Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER–/PR– Breast Cancers, a Chromosome 17 C-HPP Study

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.

Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks

“…For example, we have characterized splice isoforms of Her2/ERBB2+ breast cancers from humans and in mouse models [2, 3]. …”

The intricacy of biomarker complexity–the identification of a genuine proteomic biomarker is more complicated than believed

“…Translated into the terms of preclinical searches for proteomic biomarker, the protein altered in disease and identified by mass spectrometry very probably applies only to part of the total number of all proteoforms related to the peptides identified. This is shown impressively and discussed, for example, for splice variants , for glycoforms of apo‐lipoproteins , and of acute phase proteins . Such variants can be detected after pre‐fractionation of proteins with intact mass and by lysine counts , by pI‐variants , and by western blots .…”

Pathology-Driven Comprehensive Proteomic Profiling of the Prostate Cancer Tumor Microenvironment

“…Notably, splice isoforms of Kinectin were found to upregulated in epithelial tissue form both GS3 and GS4 tumors. The same splice isoforms of Kinectin have previously been identified as one of six overexpressed splice isoforms associated with HER2 þ /ER À /PR À breast cancer and are thought to have a role in HER þ /ER À /PR À tumor progression (23). The proteins significantly changed between the associated stroma of Gleason 3 and Gleason 4 tumor regions were also analyzed.…”