The gene regulatory system for specifying germ layers in early embryos of the simple chordate

動物胚の遺伝子発現を数式で表現 --動物の胚葉形成システムをまるごと理解--.京都大学プレスリリース. 2021-06-10.In animal embryos, gene regulatory networks control the dynamics of gene expression in cells and coordinate such dynamics among cells. In ascidian embryos, gene expression dynamics have been dissected at the single-cell resolution. Here, we revealed mathematical functions that represent the regulatory logics of all regulatory genes expressed at the 32-cell stage when the germ layers are largely specified. These functions collectively explain the entire mechanism by which gene expression dynamics are controlled coordinately in early embryos. We found that regulatory functions for genes expressed in each of the specific lineages contain a common core regulatory mechanism. Last, we showed that the expression of the regulatory genes became reproducible by calculation and controllable by experimental manipulations. Thus, these regulatory functions represent an architectural design for the germ layer specification of this chordate and provide a platform for simulations and experiments to understand the operating principles of gene regulatory networks

Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo.

Linkage logic theory provides a mathematical criterion to control network dynamics by manipulating activities of a subset of network nodes, which are collectively called a feedback vertex set (FVS). Because many biological functions emerge from dynamics of biological networks, this theory provides a promising tool for controlling biological functions. By manipulating the activity of FVS molecules identified in a gene regulatory network (GRN) for fate specification of seven tissues in ascidian embryos, we previously succeeded in reproducing six of the seven cell types. Simultaneously, we discovered that the experimentally reconstituted GRN lacked information sufficient to reproduce muscle cells. Here, we utilized linkage logic theory as a tool to find missing edges in the GRN. Then, we identified a FVS from an updated version of the GRN and confirmed that manipulating the activity of this FVS was sufficient to induce all seven cell types, even in a multi-cellular environment. Thus, linkage logic theory provides tools to find missing edges in experimentally reconstituted networks, to determine whether reconstituted networks contain sufficient information to fulfil expected functions, and to reprogram cell fate

Controlling Cell Fate Specification System by Key Genes Determined from Network Structure

遺伝子ネットワークを制御してさまざまな種類の細胞を作り出す --数学的理論に基づく細胞運命の制御に成功--. 京都大学プレスリリース. 2018-06-13.Network structures describing regulation between biomolecules have been determined in many biological systems. Dynamics of molecular activities based on such networks are considered to be the origin of many biological functions. Recently, it has been proved mathematically that key nodes for controlling dynamics in networks are identified from network structure alone. Here, we applied this theory to a gene regulatory network for the cell fate specification of seven tissues in the ascidian embryo and found that this network, which consisted of 92 factors, had five key molecules. By controlling the activities of these key molecules, the specific gene expression of six of seven tissues observed in the embryo was successfully reproduced. Since this method is applicable to all nonlinear dynamic systems, we propose this method as a tool for controlling gene regulatory networks and reprogramming cell fates

Laparoscopic Resection of Hilar Cholangiocarcinoma

Background: Surgical resection is the only curative treatment for hilar cholangiocarcinoma. Laparoscopic hepatectomy has been used to treat several types of liver neoplasms. However, technical issues have limited the adoption of laparoscopy for the treatment of hilar cholangiocarcinoma. To date there is only one report of minimally invasive procedure for hilar cholangiocarcinoma in the literature. The present video-assisted procedure shows a laparoscopic resection of hilar cholangiocarcinoma. Patient and Methods: A 43-year-old woman with progressive jaundice due to left-sided hilar cholangiocarcinoma was referred for treatment. The decision was to perform a laparoscopic left hepatectomy with lymphadenectomy and resection of extrahepatic bile ducts. Biliary reconstruction was performed using the hybrid method. Results: Operative time was 300 minutes with minimum blood loss and no need for blood transfusion. Recovery was uneventful, and the patient was discharged on postoperative Day 7. Pathology revealed a well-differentiated cholangiocarcinoma with negative lymph nodes and clear surgical margins. The patient is well with no signs of the disease 18 months after the procedure. Conclusions: Laparoscopic left hepatectomy with lymphadenectomy is safe and feasible in selected patients and when performed by surgeons with expertise in liver surgery and minimally invasive techniques. The use of a hybrid method may be needed for biliary reconstruction, especially in cases where position and size of remnant bile ducts may jeopardize the anastomosis. Further studies are still needed to confirm the benefit of this approach over conventional surgery for hilar cholangiocarcinoma

Effect of conducted adhesions on ischemic colic anastomoses in rats

PURPOSE: Evaluate the effect of conducted adhesions on the mechanical resistance of anastomoses performed in ischemic colon through the Bursting Strength Test and Breaking Strength Test. METHODS: Forty rats were divided into two groups. Group 1 was composed of 20 rats in which the anastomoses were covered with P.V.C. (Polyvinyl Chloride) to prevent the occurrence of adhesions over the anastomotic line. Group 2 was composed of 20 rats in which anastomotic line was covered with epididimal fat besides P.V.C. to prevent formation of other adhesions. RESULTS: The mean Bursting Strength of the anastomoses in the group without adhesion was 10 mmHg and this value was 55.2 mmHg in the group with adhesion (p < 0.05). The mean Breaking Strength of the anastomoses was 142.5 gf in the group without adhesion and 262 gf in the group with adhesion (p < 0.05). CONCLUSION: Based on those mechanical tests, adhesions were benefic to ischemic anastomoses, rising their intrinsic resistance both on Bursting and Breaking Strength.OBJETIVO: Avaliar o efeito das aderências dirigidas sobre a resistência mecânica de anastomoses realizadas em cólon isquêmico através da aplicação dos testes Resistência à Pressão de Explosão e Resistência à Força de Tração. MÉTODOS: Quarenta ratos foram distribuídos igualmente em dois grupos. O Grupo 1 era constituído de vinte animais em que as anastomoses cólicas isquêmicas foram recobertas por uma película de polivinilcloreto (P.V.C.) para impedir a formação de aderências sobre as linhas de sutura e o Grupo 2 era constituído por 20 animais em que as anastomoses cólicas isquêmicas foram recobertas pela gordura epididimal, de forma a constituir uma aderência dirigida sobre a linha de sutura, sendo ainda recobertas por uma película de P.V.C. para impedir a formação de outras aderências. RESULTADOS: A média da Pressão de Ruptura à Distensão por Líquidos da anastomose foi de 10 mmHg no grupo sem aderência e de 55,2 mmHg no grupo com aderência (p < 0,05). A média da Força de Ruptura à Tração das anastomoses foi de 142,5 gf no grupo sem aderências e de 262 gf no grupo com aderência (p < 0,05). CONCLUSÃO: As aderências mostraram ser benéficas, elevando a resistência intrínseca das anastomoses tanto na Resistência à Distensão por Líquido quanto na Resistência à Força de Tração.24725

Clinicopathological characteristics of patients with amyotrophic lateral sclerosis resulting in a totally locked-in state (communication Stage V)

In the present study, we performed a comprehensive analysis to clarify the clinicopathological characteristics of patients with amyotrophic lateral sclerosis (ALS) that had progressed to result in a totally locked-in state (communication Stage V), in which all voluntary movements are lost and communication is impossible. In 11 patients, six had phosphorylated TAR DNA-binding protein 43 (pTDP-43)-immunoreactive (ir) neuronal cytoplasmic inclusions (NCI), two had fused in sarcoma (FUS)-ir NCI, and three had copper/zinc superoxide dismutase (SOD1)-ir NCI. The time from ALS onset to the need for tracheostomy invasive ventilation was less than 24 months in ten patients. Regardless of accumulated protein, all the patients showed common lesions in the pallido–nigro–luysian system, brainstem reticular formation, and cerebellar efferent system, in addition to motor neurons. In patients with pTDP-43-ir NCI, patients with NCI in the hippocampal dentate granule neurons (DG) showed a neuronal loss in the cerebral cortex, and patients without NCI in DG showed a preserved cerebral cortex. By contrast, in patients with FUS-ir NCI, patients with NCI in DG showed a preserved cerebral cortex and patients without NCI in DG showed marked cerebral degeneration. The cerebral cortex of patients with SOD1-ir NCI was preserved. Together, these findings suggest that lesions of the cerebrum are probably not necessary for progression to Stage V. In conclusion, patients with ALS that had progressed to result in communication Stage V showed rapidly-progressed symptoms, and their common lesions could cause the manifestations of communication Stage V

Functional Analysis of Dendritic Cells Generated from T-iPSCs from CD4+ T Cell Clones of Sjögren\u27s Syndrome

Although it is important to clarify the pathogenic functions of T cells in human samples, their examination is often limited due to difficulty in obtaining sufficient numbers of dendritic cells (DCs), used as antigen-presenting cells, especially in autoimmune diseases. We describe the generation of DCs from induced pluripotent stem cells derived from T cells (T-iPSCs). We reprogrammed CD4+ T cell clones from a patient with Sjögren\u27s syndrome (SS) into iPSCs, which were differentiated into DCs (T-iPS-DCs). T-iPS-DCs had dendritic cell-like morphology, and expressed CD11c, HLA-DR, CD80, CD86, and also BDCA-3. Compared with monocyte-derived DCs, the capacity for antigen processing was similar, and T-iPS-DCs induced the proliferative response of autoreactive CD4+ T cells. Moreover, we could evaluate T cell functions of the patient with SS. In conclusion, we obtained adequate numbers of DCs from T-iPSCs, which could be used to characterize pathogenic T cells in autoimmune diseases such as SS

A Novel Zinc Finger Protein Zfp277 Mediates Transcriptional Repression of the Ink4a/Arf Locus through Polycomb Repressive Complex 1

Polycomb group (PcG) proteins play a crucial role in cellular senescence as key transcriptional regulators of the Ink4a/Arf tumor suppressor gene locus. However, how PcG complexes target and contribute to stable gene silencing of the Ink4a/Arf locus remains little understood.We examined the function of Zinc finger domain-containing protein 277 (Zfp277), a novel zinc finger protein that interacts with the PcG protein Bmi1. Zfp277 binds to the Ink4a/Arf locus in a Bmi1-independent manner and interacts with polycomb repressor complex (PRC) 1 through direct interaction with Bmi1. Loss of Zfp277 in mouse embryonic fibroblasts (MEFs) caused dissociation of PcG proteins from the Ink4a/Arf locus, resulting in premature senescence associated with derepressed p16(Ink4a) and p19(Arf) expression. Levels of both Zfp277 and PcG proteins inversely correlated with those of reactive oxygen species (ROS) in senescing MEFs, but the treatment of Zfp277(-/-) MEFs with an antioxidant restored the binding of PRC2 but not PRC1 to the Ink4a/Arf locus. Notably, forced expression of Bmi1 in Zfp277(-/-) MEFs did not restore the binding of Bmi1 to the Ink4a/Arf locus and failed to bypass cellular senescence. A Zfp277 mutant that could not bind Bmi1 did not rescue Zfp277(-/-) MEFs from premature senescence.Our findings implicate Zfp277 in the transcriptional regulation of the Ink4a/Arf locus and suggest that the interaction of Zfp277 with Bmi1 is essential for the recruitment of PRC1 to the Ink4a/Arf locus. Our findings also highlight dynamic regulation of both Zfp277 and PcG proteins by the oxidative stress pathways

Molecular changes in the postmortem parkinsonian brain

Parkinson disease (PD) is the second most common neurodegenerative disease after Alzheimer disease. Although PD has a relatively narrow clinical phenotype, it has become clear that its etiological basis is broad. Post-mortem brain analysis, despite its limitations, has provided invaluable insights into relevant pathogenic pathways including mitochondrial dysfunction, oxidative stress and protein homeostasis dysregulation. Identification of the genetic causes of PD followed the discovery of these abnormalities, and reinforced the importance of the biochemical defects identified post-mortem. Recent genetic studies have highlighted the mitochondrial and lysosomal areas of cell function as particularly significant in mediating the neurodegeneration of PD. Thus the careful analysis of post-mortem PD brain biochemistry remains a crucial component of research, and one that offers considerable opportunity to pursue etiological factors either by ‘reverse biochemistry’ i.e. from defective pathway to mutant gene, or by the complex interplay between pathways e.g. mitochondrial turnover by lysosomes. In this review we have documented the spectrum of biochemical defects identified in PD post-mortem brain and explored their relevance to metabolic pathways involved in neurodegeneration. We have highlighted the complex interactions between these pathways and the gene mutations causing or increasing risk for PD. These pathways are becoming a focus for the development of disease modifying therapies for PD. Parkinson's is accompanied by multiple changes in the brain that are responsible for the progression of the disease. We describe here the molecular alterations occurring in postmortem brains and classify them as: Neurotransmitters and neurotrophic factors; Lewy bodies and Parkinson's-linked genes; Transition metals, calcium and calcium-binding proteins; Inflammation; Mitochondrial abnormalities and oxidative stress; Abnormal protein removal and degradation; Apoptosis and transduction pathways