scholarly journals Classification and Treatment of Diseases in the Age of Genome Medicine Based on Pathway Pathology

2021 ◽  
Vol 22 (17) ◽  
pp. 9418
Author(s):  
Iver Petersen
Keyword(s):  
Cellular Senescence ◽  
Microscopic Analysis ◽  
Cell Types ◽  
International Classification Of Diseases ◽  
Genome Project ◽  
Treatment Modalities ◽  
Medical Work ◽  
Cells Of Origin ◽  
Essential Components ◽  
Cellular Pathology

The focus of pathology as a biomedical discipline is the identification of the pathomechanisms of diseases and the integration of this knowledge into routine diagnosis and classification. Standard tools are macroscopic and microscopic analysis complemented by immunohistochemistry and molecular pathology. So far, classification has been based on the paradigm of cellular pathology established by Rudolf Virchow and others more than 150 years ago, stating that diseases originate from diseased cells. This dogma is meanwhile challenged by the fact that cells can be fully reprogrammed. Many diseases are nowadays considered to originate from undifferentiated stem cells, induced into a diseased state by genetic or epigenetic alterations. In addition, the completion of the Human Genome Project, with the identification of more than 20.000 genes and a much higher number of gene variants and mutations, led to the concept that diseases are dominated by genetics/epigenetics rather than cells of origin. The axiom of cellular pathology, however, still holds true, as cells are the smallest animate units from which diseases originate. Medical doctors and researchers nowadays have to deal with a tremendous amount of data. The International Classification of Diseases will expand from 14.400 entities/codes in ICD-10 to more than 55.000 in ICD-11. In addition, large datasets generated by “genomics“, e.g., whole-genome sequencing, expression profiling or methylome analysis, are meanwhile not only applied in research but also introduced into clinical settings. It constitutes a major task to incorporate all the data into routine medical work. Pathway pathology may help solve this problem. It is based on the realization that diseases are characterized by three essential components: (i) cells of origin/cellular context and (ii) the alteration of cellular as well as (iii) molecular/signal transduction pathways. The concept is illustrated by elaborating on two key cellular pathways, i.e., the cellular senescence of normal cells and the immortality of cancer cells, and by contrasting single cell/single pathway diseases, such as mycoplasma and coughing pneumonia, with complex diseases such as cancer, with multiple cell types as well as multiple affected cellular and signaling pathways. Importantly, the concept of pathway pathology is not just intended to classify disease, but also to conceive new treatment modalities. This article is dedicated to Dr. Leonard Hayflick, who made basic discoveries in pathway pathology not only by identifying cells causing disease (Mycoplasma pneumoniae) and establishing cell strains for treating disease (WI-38 for viral vaccines), but also by first describing cellular senescence and immortality.

CELL AND TISSUE THERAPY OF HEART

2019 ◽  
pp. 77-84
Keyword(s):  
Extracellular Matrix ◽  
Cell Types ◽  
Heart Tissue ◽  
Decellularized Extracellular Matrix ◽  
Tissue Therapy ◽  
Essential Components ◽  
Long Time ◽  
Different Populations ◽  
A Site ◽  
Recipient Tissue

The strategy of heart tissue engineering is simple enough: first remove all the cells from a organ then take the protein scaffold left behind and repopulate it with stem cells immunologically matched to the patient in need. While various suc- cessful methods for decellularization have been developed, and the feasibility of using decellularized whole hearts and extracellular matrix to support cells has been demonstrated, the reality of creating whole hearts for transplantation and of clinical application of decellularized extracellular matrix-based scaffolds will require much more research. For example, further investigations into how lineage-restricted progenitors repopulate the decellularized heart and differentiate in a site-specific manner into different populations of the native heart would be essential. The scaffold heart does not have to be human. Pig hearts carries all the essential components of the extracellular matrix. Through trial and error, scaling up the concentration, timing and pressure of the detergents, researchers have refined the decellularization process on hundreds of hearts and other organs, but this is only the first step. Further, the framework must be populated with human cells. Most researchers in the field use a mixture of two or more cell types, such as endothelial precursor cells to line blood vessels and muscle progenitors to seed the walls of the chambers. The final challenge is one of the hardest: vasculariza- tion, placing a engineered heart into a living animal, integration with the recipient tissue, and keeping it beating for a long time. Much remains to be done before a bioartificial heart is available for transplantation in humans.

scholarly journals Expression of SOX2 and OCT4 in odontogenic cysts and tumors

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Ekarat Phattarataratip ◽  
Tarit Panitkul ◽  
Watunyoo Khodkaew ◽  
Pattarapong Anupuntanun ◽  
Jirapat Jaroonvechatam ◽  
...  
Keyword(s):  
Cell Types ◽  
Odontogenic Cysts ◽  
Positive Staining ◽  
Stem Cell Markers ◽  
Aberrant Expression ◽  
Future Studies ◽  
Sox2 Expression ◽  
Cells Of Origin ◽  
Dentigerous Cysts ◽  
Patient Prognosis

Abstract Background Aberrant expression of stem cell markers has been observed in several types of neoplasms. This trait attributes to the acquired stem-like property of tumor cells and can impact patient prognosis. The objective of this study was to comparatively analyze the expression and significance of SOX2 and OCT4 in various types of odontogenic cysts and tumors. Methods Fifty-five cases of odontogenic cysts and tumors, including 15 ameloblastomas (AM), 5 adenomatoid odontogenic tumors (AOT), 5 ameloblastic fibromas (AF), 5 calcifying odontogenic cysts (COC), 10 dentigerous cysts (DC) and 15 odontogenic keratocysts (OKC) were investigated for the expression of SOX2 and OCT4 immunohistochemically. Results Most OKCs (86.7 %) and all AFs expressed SOX2 in more than 50 % of epithelial cells. Its immunoreactivity was moderate-to-strong in all epithelial cell types in both lesions. In contrast, SOX2 expression was undetectable in AOTs and limited to the ameloblast-like cells in a minority of AM and COC cases. Most DCs showed positive staining in less than 25 % of cystic epithelium. Significantly greater SOX2 expression was noted in OKC compared with DC or AM, and in AF compared with COC or AOT. OCT4 rarely expressed in odontogenic lesions with the immunoreactivity being mild and present exclusively in OKCs. Conclusions SOX2 is differentially expressed in odontogenic cysts and tumors. This could be related to their diverse cells of origin or stages of histogenesis. The overexpression of SOX2 and OCT4 in OKC indicates the acquired stem-like property. Future studies should investigate whether the overexpression of OCT4 and SOX2 contributes to the aggressive behaviors of the tumors.

Glossary of terms used in medicinal chemistry. Part II (IUPAC Recommendations 2013)

2013 ◽  
Vol 85 (8) ◽  
pp. 1725-1758 ◽  
Author(s):  
Derek R. Buckle ◽  
Paul W. Erhardt ◽  
C. Robin Ganellin ◽  
Toshi Kobayashi ◽  
Thomas J. Perun ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Human Genome ◽  
Human Genome Project ◽  
Medicinal Chemistry ◽  
Genome Project ◽  
Scientific Disciplines ◽  
New Concepts ◽  
Essential Components ◽  
The Many ◽  
The Human Genome Project

The evolution that has taken place in medicinal chemistry practice as a result of major advances in genomics and molecular biology arising from the Human Genome Project has carried with it an extensive additional working vocabulary that has become both integrated and essential terminology for the medicinal chemist. Some of this augmented terminology has been adopted from the many related and interlocked scientific disciplines with which the modern medicinal chemist must be conversant, but many other terms have been introduced to define new concepts and ideas as they have arisen. In this supplementary Glossary, we have attempted to collate and define many of the additional terms that are now considered to be essential components of the medicinal chemist’s expanded repertoire.

scholarly journals An inexpensive, customizable microscopy system for the automated quantification and characterization of multiple adherent cell types

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4937 ◽  
Author(s):  
Vishwaratn Asthana ◽  
Yuqi Tang ◽  
Adam Ferguson ◽  
Pallavi Bugga ◽  
Anantratn Asthana ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Dynamic Range ◽  
Low Cost ◽  
Cell Types ◽  
Cell Counting ◽  
Adherent Cell ◽  
Essential Components ◽  
Automated Quantification ◽  
Automated Microscopy ◽  
Multiple Cell

Cell quantification assays are essential components of most biological and clinical labs. However, many currently available quantification assays, including flow cytometry and commercial cell counting systems, suffer from unique drawbacks that limit their overall efficacy. In order to address the shortcomings of traditional quantification assays, we have designed a robust, low-cost, automated microscopy-based cytometer that quantifies individual cells in a multiwell plate using tools readily available in most labs. Plating and subsequent quantification of various dilution series using the automated microscopy-based cytometer demonstrates the single-cell sensitivity, near-perfect R2 accuracy, and greater than 5-log dynamic range of our system. Further, the microscopy-based cytometer is capable of obtaining absolute counts of multiple cell types in one well as part of a co-culture setup. To demonstrate this ability, we recreated an experiment that assesses the tumoricidal properties of primed macrophages on co-cultured tumor cells as a proof-of-principle test. The results of the experiment reveal that primed macrophages display enhanced cytotoxicity toward tumor cells while simultaneously losing the ability to proliferate, an example of a dynamic interplay between two cell populations that our microscopy-based cytometer is successfully able to elucidate.

scholarly journals IGFBP-3, a Marker of Cellular Senescence, Is Overexpressed in Human Papillomavirus-Immortalized Cervical Cells and Enhances IGF-1-Induced Mitogenesis

2004 ◽  
Vol 78 (11) ◽  
pp. 5720-5727 ◽  
Author(s):  
Astrid C. Baege ◽  
Gary L. Disbrow ◽  
Richard Schlegel
Keyword(s):  
Cell Proliferation ◽  
Human Papillomavirus ◽  
Cellular Senescence ◽  
Cell Types ◽  
Enzyme Linked Immunosorbent Assay ◽  
Early Passage ◽  
Retroviral Transduction ◽  
Late Passage ◽  
Cervical Cells ◽  
Igfbp 3

ABSTRACT Human ectocervical cells, following retroviral transduction with the human papillomavirus type 16 E6/E7 oncogenes, are altered in their array of transcribed cellular genes, including increased mRNA for the insulin-like growth factor binding protein 3 (IGFBP-3). IGFBP-3 expression is associated with cellular senescence, and its addition to many cell types inhibits growth or induces apoptosis. By immunoblotting and enzyme-linked immunosorbent assay methods, we demonstrate that late-passage, immortalized E6/E7-transduced cells secrete high levels of IGFBP-3 (25 ng/ml), which represent a 500-fold increase compared to levels in early-passage, nonimmortalized transduced cells (<0.05 ng/ml). Concomitantly, these late-passage cervical cells exhibit an increase in sensitivity to IGF-1, including enhanced phosphorylation of the IGF receptor (IGF-R) and insulin receptor substrate as well as increased DNA synthesis (5-fold) and cell proliferation (3.7-fold). However, there was no change in the level of IGF-R in these cells (surface or total), and the cells did not synthesize IGF-1, indicating that these arms of the IGF pathway were independently regulated and not responsible for the augmented signaling. Consistent with a causal relationship between IGFBP-3 expression and enhanced IGF-1 responses, we found that early-passage cells could be converted to the late-passage, IGF-1-responsive phenotype by preincubation with IGFBP-3. Thus, in contrast to findings with some cell types, IGFBP-3 expression in cervical cells is associated with augmented IGF-1 signaling and cell proliferation and correlates with the timing of cellular immortalization.

scholarly journals What have we learned from basic science studies on idiopathic pulmonary fibrosis?

2019 ◽  
Vol 28 (153) ◽  
pp. 190029 ◽  
Author(s):  
Toyoshi Yanagihara ◽  
Seidai Sato ◽  
Chandak Upagupta ◽  
Martin Kolb
Keyword(s):  
Extracellular Matrix ◽  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Cellular Senescence ◽  
Basic Science ◽  
Science Studies ◽  
Cell Types ◽  
Age Related ◽  
Tremendous Progress

Idiopathic pulmonary fibrosis is a fatal age-related lung disease characterised by progressive and irreversible scarring of the lung. Although the details are not fully understood, there has been tremendous progress in understanding the pathogenesis of idiopathic pulmonary fibrosis, which has led to the identification of many new potential therapeutic targets. In this review we discuss several of these advances with a focus on genetic susceptibility and cellular senescence primarily affecting epithelial cells, activation of profibrotic pathways, disease-enhancing fibrogenic cell types and the role of the remodelled extracellular matrix.

Untraditional methods for targeting the kidney in transgenic mice

2003 ◽  
Vol 285 (6) ◽  
pp. F1027-F1033 ◽  
Author(s):  
Robert A. Bianco ◽  
Henry L. Keen ◽  
Julie L. Lavoie ◽  
Curt D. Sigmund
Keyword(s):  
Gene Expression ◽  
Human Genome Project ◽  
Target Gene ◽  
Cell Types ◽  
Experimental Models ◽  
Genome Project ◽  
Renal Physiology ◽  
Physiological Relevance ◽  
The Human Genome Project

With the completion of the human genome project and the sequencing of many genomes of experimental models, there is a pressing need to determine the physiological relevance of newly identified genes. Gene-targeting approaches have become an important tool in our arsenal to dissect the significance of genes expressed in many tissues. A wealth of experimental models has been made to assess the role of gene expression in renal function and development. The development of new and informative models is presently limited by the anatomic complexity of the kidney and the lack of cell-specific promoters to target the numerous diverse cell types in that organ. Because of this, new approaches may have to be developed. In this review, we will discuss several untraditional methods to target gene expression to the kidney. These approaches should provide some additional tricks and tools to help in developing additional informative models for studying renal physiology.

scholarly journals Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 276 ◽  
Author(s):  
Daniela C. Soto ◽  
Colin Shew ◽  
Mira Mastoras ◽  
Joshua M. Schmidt ◽  
Ruta Sahasrabudhe ◽  
...  
Keyword(s):  
Pan Troglodytes ◽  
Optical Mapping ◽  
Demographic History ◽  
Cell Types ◽  
Genome Project ◽  
Nanopore Sequencing ◽  
Great Ape ◽  
Single Nucleotide Variants ◽  
Short Read ◽  
Pan Troglodytes Troglodytes

Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two additional Pan troglodytes verus individuals, one of whom carries 13% admixture from Pan troglodytes troglodytes. We performed optical mapping of both individuals followed by nanopore sequencing of one individual. Filtering for larger variants (>10 kbp) and combined with genotyping of SVs using short-read data from the Great Ape Genome Project, we identified 425 deletions and 59 inversions, of which 88 and 36, respectively, were novel. Compared with gene expression in humans, we found a significant enrichment of chimpanzee genes with differential expression in lymphoblastoid cell lines and induced pluripotent stem cells, both within deletions and near inversion breakpoints. We examined chromatin-conformation maps from human and chimpanzee using these same cell types and observed alterations in genomic interactions at SV breakpoints. Finally, we focused on 56 genes impacted by SVs in >90% of chimpanzees and absent in humans and gorillas, which may contribute to chimpanzee-specific features. Sequencing a greater set of individuals from diverse subspecies will be critical to establish the complete landscape of genetic variation in chimpanzees.

scholarly journals Baculovirus Infection of Nondividing Mammalian Cells: Mechanisms of Entry and Nuclear Transport of Capsids

2001 ◽  
Vol 75 (2) ◽  
pp. 961-970 ◽  
Author(s):  
Nico-Dirk van Loo ◽  
Elisabetta Fortunati ◽  
Erich Ehlert ◽  
Martijn Rabelink ◽  
Frank Grosveld ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Fluorescent Protein ◽  
Nuclear Transport ◽  
Microscopic Analysis ◽  
Cell Types ◽  
Nuclear Pore ◽  
Fusion Event ◽  
Electron Microscopic ◽  
Cytoplasmic Transport ◽  
Baculovirus Infection

ABSTRACT We have studied the infection pathway of Autographa californica multinuclear polyhedrosis virus (baculovirus) in mammalian cells. By titration with a baculovirus containing a green fluorescent protein cassette, we found that several, but not all, mammalian cell types can be infected efficiently. In contrast to previous suggestions, our data show that the asialoglycoprotein receptor is not required for efficient infection. We demonstrate for the first time that this baculovirus can infect nondividing mammalian cells, which implies that the baculovirus is able to transport its genome across the nuclear membrane of mammalian cells. Our data further show that the virus enters via endocytosis, followed by an acid-induced fusion event, which releases the nucleocapsid into the cytoplasm. Cytochalasin D strongly reduces the infection efficiency but not the delivery of nucleocapsids to the cytoplasm, suggesting involvement of actin filaments in cytoplasmic transport of the capsids. Electron microscopic analysis shows the cigar-shaped nucleocapsids located at nuclear pores of nondividing cells. Under these conditions, we observed the viral genome, major capsid protein, and electron-dense capsids inside the nucleus. This suggests that the nucleocapsid is transported through the nuclear pore. This mode of transport seems different from viruses with large spherical capsids, such as herpes simplex virus and adenovirus, which are disassembled before nuclear transport of the genome. The implications for the application of baculovirus or its capsid proteins in gene therapy are discussed.

scholarly journals Mutation of luxS Affects Biofilm Formation in Streptococcus mutans

2003 ◽  
Vol 71 (4) ◽  
pp. 1972-1979 ◽  
Author(s):  
Justin Merritt ◽  
Fengxia Qi ◽  
Steven D. Goodman ◽  
Maxwell H. Anderson ◽  
Wenyuan Shi
Keyword(s):  
Quorum Sensing ◽  
Streptococcus Mutans ◽  
Biofilm Formation ◽  
Microscopic Analysis ◽  
Homoserine Lactone ◽  
Good Evidence ◽  
Genome Project ◽  
Bacterial Biofilm ◽  
Wild Type

ABSTRACT Quorum sensing is a bacterial mechanism for regulating gene expression in response to changes in population density. Many bacteria are capable of acyl-homoserine lactone-based or peptide-based intraspecies quorum sensing and luxS-dependent interspecies quorum sensing. While there is good evidence about the involvement of intraspecies quorum sensing in bacterial biofilm, little is known about the role of luxS in biofilm formation. In this study, we report for the first time that luxS-dependent quorum sensing is involved in biofilm formation of Streptococcus mutans. S. mutans is a major cariogenic bacterium in the multispecies bacterial biofilm commonly known as dental plaque. An ortholog of luxS for S. mutans was identified using the data available in the S. mutans genome project (http://www.genome.ou.edu/smutans.html ). Using an assay developed for the detection of the LuxS-associated quorum sensing signal autoinducer 2 (AI-2), it was demonstrated that this ortholog was able to complement the luxS negative phenotype of Escherichia coli DH5α. It was also shown that AI-2 is indeed produced by S. mutans. AI-2 production is maximal during mid- to late-log growth in batch culture. Mutant strains devoid of the luxS gene were constructed and found to be defective in producing the AI-2 signal. There are also marked phenotypic differences between the wild type and the luxS mutants. Microscopic analysis of in vitro-grown biofilm structure revealed that the luxS mutant biofilms adopted a much more granular appearance, rather than the relatively smooth, confluent layer normally seen in the wild type. These results suggest that LuxS-dependent signal may play an important role in biofilm formation of S. mutans.

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