Table 2.

Significantly upregulated nuclear matrix proteins in JL-DCIS-3 relative to non-diseased JL-Contra-3.

	Protein symbol	Fold change JL-DCIS-3 relative to JL-Contra-3 proteomics	P value Proteomics	Function	Protein expression MDA-MB231 relative to JL-Contra-3	Protein expression MCF-7 relative to JL-Contra-3
1.	SFRS3	1.334 (↑)	0.001	SFRS3 (serine and arginine-rich splicing factor 3); involved in the regulation of alternative splicing of pre-mRNA molecules	↑	↑*
2.	BAG3	1.401 (↑)	0.015	Bcl-2-associated gene 3; BAG family of co-chaperones that interact with HSP70 (heat shock protein 70)	↓	↓
3.	DDX5	1.479 (↑)	0.026	DEAD-box helicase 5; pre-mRNA splicing, mRNA export, translation, and decay	↑	↑*
4.	SNRPD3	1.616 (↑)	0.027	Small nuclear ribonucleoprotein D3; component of the spliceosome	↑	↑*
5.	PLEC1	1.946 (↑)	0.000001	Plectin 1; cell structure and organization, as well as in signaling pathways and cellular functions such as cell motility, adhesion, and survival	↑*	↓
6.	ATP5A1	2.028 (↑)	0.039	ATP synthase subunit alpha; responsible to produce ATP (adenosine triphosphate) in the mitochondria of cells, been suggested to play a role in cancer cell metabolism and survival	↑	↑*
7.	HSPB1	2.060 (↑)	0.023	Heat Shock Protein Family B Member 1, aka HSP27; induced in response to various cellular stresses, including heat shock, oxidative stress, and exposure to toxins or radiation	↓	↑*
8.	PRSS1	2.152 (↑)	0.048	Serine Protease I (trypsin); promotes cancer cell proliferation, invasion, etc.	↓	↑
9.	DSP	2.159 (↑)	0.003	Desmoplakin; obligate component of functional desmosomes, inactivated in cancer	↑	↑
10.	ANXA1	2.290 (↑)	0.014	Annexin A1 is a member of the annexin family of calcium-dependent phospholipid-binding proteins, role in inflammation, cell differentiation, and apoptosis	↑	↓*
11.	PDAP1	2.402 (↑)	0.037	Platelet-derived growth factor (PDGF); multifunctional protein that plays a role in several cellular processes, including DNA replication, repair, and apoptosis, increased in cancer, might be specific to DCIS	↓	↓*
12.	KRT1	2.960 (↑)	0.011	Keratin 1; structural protein major component of the cytoskeleton in epithelial cells.	↑	↓
13.	SFRS7	2.964 (↑)	0.012	SFRS7 (Splicing factor, arginine/serine-rich 7); involved in pre-mRNA splicing, regulation of alternative splicing, involved in the splicing of several genes related to cancer: CD44, BRCA1, and BCL-X. Dysregulation of SFRS7 expression and splicing activity has been linked to various cancers	↑	↑*
14.	RPL11	3.669 (↑)	0.021	ribosomal protein that is a component of the 60S subunit of the ribosome, implicated in cancer, interacts with MDM2	↑	↓
15.	RPL7A	3.951 (↑)	0.049	ribosomal protein: plays a regulatory role in the translation apparatus, implicated in cancer	↑	↓
16.	RPL31	4.000 (↑)	0.018	ribosomal protein: In addition to its role in protein synthesis, RPL31 has also been implicated in cancer development and progression. Studies have shown that RPL31 expression is elevated in prostate, gastric and colorectal cancers	↑	↑
17.	TPM1	4.333 (↑)	0.012	Tropomyosin 1; mechanical integrity of the cell, regulating cell shape, adhesion, and migration, may promote tumor invasion by downregulating Ecadherin and upregulating MMPs	↑	↓
18.	MECP2	4.663 (↑)	0.002	Methyl-CpG-binding protein 2; binds to methylated DNA and plays a role in silencing genes that are not needed by a particular cell type	↑*	↓
19.	RPL8	5.462 (↑)	0.002	Ribosomal Protein L8; protein component of the ribosome, role in the binding and positioning of tRNAs during translation	↑	↓
20.	ALB	6.944 (↑)	0.003	Albumin; transports hormones, fatty acids, etc.	↑	↓
21.	CKAP4	7.550 (↑)	0.0002	Cytoskeleton-Associated Protein 4; crucial role in the organization and maintenance of the cellular ER, implicated in cell proliferation and migration, vesicle transport	↑*	↓*

↓ downregulated, ↑ upregulated, * significant at P < 0.05.