scholarly journals High Content Analysis Across Signaling Modulation Treatments for Subcellular Target Identification Reveals Heterogeneity in Cellular Response

2021 ◽  
Vol 8 ◽  
Author(s):  
Sayan Biswas
Keyword(s):  
Cellular Response ◽  
Phenotypic Diversity ◽  
Target Identification ◽  
Bone Cancer ◽  
Cancer Cell Line ◽  
Bioactive Compound ◽  
Subcellular Target ◽  
Respective Treatment ◽  
Cellular Phenotypes ◽  
The Impact

Cellular phenotypes on bioactive compound treatment are a result of the downstream targets of the respective treatment. Here, a computational approach is taken for downstream subcellular target identification to understand the basis of the cellular response. This response is a readout of cellular phenotypes captured from cell-painting-based light microscopy images. The readouts are morphological profiles measured simultaneously from multiple cellular organelles. Cellular profiles generated from roughly 270 diverse treatments on bone cancer cell line form the high content screen used in this study. Phenotypic diversity across these treatments is demonstrated, depending on the image-based phenotypic profiles. Furthermore, the impact of the treatments on specific organelles and associated organelle sensitivities are determined. This revealed that endoplasmic reticulum has a higher likelihood of being targeted. Employing multivariate regression overall cellular response is predicted based on fewer organelle responses. This prediction model is validated against 1,000 new candidate compounds. Different compounds despite driving specific modulation outcomes elicit a varying effect on cellular integrity. Strikingly, this confirms that phenotypic responses are not conserved that enables quantification of signaling heterogeneity. Agonist-antagonist signaling pairs demonstrate switch of the targets in the cascades hinting toward evidence of signaling plasticity. Quantitative analysis of the screen has enabled the identification of these underlying signatures. Together, these image-based profiling approaches can be employed for target identification in drug and diseased states and understand the hallmark of cellular response.

scholarly journals Reproduction in Trypanosomatids: Past and Present

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 471
Author(s):  
Camino Gutiérrez-Corbo ◽  
Bárbara Domínguez-Asenjo ◽  
María Martínez-Valladares ◽  
Yolanda Pérez-Pertejo ◽  
Carlos García-Estrada ◽  
...  
Keyword(s):  
Low Income ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Genetic Exchange ◽  
Health Concern ◽  
Current Debate ◽  
Naturally Occurring ◽  
Experimental Works ◽  
Genomic Recombination ◽  
The Impact

Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.

scholarly journals 3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

2020 ◽  
Vol 49 (D1) ◽  
pp. D38-D46
Author(s):  
Kyukwang Kim ◽  
Insu Jang ◽  
Mooyoung Kim ◽  
Jinhyuk Choi ◽  
Min-Seo Kim ◽  
...  
Keyword(s):  
Cell Line ◽  
Large Scale ◽  
Three Dimensional ◽  
Cancer Cell Line ◽  
Cancer Genome ◽  
Structural Variations ◽  
3D Genome ◽  
Tightly Coupled ◽  
Regulatory Effects ◽  
The Impact

Abstract Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

scholarly journals Seeding of breast cancer cell line (MDA-MB-231LUC+) to the mandible induces overexpression of substance P and CGRP throughout the trigeminal ganglion and widespread peripheral sensory neuropathy throughout all three of its divisions

2021 ◽  
Vol 17 ◽  
pp. 174480692110240
Author(s):  
Silvia Gutierrez ◽  
James C Eisenach ◽  
M Danilo Boada
Keyword(s):  
Breast Cancer ◽  
Substance P ◽  
Cancer Cells ◽  
Cell Line ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Trigeminal Ganglion ◽  
Breast Cancer Cell Line ◽  
Cancer Cell Line ◽  
The Impact

Some types of cancer are commonly associated with intense pain even at the early stages of the disease. The mandible is particularly vulnerable to metastasis from breast cancer, and this process has been studied using a bioluminescent human breast cancer cell line (MDA-MB-231LUC+). Using this cell line and anatomic and neurophysiologic methods in the trigeminal ganglion (TG), we examined the impact of cancer seeding in the mandible on behavioral evidence of hypersensitivity and on trigeminal sensory neurons. Growth of cancer cells seeded to the mandible after arterial injection of the breast cancer cell line in Foxn1 animals (allogeneic model) induced behavioral hypersensitivity to mechanical stimulation of the whisker pad and desensitization of tactile and sensitization of nociceptive mechanically sensitive afferents. These changes were not restricted to the site of metastasis but extended to sensory afferents in all three divisions of the TG, accompanied by widespread overexpression of substance P and CGRP in neurons through the ganglion. Subcutaneous injection of supernatant from the MDA-MB-231LUC+ cell culture in normal animals mimicked some of the changes in mechanically responsive afferents observed with mandibular metastasis. We conclude that released products from these cancer cells in the mandible are critical for the development of cancer-induced pain and that the overall response of the system greatly surpasses these local effects, consistent with the widespread distribution of pain in patients. The mechanisms of neuronal plasticity likely occur in the TG itself and are not restricted to afferents exposed to the metastatic cancer microenvironment.

scholarly journals Impact of Carcinogenic Chromium on the Cellular Response to Proteotoxic Stress

2019 ◽  
Vol 20 (19) ◽  
pp. 4901 ◽  
Author(s):  
Leonardo M. R. Ferreira ◽  
Teresa Cunha-Oliveira ◽  
Margarida C. Sobral ◽  
Patrícia L. Abreu ◽  
Maria Carmen Alpoim ◽  
...  
Keyword(s):  
Stress Response ◽  
Health Effects ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Critical Role ◽  
Chemical Properties ◽  
Adverse Health Effects ◽  
Proteotoxic Stress ◽  
Adverse Health ◽  
The Impact

Worldwide, several million workers are employed in the various chromium (Cr) industries. These workers may suffer from a variety of adverse health effects produced by dusts, mists and fumes containing Cr in the hexavalent oxidation state, Cr(VI). Of major importance, occupational exposure to Cr(VI) compounds has been firmly associated with the development of lung cancer. Counterintuitively, Cr(VI) is mostly unreactive towards most biomolecules, including nucleic acids. However, its intracellular reduction produces several species that react extensively with biomolecules. The diversity and chemical versatility of these species add great complexity to the study of the molecular mechanisms underlying Cr(VI) toxicity and carcinogenicity. As a consequence, these mechanisms are still poorly understood, in spite of intensive research efforts. Here, we discuss the impact of Cr(VI) on the stress response—an intricate cellular system against proteotoxic stress which is increasingly viewed as playing a critical role in carcinogenesis. This discussion is preceded by information regarding applications, chemical properties and adverse health effects of Cr(VI). A summary of our current understanding of cancer initiation, promotion and progression is also provided, followed by a brief description of the stress response and its links to cancer and by an overview of potential molecular mechanisms of Cr(VI) carcinogenicity.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

EP.WE.629The effect of different anaesthetic agents in postsurgical inflammatory response in thoracic surgery: a systematic review

2021 ◽  
Vol 108 (Supplement_7) ◽  
Author(s):  
Julian Aquilina ◽  
Georgios Geropoulos ◽  
Ioannis Loufopoulos ◽  
Anaya Gupte ◽  
Sofoklis Mitsos ◽  
...  
Keyword(s):  
Systematic Review ◽  
Inflammatory Response ◽  
Thoracic Surgery ◽  
Cellular Response ◽  
Interferon Γ ◽  
Anaesthetic Agents ◽  
Systemic Inflammatory Reaction ◽  
Immunological Effects ◽  
Immune Changes ◽  
The Impact

Abstract Aims Post-operative systemic inflammatory reaction is part of the stress response caused by major thoracic surgery. Different anaesthetic agents used affect different immunological phenomena. This systematic review evaluates the impact of anaesthetic agents on the immunological profile and the associated clinical significance. Methods A systematic review of MEDLINE, EMBASE and Cohrane databases to explore how different anaesthetic agents affect post-operative inflammatory response. Results A total of nine studies were included in our analysis. Peri-operative use of dexmedetomidine, propofol, sevoflurane, isoflurane, ropivacaine, sufentanil, naloxone and clonidine were compared, based on their effect on the systemic release of inflammatory markers. Variance on the levels of the circulating inflammatory molecules such as interleukins, interferon-γ, tumor necrosis factor a and on the cellular response including natural killer, CD4 and CD8 T cells, were observed among different anaesthetic agents. Conclusions Inflammation improves immunity and regenerative cell recruitment, however excessive responses can lead to delayed wound healing, organ dysfunction and increased morbidity and mortality. There is still uncertainty regarding the role of immune changes on clinical outcomes of patients undergoing thoracic surgery, and more research is needed to explore other immunological effects related to anaesthetic agents.

scholarly journals The Impact of Genetic Variants on PTEN Molecular Functions and Cellular Phenotypes

2019 ◽  
Vol 9 (11) ◽  
pp. a036228
Author(s):  
Nicholas Hasle ◽  
Kenneth A. Matreyek ◽  
Douglas M. Fowler
Keyword(s):  
Genetic Variants ◽  
Molecular Functions ◽  
Cellular Phenotypes ◽  
The Impact

scholarly journals The impact of bone cancer on the peripheral encoding of mechanical pressure stimuli

Pain ◽  
2020 ◽  
Vol Publish Ahead of Print ◽  
Author(s):  
Mateusz W. Kucharczyk ◽  
Kim I. Chisholm ◽  
Franziska Denk ◽  
Anthony H. Dickenson ◽  
Kirsty Bannister ◽  
...  
Keyword(s):  
Bone Cancer ◽  
Mechanical Pressure ◽  
The Impact

scholarly journals UDP-glucuronosyltransferase 2B15 (UGT2B15) and UGT2B17 Enzymes Are Major Determinants of the Androgen Response in Prostate Cancer LNCaP Cells

2007 ◽  
Vol 282 (46) ◽  
pp. 33466-33474 ◽  
Author(s):  
Sarah Chouinard ◽  
Olivier Barbier ◽  
Alain Bélanger
Keyword(s):  
Culture Media ◽  
Cancer Cell Line ◽  
Mrna Levels ◽  
Uridine Diphosphate ◽  
Lncap Cells ◽  
Protein Levels ◽  
Prostate Cells ◽  
Target Probe ◽  
Interfering Rna ◽  
The Impact

Uridine diphosphate-glucuronosyltransferase 2 (UGT2)B15 and B17 enzymes conjugate dihydrotestosterone (DHT) and its metabolites androstane-3α, 17β-diol (3α-DIOL) and androsterone (ADT). The presence of UGT2B15/B17 in the epithelial cells of the human prostate has been clearly demonstrated, and significant 3α-DIOL glucuronide and ADT-glucuronide concentrations have been detected in this tissue. The human androgen-dependent cancer cell line, LNCaP, expresses UGT2B15 and -B17 and is also capable of conjugating androgens. To assess the impact of these two genes in the inactivation of androgens in LNCaP cells, their expression was inhibited using RNA interference. The efficient inhibitory effects of a UGT2B15/B17 small interfering RNA (siRNA) probe was established by the 70% reduction of these UGT mRNA levels, which was further confirmed at the protein levels. The glucuronidation of dihydrotestosterone (DHT), 3α-DIOL, and ADT by LNCaP cell homogenates was reduced by more than 75% in UGT2B15/B17 siRNA-transfected LNCaP cells when compared with cells transfected with a non-target probe. In UGT2B15/B17-deficient LNCaP cells, we observe a stronger response to DHT than in control cells, as determined by cell proliferation and expression of eight known androgen-sensitive genes. As expected, the amounts of DHT in cell culture media from control cells were significantly lower than that from UGT2B15/B17 siRNA-treated cells, which was caused by a higher conversion to its corresponding glucuronide derivative. Taken together these data support the idea that UGT2B15 and -B17 are critical enzymes for the local inactivation of androgens and that glucuronidation is a major determinant of androgen action in prostate cells.

Effect of Color Coding on Visually and Verbally Oriented Tests with Students of Different Field Dependence Levels

1992 ◽  
Vol 20 (4) ◽  
pp. 311-320 ◽  
Author(s):  
Francis M. Dwyer ◽  
David M. Moore
Keyword(s):  
Field Dependence ◽  
Information Acquisition ◽  
Color Coding ◽  
Treatment Groups ◽  
Black And White ◽  
Field Dependent ◽  
Different Types ◽  
Respective Treatment ◽  
The Impact ◽  
Instructional Variable

To assess the impact of instructional color coding on visually and verbally oriented tests and on field-dependent-independent subjects, undergraduate college students (119) were randomly assigned to two treatment groups (color—black and white). These subjects received their respective treatment and received four dependent measures measuring four different types of educational objectives. Results indicated that the subject's level of field dependence is an important instructional variable and that color coding is an effective variable for maximizing information acquisition levels for field dependent over oriented subjects.

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