An Integrated View of Virus-Triggered Cellular Plasticity Using Boolean Networks.

Virus-related mortality and morbidity are due to cell/tissue damage caused by replicative pressure and resource exhaustion, e.g., HBV or HIV; exaggerated immune responses, e.g., SARS-CoV-2; and cancer, e.g., EBV or HPV. In this context, oncogenic and other types of viruses drive genetic and epigenetic changes that expand the tumorigenic program, including modifications to the ability of cancer cells to migrate. The best-characterized group of changes is collectively known as the epithelial-mesenchymal transition, or EMT. This is a complex phenomenon classically described using biochemistry, cell biology and genetics. However, these methods require enormous, often slow, efforts to identify and validate novel therapeutic targets. Systems biology can complement and accelerate discoveries in this field. One example of such an approach is Boolean networks, which make complex biological problems tractable by modeling data ("nodes") connected by logical operators. Here, we focus on virus-induced cellular plasticity and cell reprogramming in mammals, and how Boolean networks could provide novel insights into the ability of some viruses to trigger uncontrolled cell proliferation and EMT, two key hallmarks of cancer.

Transcriptional signatures underlying dynamic phenotypic switching and novel disease biomarkers in a linear cellular model of melanoma progression.

Despite advances in therapeutics, the progression of melanoma to metastasis still confers a poor outcome to patients. Nevertheless, there is a scarcity of biological models to understand cellular and molecular changes taking place along disease progression. Here, we characterized the transcriptome profiles of a multi-stage murine model of melanoma progression comprising a nontumorigenic melanocyte lineage (melan-a), premalignant melanocytes (4C), nonmetastatic (4C11-) and metastasis-prone (4C11+) melanoma cells. Clustering analyses have grouped the 4 cell lines according to their differentiated (melan-a and 4C11+) or undifferentiated/"mesenchymal-like" (4C and 4C11-) morphologies, suggesting dynamic gene expression patterns associated with the transition between these phenotypes. The cell plasticity observed in the murine melanoma progression model was corroborated by molecular markers described during stepwise human melanoma differentiation, as the differentiated cell lines in our model exhibit upregulation of transitory and melanocytic markers, whereas "mesenchymal-like" cells show increased expression of undifferentiated and neural crest-like markers. Sets of differentially expressed genes (DEGs) were detected at each transition step of tumor progression, and transcriptional signatures related to malignancy, metastasis and epithelial-to-mesenchymal transition were identified. Finally, DEGs were mapped to their human orthologs and evaluated in uni- and multivariate survival analyses using gene expression and clinical data of 703 drug-naïve primary melanoma patients, revealing several independent candidate prognostic markers. Altogether, these results provide novel insights into the molecular mechanisms underlying the phenotypic switch taking place during melanoma progression, reveal potential drug targets and prognostic biomarkers, and corroborate the translational relevance of this unique sequential model of melanoma progression.

Dynamic Transcriptional and Epigenetic Changes Drive Cellular Plasticity in the Liver.

BACKGROUND AND AIMS: Following liver injury, a fraction of hepatocytes adopt features of biliary epithelial cells (BECs) in a process known as biliary reprogramming. The aim of this study was to elucidate the molecular events accompanying this dramatic shift in cellular identity. APPROACH AND RESULTS: We applied the techniques of bulk RNA-sequencing (RNA-seq), single-cell RNA-seq, and assay for transposase-accessible chromatin with high-throughput sequencing to define the epigenetic and transcriptional changes associated with biliary reprogramming. In addition, we examined the role of TGF-ß signaling by profiling cells undergoing reprogramming in mice with hepatocyte-specific deletion in the downstream TGF-ß signaling component mothers against decapentaplegic homolog 4 (Smad4). Biliary reprogramming followed a stereotyped pattern of altered gene expression consisting of robust induction of biliary genes and weaker repression of hepatocyte genes. These changes in gene expression were accompanied by corresponding modifications at the chromatin level. Although some reprogrammed cells had molecular features of "fully differentiated" BECs, most lacked some biliary characteristics and retained some hepatocyte characteristics. Surprisingly, single-cell analysis of Smad4 mutant mice revealed a dramatic increase in reprogramming. CONCLUSION: Hepatocytes undergo widespread chromatin and transcriptional changes during biliary reprogramming, resulting in epigenetic and gene expression profiles that are similar to, but distinct from, native BECs. Reprogramming involves a progressive accumulation of biliary molecular features without discrete intermediates. Paradoxically, canonical TGF-ß signaling through Smad4 appears to constrain biliary reprogramming, indicating that TGF-ß can either promote or inhibit biliary differentiation depending on which downstream components of the pathway are engaged. This work has implications for the formation of BECs and bile ducts in the adult liver.

Osteopontin­c isoform inhibition modulates ovarian cancer cell cisplatin resistance, viability and plasticity.

Osteopontin (OPN) is upregulated in several types of tumor and has been associated with chemoresistance. However, the contribution of OPN splicing isoforms (OPN­SIs) to chemoresistance requires further investigation. The present study aimed to evaluate the expression patterns of each tested OPN­SI in cisplatin (CDDP)­resistant ovarian carcinoma cell lines, focusing on the role of the OPN­c isoform (OPNc) in drug resistance. ACRP ovarian cancer cells resistant to CDDP, as well as their parental cell line A2780, were used. Analyses of the transcriptional expression of OPN­SIs, epithelial­mesenchymal transition (EMT) markers and EMT­related cytokines were performed using reverse transcription­quantitative PCR. OPNc was silenced in ACRP cells using anti­OPNc DNA oligomers and stably overexpressed by transfecting A2780 cells with a mammalian expression vector containing the full length OPNc cDNA. Functional assays were performed to determine cell proliferation, viability and colony formation. The results demonstrated that among the three tested OPN­SIs, OPNc was the most upregulated transcript in the ACRP cells compared with the parental A2780 cells. In addition, the expression levels of P­glycoprotein multidrug transporter were upregulated in CDDP­resistant ACRP cells compared with those in A2780 cells. OPNc knockdown sensitized ACRP cells to CDDP treatment and downregulated P­gp expression levels compared with those in the negative control group. Additionally, silencing of OPNc impaired cell proliferative and colony formation abilities, as well as reversed the expression levels of EMT markers and EMT­related cytokines compared with those in the negative control cells. Notably, although stable OPNc overexpression resulted in increased A2780 cell proliferation, it notably increased CDDP sensitivity compared with that in the cells transfected with a control vector. These results suggested that OPNc silencing may represent a putative approach to sensitize resistant ovarian cancer cells to chemotherapeutic agents.

Epigenetic Therapy as a Putative Molecular Target to Modulate B Cell Biology and Behavior in the Context of Immunological Disorders.

Histone Deacetylase- (HDAC-) dependent epigenetic mechanisms have been widely explored in the last decade in different types of malignancies in preclinical studies. This effort led to the discovery and development of a range of new HDAC inhibitors (iHDAC) with different chemical properties and selective abilities. In fact, hematological malignancies were the first ones to have new iHDACs approved for clinical use, such as Vorinostat and Romidepsin for cutaneous T cell lymphoma and panobinostat for multiple myeloma. Besides these promising already approved iHDACs, we highlight a range of studies focusing on the HDAC-dependent epigenetic control of B cell development, behavior, and/or function. Here, we highlight 21 iHDACs which have been studied in the literature in the context of B cell development and/or dysfunction mostly focused on B cell lymphomagenesis. Regardless, we have identified 55 clinical trials using 6 out of 21 iHDACs to approach their putative roles on B cell malignancies; none of them focuses on peritoneal B cell populations. Since cells belonging to this peculiar body compartment, named B1 cells, may contribute to the development of autoimmune pathologies, such as lupus, a better understanding of the HDAC-dependent epigenetic mechanisms that control its biology and behavior might shed light on iHDAC use to manage these immunological dysfunctions. In this sense, iHDACs might emerge as a promising new approach for translational studies in this field. In this review, we discuss a putative role of iHDACs in the modulation of peritoneal B cell subpopulation's balance as well as their role as therapeutic agents in the context of chronic diseases mediated by peritoneal B cells.

Production and leaf plasticity of rose plants sprayed with paclobutrazol and daminozide / Produção e plasticidade anatômica foliar de roseiras pulverizadas com paclobutrazol e daminozide

The aim of this work was to evaluate morphological and anatomical alterations in leaves of Yellow Terrazza® and Red White Terrazza® pot roses sprayed with paclobutrazol (0, 40, 60, 80 mg L-1) and daminozide (0, 2000, 4000, 6000, 8000 mg L-1). The experiments were conducted under greenhouse conditions using a factorial treatment design (cultivars x growth retardant doses) with five replications and experimental units arranged in randomized blocks. Cv. Yellow Terrazza ® presented higher plants, greater floral diameter and leaf area than cv. Red White Terrazza ®. Plant height, leaf area, and flower diameter decreased linearly with paclobutrazol and daminozide doses. In addition, paclobutrazol and daminozide applications changed leaf tissue proportions by increasing the thickness of leaf blade, mesophyll, palisade parenchyma, and spongy parenchyma but did not influence the thickness of leaf epidermis.(AU)

Objetivou-se com esse trabalho avaliar características fitotécnicas e alterações anatômicas quantitativas nas folhas de duas cultivares de roseira (Yellow Terrazza® e Red White Terrazza®), cultivadas em vaso em função da pulverização foliar de doses de paclobutrazol (0, 40, 60, 80 mg L-1) em um experimento e doses de daminozide (0, 2000, 4000, 6000, 8000 mg L-1) em outro. Os experimentos foram conduzidos em ambiente protegido e os tratamentos dispostos em esquema fatorial (cultivares x doses dos retardantes), em delineamento de blocos casualizados com cinco repetições. A cultivar Yellow Terrazza® apresentou plantas com maior altura, diâmetro floral e área foliar que a Red White Terrazza®. O aumento da dose dos retardantes nas duas cultivares reduziu altura e área foliar, promoveu mudanças na proporção dos tecidos, aumentou a espessura da lâmina foliar, mesofilo e dos parênquimas paliçádico e lacunoso. Os retardantes não influenciaram a espessura das epidermes das cultivares. O tecido parenquimático das cultivares apresenta plasticidade com aplicação dos retardantes.(AU)

Production and leaf plasticity of rose plants sprayed with paclobutrazol and daminozide / Produção e plasticidade anatômica foliar de roseiras pulverizadas com paclobutrazol e daminozide

The aim of this work was to evaluate morphological and anatomical alterations in leaves of Yellow Terrazza® and Red White Terrazza® pot roses sprayed with paclobutrazol (0, 40, 60, 80 mg L-1) and daminozide (0, 2000, 4000, 6000, 8000 mg L-1). The experiments were conducted under greenhouse conditions using a factorial treatment design (cultivars x growth retardant doses) with five replications and experimental units arranged in randomized blocks. Cv. Yellow Terrazza ® presented higher plants, greater floral diameter and leaf area than cv. Red White Terrazza ®. Plant height, leaf area, and flower diameter decreased linearly with paclobutrazol and daminozide doses. In addition, paclobutrazol and daminozide applications changed leaf tissue proportions by increasing the thickness of leaf blade, mesophyll, palisade parenchyma, and spongy parenchyma but did not influence the thickness of leaf epidermis.

Objetivou-se com esse trabalho avaliar características fitotécnicas e alterações anatômicas quantitativas nas folhas de duas cultivares de roseira (Yellow Terrazza® e Red White Terrazza®), cultivadas em vaso em função da pulverização foliar de doses de paclobutrazol (0, 40, 60, 80 mg L-1) em um experimento e doses de daminozide (0, 2000, 4000, 6000, 8000 mg L-1) em outro. Os experimentos foram conduzidos em ambiente protegido e os tratamentos dispostos em esquema fatorial (cultivares x doses dos retardantes), em delineamento de blocos casualizados com cinco repetições. A cultivar Yellow Terrazza® apresentou plantas com maior altura, diâmetro floral e área foliar que a Red White Terrazza®. O aumento da dose dos retardantes nas duas cultivares reduziu altura e área foliar, promoveu mudanças na proporção dos tecidos, aumentou a espessura da lâmina foliar, mesofilo e dos parênquimas paliçádico e lacunoso. Os retardantes não influenciaram a espessura das epidermes das cultivares. O tecido parenquimático das cultivares apresenta plasticidade com aplicação dos retardantes.

Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Muchos peces carácidos sudamericanos desarrollan protuberancias dérmicas reversibles en las mandíbulas para optimizar la respiración acuática superficial (RAS) durante la hipoxia. Actualmente, aspectos básicos de esta adaptación permanecen desconocidos, principalmente debido a la escasez de estudios experimentales. En experiencias de laboratorio, determinamos el tiempo necesario para el desarrollo y la reversión completos de estas estructuras en Piaractus mesopotamicus , y estudiamos comparativamente respuestas conductuales, morfológicas, y respiratorias en un gradiente de concentración de oxígeno disuelto (OD). Los cambios morfológicos durante la hipoxia consistieron en protuberancias dérmicas del labio inferior, el borde anterior del maxilar, y el borde distal de la válvula opercular, incrementando el número conocido de estructuras modificadas. Éstas se desarrollaron completamente en menos de 6 horas y se revirtieron en menos de 3 horas. La mayoría de los rasgos observados siguieron una curva de respuesta logística, con valores críticos entre 0,90 y 2,70 mgL-1 de OD. La frecuencia respiratoria y el desarrollo de la válvula opercular presentaron valores críticos similares ubicados por encima del nivel de tolerancia al OD, mientras que la RAS y las protuberancias dérmicas mandibulares presentaron críticos por debajo de dicho nivel. Estas observaciones apoyan la relación funcional existente entre estos grupos de rasgos conductuales y morfológicos. Este estudio demuestra que esta especie puede modificar reversiblemente porciones del sistema respiratorio para optimizar las respuestas a la hipoxia.(AU)

Many South American characid fishes develop reversible dermal protuberances in the jaws to optimize aquatic surface respiration (ASR) during hypoxia. To date, basic aspects of this adaptation remain unknown, mainly due to the scarcity of experimental studies. In laboratory experiments, we determined time necessary for the complete formation and reversion of these structures in Piaractus mesopotamicus , and studied comparatively behavioral, morphological, and respiratory responses along gradients of dissolved oxygen (DO) concentration. Morphological changes during hypoxia consisted in dermal protuberances of lower lip, anterior border of maxillary and distal border of opercular valve, increasing the known number of structures modified. These structures developed completely in less than 6 hours and reversed in less than 3 hours. Most of observed traits showed a logistic response curve with threshold DO values between 0.90 and 2.70 mgL-1. Respiratory frequency and opercular valve development showed similar threshold values above the level of tolerance of DO, whereas ASR and dermal protuberances of the jaws showed threshold values below this level. This observation supports the functional link between these groups of behavioral and morphological traits. This study demonstrates that this species is able to modify reversibly portions of the respiratory system to optimize responses to hypoxia.(AU)

Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Muchos peces carácidos sudamericanos desarrollan protuberancias dérmicas reversibles en las mandíbulas para optimizar la respiración acuática superficial (RAS) durante la hipoxia. Actualmente, aspectos básicos de esta adaptación permanecen desconocidos, principalmente debido a la escasez de estudios experimentales. En experiencias de laboratorio, determinamos el tiempo necesario para el desarrollo y la reversión completos de estas estructuras en Piaractus mesopotamicus , y estudiamos comparativamente respuestas conductuales, morfológicas, y respiratorias en un gradiente de concentración de oxígeno disuelto (OD). Los cambios morfológicos durante la hipoxia consistieron en protuberancias dérmicas del labio inferior, el borde anterior del maxilar, y el borde distal de la válvula opercular, incrementando el número conocido de estructuras modificadas. Éstas se desarrollaron completamente en menos de 6 horas y se revirtieron en menos de 3 horas. La mayoría de los rasgos observados siguieron una curva de respuesta logística, con valores críticos entre 0,90 y 2,70 mgL-1 de OD. La frecuencia respiratoria y el desarrollo de la válvula opercular presentaron valores críticos similares ubicados por encima del nivel de tolerancia al OD, mientras que la RAS y las protuberancias dérmicas mandibulares presentaron críticos por debajo de dicho nivel. Estas observaciones apoyan la relación funcional existente entre estos grupos de rasgos conductuales y morfológicos. Este estudio demuestra que esta especie puede modificar reversiblemente porciones del sistema respiratorio para optimizar las respuestas a la hipoxia.

Many South American characid fishes develop reversible dermal protuberances in the jaws to optimize aquatic surface respiration (ASR) during hypoxia. To date, basic aspects of this adaptation remain unknown, mainly due to the scarcity of experimental studies. In laboratory experiments, we determined time necessary for the complete formation and reversion of these structures in Piaractus mesopotamicus , and studied comparatively behavioral, morphological, and respiratory responses along gradients of dissolved oxygen (DO) concentration. Morphological changes during hypoxia consisted in dermal protuberances of lower lip, anterior border of maxillary and distal border of opercular valve, increasing the known number of structures modified. These structures developed completely in less than 6 hours and reversed in less than 3 hours. Most of observed traits showed a logistic response curve with threshold DO values between 0.90 and 2.70 mgL-1. Respiratory frequency and opercular valve development showed similar threshold values above the level of tolerance of DO, whereas ASR and dermal protuberances of the jaws showed threshold values below this level. This observation supports the functional link between these groups of behavioral and morphological traits. This study demonstrates that this species is able to modify reversibly portions of the respiratory system to optimize responses to hypoxia.

Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation.

BACKGROUND: The endogenous ability to dedifferentiate, re-pattern, and re-differentiate adult cells to repair or replace damaged or missing structures is exclusive to only a few tetrapod species. The Mexican axolotl is one example of these species, having the capacity to regenerate multiple adult structures including their limbs by generating a group of progenitor cells, known as the blastema, which acquire pattern and differentiate into the missing tissues. The formation of a limb regenerate is dependent on cells in the connective tissues that retain memory of their original position in the limb, and use this information to generate the pattern of the missing structure. Observations from recent and historic studies suggest that blastema cells vary in their potential to pattern distal structures during the regeneration process; some cells are plastic and can be reprogrammed to obtain new positional information while others are stable. Our previous studies showed that positional information has temporal and spatial components of variation; early bud (EB) and apical late bud (LB) blastema cells are plastic while basal-LB cells are stable. To identify the potential cellular and molecular basis of this variation, we compared these three cell populations using histological and transcriptional approaches. RESULTS: Histologically, the basal-LB sample showed greater tissue organization than the EB and apical-LB samples. We also observed that cell proliferation was more abundant in EB and apical-LB tissue when compared to basal-LB and mature stump tissue. Lastly, we found that genes associated with cellular differentiation were expressed more highly in the basal-LB samples. CONCLUSIONS: Our results characterize histological and transcriptional differences between EB and apical-LB tissue compared to basal-LB tissue. Combined with our results from a previous study, we hypothesize that the stability of positional information is associated with tissue organization, cell proliferation, and pathways of cellular differentiation.