Table 1.
Significantly downregulated 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. | KRT8 | 1.454(↓) | 0.038 | Keratin, type II cytoskeletal 8; dimerizes with keratin 18 to form an intermediate filament in simple single-layered epithelial cells | ↓ | ↑* |
| 2. | HNRNPM | 1.541 (↓) | 0.034 | Isoform 1 of Heterogeneous nuclear ribonucleoprotein M; RNA binding, complexes with hnRNA. Associated with pre-mRNAs, influence pre-mRNA processing and aspects of mRNA metabolism and transport. Shuttles between the nucleus and the cytoplasm. | ↓ | ↑ |
| 3. | VIM | 1.693 (↓) | 0.00007 | Vimentin; organizer other critical proteins involved in attachment, migration, and signaling | ↓* | ↓* |
| 4. | RPS7 | 1.811 (↓) | 0.007 | 40S ribosomal protein S7; involved in protein synthesis | ↓ | ↑ |
| 5. | RBMX | 1.902 (↓) | 0.037 | RNA binding motif protein X-linked; Involved in RNA processing, splicing, cellular stress responses | ↓ | ↓ |
| 6. | SPTAN1 | 1.992 (↓) | 0.0001 | Isoform 3 of Spectrin alpha chain; filamentous cytoskeletal protein implicated in cell polarity, DNA repair (enables repair of cisplatin crosslinks) and cell cycle regulation, possible tumor suppressor, enhanced in some cancers decreased in others | ↓* | ↓* |
| 7. | RPS21 | 2.121 (↓) | 0.041 | 40S ribosomal protein S21; a component of the ribosome and is involved in protein synthesis | ↓* | ↓* |
| 8. | HNRNPA3 | 2.135 (↓) | 0.001 | Isoform 1 of Heterogeneous nuclear ribonucleoprotein A3; Enables RNA binding activity. Involved in mRNA splicing, via spliceosome. | ↑ | ↑* |
| 9. | HNRNPK | 2.204 (↓) | 0.034 | similar to Heterogeneous nuclear ribonucleoprotein K; involved in RNA processing, splicing, and transcriptional regulation. | ↓* | ↓* |
| 10. | HSP90B1 | 2.296 (↓) | 0.005 | HSP90B1 Endoplasmin; involved in protein folding, maturation, and stabilization. | ↑ | ↑* |
| 11. | CLTB | 2.308 (↓) | 0.005 | Component of the clathrin-coated vesicles and is involved in endocytosis and intracellular trafficking. | ↓* | ↓* |
| 12. | NONO | 2.313 (↓) | 0.002 | Non-POU domain-containing octamer-binding protein | ↑ | ↑* |
| 13. | SFPQ | 2.341 (↓) | 0.0002 | Isoform Long of Splicing factor; involved in DNA repair, telomere maintenance, neuronal development, promote proper splicing of pre-mRNA | ↑ | ↑* |
| 14. | RP11 | 2.439 (↓) | 0.035 | Isoform 1 of 60S ribosomal protein L11 | ↓ | ↓ |
| 15. | TPM4 | 2.457 (↓) | 0.031 | Isoform 1 of Tropomyosin alpha-4 chain; component of the cytoskeleton, maintains cell shape and integrity | ↓* | ↓* |
| 16. | BUD31 | 2.524 (↓) | 0.004 | Protein BUD31 homolog; involved in RNA processing and splicing | ↑ | ↑ |
| 17. | HNRNPAB | 2.599 (↓) | 0.002 | Isoform 3 of Heterogeneous nuclear ribonucleoprotein A/B; involved in RNA metabolism, including pre-mRNA splicing, mRNA transport, and translation | ↑ | ↑* |
| 18. | CBX3 | 2.709 (↓) | 0.047 | chromobox protein homolog 3; involved in chromatin remodeling and gene expression regulation | ↓ | ↓* |
| 19. | NUDC | 2.843 (↓) | 0.020 | Nuclear migration protein C; involved in mitosis and cell division. | ↓* | ↓ |
| 20. | EEF1B2 | 3.035 (↓) | 0.002 | Elongation factor 1-beta 2; involved in protein synthesis and elongation | ↓* | ↓* |
| 21. | TXLNA | 3.385 (↓) | 0.031 | Alpha-taxilin; involved in intracellular transport and vesicles | ↓ | ↓ |
| 22. | NCL | 3.651 (↓) | 3.51E-10 | Nucleolin; ribosome biogenesis and RNA processing | ↓* | ↓ |
| 23. | HNRNPH1 | 3.731 (↓) | 0.041 | heterogeneous nuclear ribonucleoprotein H1, which is involved in RNA splicing and processing | ↑ | ↑ |
| 24. | HMGA1 | 4.032 (↓) | 0.006 | Isoform HMG-I of High mobility group protein; involved in chromatin structure and transcriptional regulation | ↑ | ↓* |
| 25. | DNAJB1 | 4.057 (↓) | 0.005 | DNAJ homolog subfamily B member 1; a chaperone protein subclass of HSP 40 family, that helps to fold and stabilize other proteins, stabilizes MDM2, can serve as a metastasis promoter or suppressor | ↓* | ↓ |
| 26. | LIMA1 | 4.161 (↓) | 0.023 | Isoform Beta of LIM domain and actin-binding protein 1; cytoskeletal organization and cell motility | ↓ | ↓ |
| 27. | PABPN1 | 4.202 (↓) | 0.041 | Isoform 1 of Polyadenylate-binding protein nuclear 2; involved in mRNA processing and transport | ↑ | ↑ |
| 28. | HMGB1 | 4.514 (↓) | 0.039 | High mobility group protein B1; involved in chromatin structure and transcriptional regulation. | ↓ | ↑ |
| 29. | EZR | 4.596 (↓) | 0.0005 | Ezrin; cytoskeletal protein that plays a role in cell adhesion, migration, and signaling. | ↓* | ↓* |
| 30. | THOC4 | 4.781 (↓) | 0.043 | THO complex 4; involved in RNA metabolism, particularly in the export of mRNA from the nucleus to the cytoplasm. Implicated in cancer. | ↓* | ↓* |
| 31. | NPM1 | 4.983 (↓) | 8.05E-08 | Isoform 1 of Nucleophosmin; Involved in ribosome assembly, DNA repair, and regulation of gene expression. | ↓* | ↓* |
| 32. | STMN1 | 5.065 (↓) | 0.024 | Stathmin; cytosolic phosphoprotein that promotes disassembly of microtubules. | ↓* | ↓* |
| 33. | ZNF185 | 5.074 (↓) | 0.033 | zinc finger protein 185; functions as a tumor suppressor by inhibiting cell proliferation, migration, and invasion. Lost in cancers. | ↓* | ↓* |
| 34. | AHNAK | 5.358 (↓) | 1.35E-13 | Neuroblast differentiation-associated protein; large scaffold protein involved in cell adhesion, cytoskeletal organization, signal transduction, tumor suppressor, negatively regulates TNBC proliferation, downreg prognostically neg in cancer | ↓ * | ↓ * |
| 35. | HIST1H1E | 5.571 (↓) | 0.023 | Histone H1.4; linker histone that binds to nucleosomes and promotes higher-order chromatin folding, essential for the regulation of gene expression | ↓ | ↓ * |
| 36. | HNRNPA1 | 6.420 (↓) | 0.008 | Isoform A1-B of Heterogeneous nuclear ribonucleoprotein A1; regulation of mRNA processing, transport, and translation | ↓* | ↓ |
| 37. | CAST | 6.740 (↓) | 0.012 | Calpastatin; inhibitor of calpains, a family of calcium-dependent proteases involved in cell motility, signal transduction, and apoptosis | ↓ * | ↓ * |
| 38. | HNRPDL | 8.417 (↓) | 0.015 | Isoform 1 of Heterogeneous nuclear ribonucleoprotein D-like; | ↑ | ↑* |
| 39. | CDC37 | 9.364 (↓) | 0.043 | Hsp90 co-chaperone; forms complex with Hsp90 and a variety of protein kinases including EGFR, MET, CDK4, CDK6, SRC, RAF-1, MOK, as well as eIF2 alpha kinases; oncogene | ↓ * | ↓ * |
↓ downregulated, ↑ upregulated, * significant at P < 0.05.