Probably less than one-tenth of the genes produce only the wild type protein without at least one additional protein isoform in some human cancer cell lines

// Rui Yan 1 , Ju Zhang 2 , Lucas Zellmer 3 , Lichan Chen 3 , Di Wu 4 , Siqi Liu 2 , Ningzhi Xu 5 and Joshua D. Liao 6 1 Nephrology Department, Guizhou Medical University Hospital, Guiyang, P.R. China 2 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China 3 Hormel Institute, University of Minnesota, Austin, Minnesota, USA 4 Beijing Protein Innovation Co., Ltd, Beijing, P.R. China 5 Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China 6 Department of Pathology, Guizhou Medical University Hospital, Guiyang, P.R. China Correspondence to: Rui Yan, email: yanrui@gmc.edu.cn Siqi Liu, email: siqiliu@genomics.cn Ningzhi Xu, email: xuningzhi@cicams.ac.cn Joshua D. Liao, email: djliao@gmc.edu.cn Keywords: proteomics, mass spectrometry, protein isoform, western blotting, immunohistochemical staining Received: March 14, 2017     Accepted: June 30, 2017     Published: August 07, 2017 ABSTRACT To estimate how many genes produce multiple protein isoforms, we electrophoresed proteins from MCF7 and MDA-MB231 (MB231) human breast cancer cells in SDS-PAGE and excised narrow stripes of the gel at the 48kD, 55kD and 72kD. Proteins in these stripes were identified using liquid chromatography and tandem mass spectrometry. A total of 765, 750 and 679 proteins from MB231 cells, as well as 470, 390 and 490 proteins from MCF7 cells, were identified from the 48kD, 55kD and 72kD stripes, respectively. We arbitrarily allowed a 10% technical variation from the proteins’ theoretical molecular mass (TMM) and considered those proteins with their TMMs within the 43-53 kD, 49-61 kD and 65-79 kD ranges as the wild type (WT) expected from the corresponding stripe, whereas those with a TMM above or below this range as a smaller- or larger-group, respectively. Only 263 (34.4%), 269 (35.9%) and 151 (22.2%) proteins from MB231 cells and 117 (24.9%), 135 (34.6%) and 130 (26.5%) proteins from MCF7 cells from the 48kD, 55kD and 72kD stripes, respectively, belonged to the WT, while the remaining majority belonged to the smaller- or larger-groups. Only about 3-16%, on average about 10% regardless of the stripe and cell line, of the proteins appeared in only one stripe and within the WT range, while the remaining preponderance appeared also in additional stripe(s) or had a larger or smaller TMM. We conclude that few (fewer than 10%) of the human genes produce only the WT protein without additional isoform(s).