COVID-19 engages clinical markers for the management of cancer and cancer-relevant regulators of cell proliferation, death, migration, and immune response.

Clinical reports show that the management of cancer patients infected with SARS-CoV-2 requires modifications. Understanding of cancer-relevant mechanisms engaged by the virus is essential for the evidence-based management of cancer. The network of SARS-CoV-2 regulatory mechanisms was used to study potential engagement of oncogenes, tumor suppressors, other regulators of tumorigenesis and clinical markers used in the management of cancer patients. Our network analysis confirms links between COVID-19 and tumorigenesis that were predicted in epidemiological reports. The COVID-19 network shows the involvement of tumorigenesis regulators and clinical markers. Regulators of cell proliferation, death, migration, and the immune system were retrieved. Examples are pathways initiated by EGF, VEGF, TGFß and FGF. The SARS-CoV-2 network engages markers for diagnosis, prognosis and selection of treatment. Intersection with cancer diagnostic signatures supports a potential impact of the virus on tumorigenesis. Clinical observations show the diversity of symptoms correlating with biological processes and types of cells engaged by the virus, e.g. epithelial, endothelial, smooth muscle, glial and immune system cells. Our results describe an extensive engagement of cancer-relevant mechanisms and clinical markers by COVID-19. Engagement by the virus of clinical markers provides a rationale for clinical decisions based on these markers.

Acquisition of Invasiveness by Breast Adenocarcinoma Cells Engages Established Hallmarks and Novel Regulatory Mechanisms.

BACKGROUND/AIM: Proteomics of invasiveness opens a window on the complexity of the metastasis-engaged mechanisms. The extend and types of this complexity require elucidation. MATERIALS AND METHODS: Proteomics, immunohistochemistry, immunoblotting, network analysis and systems cancer biology were used to analyse acquisition of invasiveness by human breast adenocarcinoma cells. RESULTS: We report here that invasiveness network highlighted the involvement of hallmarks such as cell proliferation, migration, cell death, genome stability, immune system regulation and metabolism. Identified involvement of cell-virus interaction and gene silencing are potentially novel cancer mechanisms. Identified 6,113 nodes with 11,055 edges affecting 1,085 biological processes show extensive re-arrangements in cell physiology. These high numbers are in line with a similar broadness of networks built with diagnostic signatures approved for clinical use. CONCLUSION: Our data emphasize a broad systemic regulation of invasiveness, and describe the network of this regulation.

Proteomic Profiling of Diffuse Large B-Cell Lymphomas.

OBJECTIVE: The aim of this study was to identify differences in proteome profiles of diffuse large B-cell lymphoma (DLBCL) of nongerminal center (non-GC) versus GC type in the search for new markers and drug targets. METHODS: Six DLBCL, with 3 repeats for each, were used for the initial study by proteomics: 3 non-GC and 3 GC DLBCL cases. For immunohistochemistry, tissue microarrays were made from 31 DLBCL samples: 16 non-GC de novo lymphomas and 15 GC cases (11 transformed from follicular lymphomas and 4 de novo GC lymphomas). Proteome profiling was performed by two-dimensional gel electrophoresis and MALDI-TOF mass spectrometry. RESULTS: Ninety-one proteins were found differentially expressed in non-GC compared to GC type. The Cytoscape tool was used for systemic analysis of proteomics data, revealing 19 subnetworks representing functions affected in non-GC versus GC types of DLBCL. CONCLUSION: A validation study of 3 selected proteins (BiP/Grp78, Hsp90, and cyclin B2) showed the enhanced expression in non-GC DLBCL, supporting the proteomics data.

Proteomic study of retinal proteins associated with transcorneal electric stimulation in rats.

Background. To investigate how transcorneal electric stimulation (TES) affects the retina, by identifying those proteins up- and downregulated by transcorneal electric stimulation (TES) in the retina of rats. Methods. Adult Wistar rats received TES on the left eyes at different electrical currents while the right eyes received no treatment and served as controls. After TES, the eye was enucleated and the retina was isolated. The retinas were analyzed by proteomics. Results. Proteomics showed that twenty-five proteins were upregulated by TES. The identified proteins included cellular signaling proteins, proteins associated with neuronal transmission, metabolic proteins, immunological factors, and structural proteins. Conclusions. TES induced changes in expression of various functional proteins in the retina.

Proteome profiling of immortalization-to-senescence transition of human breast epithelial cells identified MAP2K3 as a senescence-promoting protein which is downregulated in human breast cancer.

PURPOSE: immortalization is one of the first changes in cells undergoing carcinogenic transformation. Proteome profiling of the immortalization-senescence transition is expected to provide insights into the molecular mechanisms of early tumorigenesis. EXPERIMENTAL DESIGN: 2-DE and MALDI-MS were used to identify proteins in primary human breast epithelial cells, relevant to the immortalization-senescence transition. Cell and molecular biology and immunohistochemistry were used to validate involvement of mitogen-activated protein kinase kinase 3 (MAP2K3) in the immortalization-senescence transition. RESULTS: we identified 71 proteins whose expression changed upon induction of senescence. The identified proteins include regulators of cell growth, death, cell assembly and organization. Analysis of the network formed by the identified proteins suggested that the immortalization-to-senescence transition could affect regulators of the cell cycle, protein synthesis, transport, post-translational modifications, DNA recombination and repair, and lipid and amino acid metabolism. We observed that MAP2K3 was downregulated in immortal human breast epithelial cells and that upregulation of MAP2K3 expression promoted cell senescence. Decreased expression of MAP2K3 was observed in human breast infiltrating ductal carcinomas, as compared to non-cancerous human breast tissues. CONCLUSION AND CLINICAL RELEVANCE: we described a proteome profile of the immortalization-to-senescence transition for human breast epithelial cells, and identified MAP2K3 as a protein that promotes senescence in these cells.

Functional proteomics of failed filtering blebs.

PURPOSE: To identify and determine the function of the proteins associated with failed filtering blebs following trabeculectomy. METHODS: Tenon's tissues, obtained during surgery for failed filtering blebs or obtained during cataract surgery on normal eyes, were analyzed by proteomics. The proteins showing significant differences between the two tissues were selected for identification by mass spectrometry. The location and expression pattern of ribosomal S6 kinase 2 (RSK2), one of the altered proteins, were determined. The effect of basic fibroblast growth factor (bFGF) on the expression pattern and function of RSK2 in NIH3T3 fibroblast cells was then investigated by an RNA knockdown technique. RESULTS: Eight proteins were found differentially expressed in failed filtering blebs; the identified proteins included those associated with intracellular signaling pathways. The expression of RSK2, one of the identified proteins, was found to be decreased compared with that of the control. RSK2 was located in Tenon's tissue using an immunohistochemical technique. In culture, the bFGF-induced cell proliferation was inhibited by the RNA knockdown of RSK2. The level of mRNA and protein expression of actin was increased by RSK2 RNA knockdown, but bFGF-induced protein expression of actin was not promoted by RSK2 RNA knockdown. Whereas RSK2 RNA knockdown increased the expression and activity of mitogen-activated protein kinase (MAPK), activation of MAPK induced by bFGF was not promoted by RSK2 knockdown. CONCLUSIONS: The expression of eight proteins in the failed filtering blebs was significantly different from that in the Tenon's capsules used as a control. The effect of RSK2 expression on fibroblast cells suggests that RSK2 may be associated with wound healing in filtering blebs.

Proteomic study of DBA/2J mice retina: Down-regulation of Integrin beta7 correlated with retinal ganglion cell death.

To identify and determine the function of the proteins associated with the death of retinal ganglion cells (RGCs) in DBA/2J mice, an animal model of glaucoma, retinas of DBA/2J mice, were analyzed by proteomics at 5-, 7-, and 11-months-of-age. The proteins showing significant alterations were selected for identification by MS and 18 proteins were differentially expressed and the identified proteins included cell membrane receptors and proteins associated with intracellular signaling pathways. Among of identified proteins, the expression of Integrin beta7 at 7-months-of-age was decreased by about 89% of that at 5-months-of-age. Integrin beta7 was expressed in the RGCs. The effect of glutamate toxicity on the expression pattern of Integrin beta7 in a RGC line was also investigated and the glutamate-induced death of RGC was inhibited by the RNA knockdown of Integrin beta7. Our data showed also that the expression of 18 proteins in the DBA/2J was significantly altered in DBA2 mice and down-regulation of Integrin beta7 may have a protective effect on glutamate-induced death of RGCs.

Wnt14 inhibits death of retinal precursor cells.

An earlier proteomics study from our laboratory showed that Wnt14, a member of the Wnt family that regulates the development of vertebrates, was one of the proteins expressed transiently during the development of the chick retina. The purpose of this study was to determine in more detail the changes in the expression of Wnt14 during the development of the chick retina, and to investigate the biological function of Wnt14. Endogenous Wnt14 is located in the retinal ganglion cell layer, and is expressed in the chick retina on embryonic days (ED) 7, ED11, and ED15. The level of Wnt14 is transiently decreased on ED11. In vitro analysis showed that an over-expression of Wnt14 reduced the activation of caspase-3 and inhibited the death of R28 cells induced by serum deprivation or exposure to glutamate. An interferon-induced protein was identified as the protein that was bound to Wnt14. These results suggest that a stable expression of Wnt14 inhibits cell death by inactivating caspase-3 in the developing retina.

Elevated intraocular pressure, optic nerve atrophy, and impaired retinal development in ODAG transgenic mice.

PURPOSE: In an earlier study, a cDNA was cloned that showed abundant expression in the eye at postnatal day (P)2 but was downregulated at P10; it was named ODAG (ocular development-associated gene). Its biological function was examined by generating and analyzing transgenic mice overexpressing ODAG (ODAG Tg) in the eye and by identifying ODAG-binding proteins. METHODS: Transgenic mice were generated by using the mouse Crx promoter. EGFP was designed to be coexpressed with transgenic ODAG, to identify transgene-expressing cells. Overexpression of ODAG was confirmed by Northern and Western blot analysis. IOP was measured with a microneedle technique. The eyes were macroscopically examined and histologically analyzed. EGFP expression was detected by confocal microscope. Proteins associated with ODAG were isolated by pull-down assay in conjugation with mass spectrometry. RESULTS: Macroscopically, ODAG Tg exhibited gradual protrusion of the eyeballs. The mean IOP of ODAG Tg was significantly higher than that of wild-type (WT) littermates. Histologic analysis exhibited optic nerve atrophy and impaired retinal development in the ODAG Tg eye. EGFP was expressed highly in the presumptive outer nuclear layer and weakly in the presumptive inner nuclear layer in the ODAG Tg retina. Rab6-GTPase-activating protein (Rab6-GAP) and its substrate, Rab6, were identified as ODAG-binding proteins. CONCLUSIONS: Deregulated expression of ODAG in the eye induces elevated intraocular pressure and optic nerve atrophy and impairs retinal development, possibly by interfering with the Rab6/Rab6-GAP-mediated signaling pathway. These results provide new insights into the mechanisms regulating ocular development, and ODAG Tg would be a novel animal model for human diseases caused by ocular hypertension.

Proteome profiling of embryo chick retina.

BACKGROUND: Little is known regarding the molecular pathways that underlie the process of retinal development. The purpose of this study was to identify proteins which may be involved in development of retina. We used a proteomics-based approach to identify proteins that are up- or down-regulated during the development of the embryo chick retina. RESULTS: Two-dimensional gel electrophoresis was performed with the retina of embryo chicken, which was obtained from embryos of day 7 (ED7) and of day 11 (ED11). The protein spots showing significant differences were selected for identification by MALDI mass spectrometry. Thirteen proteins were differentially expressed; seven proteins were up-regulated in embryo retina of chicken at ED 11 and six proteins were down-regulated. Significant proteins were also evaluated in embryo day 15 (ED15). Some of identified proteins were known to regulate cell proliferation, cell death, transport, metabolism, organization and extracellular matrix, and others also included novel proteins. CONCLUSION: We identified thirteen proteins which differentially expressed in embryonal retina of chicken at day 7, as compared to the retina of embryo of day 11. They were various regulatory proteins for cellular signaling.

Proteomic analyses of retina of excitatory amino acid carrier 1 deficient mice.

BACKGROUND: Excitatory amino acid carrier 1 (EAAC1) is a glutamate transporter found in neuronal tissues and is extensively expressed in the retina. EAAC1 plays a role in a variety of neural functions, but its biological functions in the retina has not been fully determined. The purpose of this study was to identify proteins regulated by EAAC1 in the retina of mice. To accomplish this, we used a proteomics-based approach to identify proteins that are up- or down-regulated in EAAC1-deficient (EAAC1-/-) mice. RESULTS: Proteomic analyses and two-dimensional gel electorphoresis were performed on the retina of EAAC1-/- mice, and the results were compared to that of wild type mice. The protein spots showing significant differences were selected for identification by mass spectrometric analyses. Thirteen proteins were differentially expressed; nine proteins were up-regulated and five proteins were down-regulated in EAAC1-/- retina. Functional clustering showed that identified proteins are involved in various cellular process, e.g. cell cycle, cell death, transport and metabolism. CONCLUSION: We identified thirteen proteins whose expression is changed in EAAC-/- mice retinas. These proteins are known to regulate cell proliferation, death, transport, metabolism, cell organization and extracellular matrix.