Pleiotropic combinatorial transcriptomes of human breast cancer cells exposed to mixtures of dietary phytoestrogens

Dip, Ramiro; Lenz, Sarah; Gmuender, Hans; Naegeli, Hanspeter

doi:10.1016/j.fct.2009.01.008

Cited by 15 publications

(6 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Human H3C1 acts as a client protein of liquid-liquid phase separation (LLPS) in nucleolus ( 54 ), interacts with 2790 other proteins, is post-transcriptionally targeted by 14 miRNAs according to the annotations in miRTarBase ( 55 ). With 221 resolved 3D structures in PDB ( 38 ), H3C1 could be targeted by 65 chemicals, such as calcitriol ( 56 ), berberine ( 57 ) and coumestrol ( 58 ). According to the annotations of The Cancer Genome Atlas (TCGA) ( 59 ), the mRNA of H3C1 was highly expressed in thymoma (THYM), UCEC, and uterine carcinosarcoma (UCS).…”

Section: Discussionmentioning

confidence: 99%

CPLM 4.0: an updated database with rich annotations for protein lysine modifications

Zhang

Tan

Lin

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

Here, we reported the compendium of protein lysine modifications (CPLM 4.0, http://cplm.biocuckoo.cn/), a data resource for various post-translational modifications (PTMs) specifically occurred at the side-chain amino group of lysine residues in proteins. From the literature and public databases, we collected 450 378 protein lysine modification (PLM) events, and combined them with the existing data of our previously developed protein lysine modification database (PLMD 3.0). In total, CPLM 4.0 contained 592 606 experimentally identified modification events on 463 156 unique lysine residues of 105 673 proteins for up to 29 types of PLMs across 219 species. Furthermore, we carefully annotated the data using the knowledge from 102 additional resources that covered 13 aspects, including variation and mutation, disease-associated information, protein-protein interaction, protein functional annotation, DNA & RNA element, protein structure, chemical-target relation, mRNA expression, protein expression/proteomics, subcellular localization, biological pathway annotation, functional domain annotation, and physicochemical property. Compared to PLMD 3.0 and other existing resources, CPLM 4.0 achieved a >2-fold increase in collection of PLM events, with a data volume of ∼45GB. We anticipate that CPLM 4.0 can serve as a more useful database for further study of PLMs.

show abstract

Section: Discussionmentioning

confidence: 99%

CPLM 4.0: an updated database with rich annotations for protein lysine modifications

Zhang

Tan

Lin

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…The effects of the phytoestrogens may well be related to the particular components and doses in the diet [ 609 ], and cellular effects may vary depending on concentration and timing. In a study examining the effects of different types and concentrations of phytoestrogens on the expression of estrogen-dependent gene activity in human breast cancer cells grown in vitro (MCF-7 cells), low doses of genistein resulted in a pattern of expression that indicated increased cell proliferation, while somewhat higher concentrations led to increased apoptosis [ 610 ].…”

Section: Evidence Linking Environmental Factors and Breast Cancermentioning

confidence: 99%

State of the evidence 2017: an update on the connection between breast cancer and the environment

et al. 2017

View full text Add to dashboard Cite

BackgroundIn this review, we examine the continually expanding and increasingly compelling data linking radiation and various chemicals in our environment to the current high incidence of breast cancer.AbstractSingly and in combination, these toxicants may have contributed significantly to the increasing rates of breast cancer observed over the past several decades. Exposures early in development from gestation through adolescence and early adulthood are particularly of concern as they re-shape the program of genetic, epigenetic and physiological processes in the developing mammary system, leading to an increased risk for developing breast cancer. In the 8 years since we last published a comprehensive review of the relevant literature, hundreds of new papers have appeared supporting this link, and in this update, the evidence on this topic is more extensive and of better quality than that previously available.ConclusionIncreasing evidence from epidemiological studies, as well as a better understanding of mechanisms linking toxicants with development of breast cancer, all reinforce the conclusion that exposures to these substances – many of which are found in common, everyday products and byproducts – may lead to increased risk of developing breast cancer. Moving forward, attention to methodological limitations, especially in relevant epidemiological and animal models, will need to be addressed to allow clearer and more direct connections to be evaluated.

show abstract

“…It is a damage-specific DNA binding protein, which involves various biological functions including protein autoubiquitination, protein polyubiquitination, pyrimidine dimer repair and participates in the nucleotide excision repair pathway. It interacts with 17β-estradiol [ 16 ], an endogenous estrogen that usually undergoes a substantial metabolic process in rat livers regulated by cychrome P450. It also interacts with TCDD (2,3,7,8-tetrachlorodibenzodioxine) and 2,4-D (2,4-Dichlorophenoxyacetic acid), two well-known environmental toxicants [ 17 ].…”

Section: Resultsmentioning

confidence: 99%

Of text and gene – using text mining methods to uncover hidden knowledge in toxicogenomics

et al. 2014

View full text Add to dashboard Cite

BackgroundToxicogenomics studies often profile gene expression from assays involving multiple doses and time points. The dose- and time-dependent pattern is of great importance to assess toxicity but computational approaches are lacking to effectively utilize this characteristic in toxicity assessment. Topic modeling is a text mining approach, but may be used analogously in toxicogenomics due to the similar data structures between text and gene dysregulation.ResultsTopic modeling was applied to a very large toxicogenomics dataset containing microarray gene expression data from >15,000 samples associated with 131 drugs tested in three different assay platforms (i.e., in vitro assay, in vivo repeated dose study and in vivo single dose experiment) with a design including multiple doses and time points. A set of “topics” which each consist of a set of genes was determined, by which the varying sensitivity of three assay systems was observed. We found that the drug-dependent effect was more pronounced in the two in vivo systems than the in vitro system, while the time-dependent effect was most strongly reflected in the in vitro system followed by the single dose study and lastly the repeated dose experiment. The dose-dependent effect was similar across three assay systems. Although the results indicated a challenge to extrapolate the in vitro results to the in vivo situation, we did notice that, for some drugs but not for all the drugs, the similarity in gene expression patterns was observed across all three assay systems, indicating a possibility of using in vitro systems with careful designs (such as the choice of dose and time point), to replace the in vivo testing strategy. Nonetheless, a potential to replace the repeated dose study by the single-dose short-term methodology was strongly implied.ConclusionsThe study demonstrated that text mining methodologies such as topic modeling provide an alternative method compared to traditional means for data reduction in toxicogenomics, enhancing researchers’ capabilities to interpret biological information.

show abstract

Pleiotropic combinatorial transcriptomes of human breast cancer cells exposed to mixtures of dietary phytoestrogens

Cited by 15 publications

References 44 publications

CPLM 4.0: an updated database with rich annotations for protein lysine modifications

CPLM 4.0: an updated database with rich annotations for protein lysine modifications

State of the evidence 2017: an update on the connection between breast cancer and the environment

Of text and gene – using text mining methods to uncover hidden knowledge in toxicogenomics

Contact Info

Product

Resources

About