression of the myosin heavy chains. A shift of the ratio of myosin isoforms toward the β isoform that has an ATPase activity several times lower than the α isoform is the commonly accepted indicator of human heart failure; therefore, the cryptosporidial gastroenteritis can be considered a novel risk factor for decrease of the heart's contractile ability. Our data may be of interest for clinical and preventive medicine.
Changes in gene expression play an important role in evolution and can be relevant to evolutionar... more Changes in gene expression play an important role in evolution and can be relevant to evolutionary medicine. In this work, a strong relationship was found between the statistical significance of evolutionary changes in the expression of orthologous genes in the five or six homologous mammalian tissues and the across-tissues unidirectionality of changes (i.e., they occur in the same direction in different tissues -- all upward or all downward). In the area of highly significant changes, the fraction of unidirectionally changed genes (UCG) was above 0.9 (random expectation is 0.03). This observation indicates that the most pronounced evolutionary changes in mammalian gene expression are systemic (i.e., they operate at the whole-organism level). The UCG are strongly enriched in the housekeeping genes. More specifically, in the human-chimpanzee comparison, the UCG are enriched in the pathways belonging to gene expression (translation is prominent), cell cycle control, ubiquitin-dependent protein degradation (mostly related to cell cycle control), apoptosis, and Parkinson's disease. In the human-macaque comparison, the two other neurodegenerative diseases (Alzheimer's and Huntington's) are added to the enriched pathways. The consolidation of gene expression changes at the level of pathways indicates that they are not neutral but functional. The systemic expression changes probably maintain the across-tissues balance of basic physiological processes in the course of evolution (e.g., during the movement along the fast-slow life axis). These results can be useful for understanding the variation in longevity and susceptibility to cancer and widespread neurodegenerative diseases. This approach can also guide the choice of prospective genes for studies aiming to decipher cis-regulatory code (the gene list is provided).
International Journal of Molecular Sciences, Nov 19, 2020
Tumours were recently revealed to undergo a phylostratic and phenotypic shift to unicellularity. ... more Tumours were recently revealed to undergo a phylostratic and phenotypic shift to unicellularity. As well, aggressive tumours are characterized by an increased proportion of polyploid cells. In order to investigate a possible shared causation of these two features, we performed a comparative phylostratigraphic analysis of ploidy-related genes, obtained from transcriptomic data for polyploid and diploid human and mouse tissues using pairwise cross-species transcriptome comparison and principal component analysis. Our results indicate that polyploidy shifts the evolutionary age balance of the expressed genes from the late metazoan phylostrata towards the upregulation of unicellular and early metazoan phylostrata. The up-regulation of unicellular metabolic and drug-resistance pathways and the downregulation of pathways related to circadian clock were identified. This evolutionary shift was associated with the enrichment of ploidy with bivalent genes (p < 10 −16). The protein interactome of activated bivalent genes revealed the increase of the connectivity of unicellulars and (early) multicellulars, while circadian regulators were depressed. The mutual polyploidy-c-MYC-bivalent genes-associated protein network was organized by gene-hubs engaged in both embryonic development and metastatic cancer including driver (proto)-oncogenes of viral origin. Our data suggest that, in cancer, the atavistic shift goes hand-in-hand with polyploidy and is driven by epigenetic mechanisms impinging on development-related bivalent genes.
Design and development of highly sensitive method bioinformatics are important for investigation ... more Design and development of highly sensitive method bioinformatics are important for investigation of casual relationships between epigenetic changes and gene activity. Cell polyploidy may trigger such changes. However, maintaining the balance of gene dosage, polyploidy may provide only a rather weak effect on their expression. Currently, there is no comprehensive and concordant data in regard to ploidy-associated transcriptomic changes. To find out how polypoidy affects gene activity, we have developed an integrative bioinformatic method of pairwise cross-species transcriptome analysis of mammalian tissues with various polyploidy degrees. The main benefit of this approach is its ability to separate species- and tissue-specific noises of evolutionary conserved effects. We demonstrat the application of the method for the analysis of gene modules and protein interactions networks coordinating programs of development, differentiation and pluripotency. The analysis was performed with transcriptomes of polyploid and diploid organs (human and mouse heart and liver). Our data indicate that ploidy-induced genes enrich Gene Ontology (GO) biological processes and KEGG pathways related to development, morphogenesis and stem cells biology (including Hippo, Pi3K, WNT, Hedgehog and TGF-β pathways) with higher degree than ploidy-inhibited genes. Thas, our data are the first to show that polyploidy may induce and coordinate developmental modules.
Journal of Evolutionary Biochemistry and Physiology, Sep 1, 2013
Disturbances at the childhood age increase risk of the appearance of cardiovascular diseases deca... more Disturbances at the childhood age increase risk of the appearance of cardiovascular diseases decades later. The nature of this interconnection called ontogenetic programming is not completely understood. Valuable sources of knowledge about mechanisms of ontogenetic programming are data of interspecies study of biology of the body life cycles and of heart physiological capabilities. Taken into account the interspecies differences, these data allow finding the correct direction of experimental investigations. Results of studies of almost 100 homoiothermal species have shown the slow growth and a high loading on the heart at postnatal development to decrease its aerobic capability in adults. Basing on these data, we suggested that the neonatal gastroenteritis causing tachyarrhythmia, malabsorption, and the growth deceleration might lead to pathological changes in the heart. Our task was to evaluate the effect of cryptosporidial gastroenteritis of different degrees of severity on heart of the neonatal rats. By using methods of Real-Time PCR, immunocytochemistry, image analysis, and study of interatrial septum, we have established that a gradual increase of intensity of infestation with Cryptosporidium parvum oocytes causes sharp changes corresponding to the &quot;all or nothing&quot; response. At a weak infestation the interatrial septum was close (like in control), while significant changes in expression of isoforms of heavy chains of alpha- and beta-myosin were absent. At the intermediate and severe infestation, in the interatrial septum the foramen ovale was visualized and there were observed cardiac atrophy and a strong shift of ration of expression of myosin heavy chains toward the low-velocity beta chain. Thus, by disturbing the frequency-strength ratios and causing outflow of resources from the formed heart, the neonatal gastroenteritis produces pathological changes of the organ molecular and anatomical structures. Our results can be interest to evolutionary biologists and physicians, as they show importance of knowledge of evolutionary-comparative investigations for the search for novel risk factors of heart diseases and demonstrate interconnection between gastroenteritis, pathology of interatrial septum, and a change of composition of the main contractile proteins in cardiomyocytes.
Inflammation, malnutrition and growth retardation during critical time-windows of development pla... more Inflammation, malnutrition and growth retardation during critical time-windows of development play a powerful role in ontogenetic programming of the lifelong risk to many adult diseases (including metabolic syndrome, obesity and diabetes). Cellular mechanisms and the accurate timing and duration of critical periods for the liver remain obscure. To resolve this problem, we developed a postnatal suckling-weanling rat model of mild, moderate, and acute gastroenteritis challenged by a protozoan parasitic spread throughout the whole world, namely Cryptosporidium parvum. The physiological state of the liver was evaluated by hepatocyte ploidy and protein content that were measured by cytophotometry and image analysis on isolated cells. Hepatocyte ploidy is known to irreversibly increase after stress and is associated with the decrease in liver physiological capacity. Hepatocyte hypertrophy reflects cell functional loading. From our results, cryptosporidiosis is able to provoke a burst in premature hepatocyte polyploidization and hypertrophy (in proportion to parasitic load), and thus plays an important role in epigenetic programming of hepatocyte structure and function. We revealed two sensitive periods in liver growth. The first period (the less sensitive) covers the time before the establishment of homoiothermy, i.e. 6e9 days after birth. The second period (the more sensitive) covers the time of weaning when the change of type of nutrition and the peak of hepatocyte polyploidization and differentiation occurs. Thus, our data provide direct evidence that phenomenon of ontogenetic programming is reflected at the cellular level.
Background: The aim of our study was to find out, whether cardiomyocyte genome duplication partic... more Background: The aim of our study was to find out, whether cardiomyocyte genome duplication participates in developmental programming of adult hypertension and impaired heart aerobic capacity, and if it does, whether ploidy-related programming is reversible and what are the timeframes of the most critical window. For this propose we studied the effect of the well-known factors of programming, including growth retardation, infection, and cardiac overload on the level of neonatal cardiomyocyte ploidy, protein content and shape. Methods: Using the model of rat cryptosporidial gastroenteritis, we shifted the time point of infection day by day through the neonatal period and traced the immediate and postponed effects of disease on isolated cardiomyocyte ploidy, phenotype, and protein content. Results: We found that gastroenteritis caused cardiac atrophy and a burst-like premature genome accumulation, elongation, narrowing and protein loss in the cardiomyocytes. These changes resulted in sharp increase of DNA content at the expense of contractile proteins. We also revealed clear indications of critical window of heart development during the peak of cardiomyocyte transition from proliferation to hypertrophy. After the rehabilitation, the atrophy of heart and cardiomyocyte remodelling showed a conspicuous restoration, whereas the hyperpolyploidization did not regress. An irreversible manner of excessive genome duplication and its well-known ability to alter gene expression confirm our suggestion that it is implicated in the ontogenetic programming of heart development. Conclusion: We provided the first evidence that developmental programming can operate through cardiomyocyte genome duplication and that the critical window coincides with cell transition from proliferation to hypertrophy. Our data help determine the timing of critical window for human heart and would allow successful prevention of human cardiac abnormalities even before they become tangible.
Cytofluorimetric study of ploidy levels in ventricular cardiomyocytes was carried out on 36 adult... more Cytofluorimetric study of ploidy levels in ventricular cardiomyocytes was carried out on 36 adult bird species belonging to 10 orders as well as on the quail Coturnix coturnix, of different ages. It was shown that polyploidization of quail cardiomyocytes occurs during the first 40 days after hatching and ends by the time growth is completed. In adult birds, the cardiomyocyte ploidy hardly changed at all. Interspecies comparison revealed that in the adult bird myocardium 2cx2 myocytes are predominant, accounting for at least 50% of the cell population. Multinuclear cells with three to eight diploid nuclei were widespread. The percentage of such cells was five to six times higher in precocial species than in altricial birds of the same weight. Myocytes with polyploid nuclei were rare. A significant interspecies variability of cardiomyocyte ploidy levels was observed. The most prominent differences were found between the precocial and the altricial birds. The mean number of genomes in cells correlated both with the body mass and with the growth rate of the birds. The differences between the precocial and altricial birds disappeared when a statistical method was used to eliminate the effect of the growth rate, but did not when the effect of body mass was eliminated. Among the altricial birds, which are generally immobile during growth, the cardiomyocyte ploidy levels also correlated more closely with growth rate than with body mass. The opposite was observed in the precocial birds, which are highly mobile from the first minutes of life. We conclude that the interspecies variability of bird cardiomyocyte ploidy levels is a result of changes in the balance between the cardiac functional load and the growth rate; this is manifested at the cellular level as a competition between the proliferation and differentiation of cardiomyocytes.
International Journal of Molecular Sciences, Sep 29, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cryptosporidiosis causes persistent diarrhea in infants, immunocompromised patients and elderly p... more Cryptosporidiosis causes persistent diarrhea in infants, immunocompromised patients and elderly persons. Long-term consequences of the disease include increased risk of malignancy, cardiomyopathy and gastrointestinal inflammation. This study aimed to investigate prolonged effects of cryptosporidiosis on innate immunity and growth in neonatal C3HA mice. The disease was challenged by Cryptosporidium parvum oocyst inoculation into 7-days old animals. The mice whose intestine smears contained 3-5 or 6 and more oocysts per microscopic field at the day 5 after infection were considered as mildly or Accepted Article This article is protected by copyright. All rights reserved. severely infected, correspondingly. To determine natural killer cell (NK) activity, we applied 3 H-uridine cytotoxic assay to the animals at 5-68 days after infection using K562 cells as targets. At severe infection, there was a statistically significant 1.5-2.0 fold decline of body mass, spleen mass and spleen cellularity that persisted in animals of all ages. Accordingly, NK cytotoxicity showed even more drastic drop reaching 2.7-3.0 folds that was statistically significant in all animals. At mild infection, the discovered effects were less pronounced and reached significance only in some age groups. Thus, our study provides evidence that NK cells show long-term cytotoxic activity decrease following Cryptosporidium infection in neonatal mice, particularly in severe disease.
Whole-genome duplication (WGD), or polyploidy, increases the amount of genetic information in the... more Whole-genome duplication (WGD), or polyploidy, increases the amount of genetic information in the cell. WGDs of whole organisms are found in all branches of eukaryotes and act as a driving force of speciation, complication, and adaptations. Somatic-cell WGDs are observed in all types of tissues and can result from normal or altered ontogenetic programs, regeneration, pathological conditions, aging, malignancy, and metastasis. Despite the versatility of WGDs, their functional significance, general properties, and causes of their higher adaptive potential are unclear. Comparisons of whole-transcriptome data and information from various fields of molecular biology, genomics, and molecular medicine showed several common features for polyploidy of organisms and somatic and cancer cells, making it possible to understand what WGD properties lead to the emergence of an adaptive phenotype. The adaptation potential of WGDs may be associated with an increase in the complexity of the regulation of networks and signaling systems; a higher resistance to stress; and activation of ancient evolutionary programs of unicellularity and pathways of morphogenesis, survival, and life extension. A balance between the cell and organismal levels in controlling gene regulation may shift in stress towards the priority of cell survival, and the shift can lead to cardiovascular diseases and carcinogenesis. The presented information helps to understand how polyploidy creates new phenotypes and why it acts as a driving force of evolution and an important regulator of biological processes in somatic cells during ontogeny, pathogenesis, regeneration, and transformation.
The prevalence of purifying selection in the nature suggests that larger organisms bear a higher ... more The prevalence of purifying selection in the nature suggests that larger organisms bear a higher number of slightly deleterious mutations because of smaller populations and therefore weaker selection. In this work redistribution of purifying selection in favor of information genes, pathways and processes was found in primates compared with treeshrew and rodents on the ground of genome-wide analysis. The genes which are more favored in primates belong mainly to regulation of gene expression and development, in treeshrew and rodents, to metabolism, transport, energetics, reproduction and olfaction. The former occur predominantly in the nucleus, the latter, in the cytoplasm and membranes. Thus, although purifying selection is on average weaker in the primates, it is stronger concentrated on the 'information technology' of life (regulation of gene expression and development). Increased accuracy of information processes probably allows escaping 'error catastrophes' in spite of more complex organization, larger body size and higher longevity.
International Journal of Molecular Sciences, Oct 28, 2021
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Temperature is an important exogenous factor capable of leading to irreversible processes in the ... more Temperature is an important exogenous factor capable of leading to irreversible processes in the vital activity of cells. However, the long-term effects of heat shock (HS) on mesenchymal stromal cells (MSC) remain unstudied. We investigated the karyotype and DNA repair drivers and pathways in the human endometrium MSC (eMSC) survived progeny at passage 6 after sublethal heat stress (sublethal heat stress survived progeny (SHS-SP)). G-banding revealed an outbreak of random karyotype instability caused by chromosome breakages and aneuploidy. Molecular karyotyping confirmed the random nature of this instability. Transcriptome analysis found homologous recombination (HR) deficiency that most likely originated from the low thermostability of the AT-rich HR driving genes. SHS-SP protection from transformation is provided presumably by low oncogene expression maintained by tight co-regulation between thermosensitive HR drivers BRCA, ATM, ATR, and RAD51 (decreasing expression after SHS), and oncogenes mTOR, MDM2, KRAS, and EGFR. The cancer-related transcriptomic features previously identified in hTERT transformed MSC in culture were not found in SHS-SP, suggesting no traits of malignancy in them. The entrance of SHS-SP into replicative senescence after 25 passages confirms their mortality and absence of transformation features. Overall, our data indicate that SHS may trigger non-tumorigenic karyotypic instability due to HR deficiency and decrease of oncogene expression in progeny of SHS-survived MSC. These data can be helpful for the development of new therapeutic approaches in personalized medicine.
Whole-genome duplications are important for the growth of genome complexity. We investigated vari... more Whole-genome duplications are important for the growth of genome complexity. We investigated various factors involved in the evolution of yeast whole-genome duplicates (ohnologs) making emphasis on the analysis of protein interactions. We found that ohnologs have a lower number of protein interactions compared with small-scale duplicates and singletons (by about − 40%). The loss of interactions was proportional to their initial number and independent of ohnolog position in the protein interaction network. A faster evolving member of an ohnolog pair has a lower number of interactions compared to its counterpart. The Gene Ontology mapping of non-overlapping and overlapping interactants of paired ohnologs reveals a sharp asymmetry in GO terms related to regulation. The fraction of these terms is much higher in nonoverlapping interactants (compared to overlapping interactants and total dataset). Network clustering coefficient is lower in ohnologs, yet they show an increased density of protein interactions restricted within the whole ohnologs set. These facts suggest that subfunctionalization (or subneofunctionalization) reflected in the loss of protein interactions was a prevailing process in the divergence of ohnologs, which distinguishes them from small-scale duplicates. The loss of protein interactions was associated with the regulatory divergence between the members of an ohnolog pair. A small-scale modularity (reflected in clustering coefficient) probably was not important for ohnologs retention, yet a larger-scale modularity could be involved in their evolution.
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