ArticleJournal of proteome research2015
Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 14 citations in OpenAlex.
- Identification and validation of hub genes and molecular classifications associated with chronic myeloid leukemia.Frontiers in immunology · 2023Article
- Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts.Frontiers in public health · 2023Article
- Cellular, transcriptomic and isoform heterogeneity of breast cancer cell line revealed by full-length single-cell RNA sequencing.Computational and structural biotechnology journal · 2020Article
- Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17.Journal of proteome research · 2018Article
- Alternative Splicing as a Target for Cancer Treatment.International journal of molecular sciences · 2018Review
- Advances in the Chromosome-Centric Human Proteome Project: looking to the future.Expert review of proteomics · 2017Review
- ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly.Nucleic acids research · 2017Article
- Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.Methods in molecular biology (Clifton, N.J.) · 2017Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
This study was conducted as a part of the Chromosome-Centric Human Proteome Project (C-HPP) of the Human Proteome Organization. The main objective is to identify and evaluate functionality of a set of specific noncanonical isoforms expressed in HER2-neu positive, estrogen receptor negative (ER-), and progesterone receptor negative (PR-) breast cancers (HER2+/ER-/PR- BC), an aggressive subtype of breast cancers that cause significant morbidity and mortality. We identified 11 alternative splice isoforms that were differentially expressed in HER2+/ER-/PR- BC compared to normal mammary, triple negative breast cancer and triple positive breast cancer tissues (HER2+/ER+/PR+). We used a stringent criterion that differentially expressed noncanonical isoforms (adjusted p value < 0.05) and have to be expressed in all replicates of HER2+/ER-/PR- BC samples, and the trend in differential expression (up or down) is the same in all comparisons. Of the 11 protein isoforms, six were overexpressed in HER2+/ER-/PR- BC. We explored possible functional roles of these six proteins using several complementary computational tools. Biological processes including cell cycle events and glycolysis were linked to four of these proteins. For example, glycolysis was the top ranking functional process for DMXL2 isoform 3, with a fold change of 27 compared to just two for the canonical protein. No previous reports link DMXL2 with any metabolic processes; the canonical protein is known to participate in signaling pathways. Our results clearly indicate distinct functions for the six overexpressed alternative splice isoforms, and these functions could be specific to HER2+/ER-/PR- tumor progression. Further detailed analysis is warranted as these proteins could be explored as potential biomarkers and therapeutic targets for HER2+/ER-/PR- BC patients.
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Registered trials
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