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Finding New Ways How to Control BACE1. J Membr Biol 2022; 255:293-318. [PMID: 35305135 DOI: 10.1007/s00232-022-00225-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/24/2022] [Indexed: 01/18/2023]
Abstract
Recently, all applications of BACE1 inhibitors failed as therapeutical targets for Alzheimer´s disease (AD) due to severe side effects. Therefore, alternative ways for treatment development are a hot research topic. The present analysis investigates BACE1 protein-protein interaction networks and attempts to solve the absence of complete knowledge about pathways involving BACE1. A bioinformatics analysis matched the functions of the non-substrate interaction network with Voltage-gated potassium channels, which also appear as top priority protein nodes. Targeting BACE1 interactions with PS1 and GGA-s, blocking of BACE1 access to APP by BRI3 and RTN-s, activation of Wnt signaling and upregulation of β-catenin, and brain delivery of the extracellular domain of p75NTR, are the main alternatives to the use of BACE 1 inhibitors highlighted by the analysis. The pathway enrichment analysis also emphasized substrates and substrate candidates with essential biological functions, which cleavage must remain controlled. They include ephrin receptors, ROBO1, ROBO2, CNTN-s, CASPR-s, CD147, CypB, TTR, APLP1/APLP2, NRXN-s, and PTPR-s. The analysis of the interaction subnetwork of BACE1 functionally related to inflammation identified a connection to three cardiomyopathies, which supports the hypothesis of the common molecular mechanisms with AD. A lot of potential shows the regulation of BACE1 activity through post-translational modifications. The interaction network of BACE1 and its phosphorylation enzyme CSNK1D functionally match the Circadian clock, p53, and Hedgehog signaling pathways. The regulation of BACE1 glycosylation could be achieved through N-acetylglucosamine transferases, α-(1→6)-fucosyltransferase, β-galactoside α-(2→6)-sialyltransferases, galactosyltransferases, and mannosidases suggested by the interaction network analysis of BACE1-MGAT3. The present analysis proposes possibilities for the alternative control of AD pathology.
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Becherini P, Caffa I, Piacente F, Damonte P, Vellone VG, Passalacqua M, Benzi A, Bonfiglio T, Reverberi D, Khalifa A, Ghanem M, Guijarro A, Tagliafico L, Sucameli M, Persia A, Monacelli F, Cea M, Bruzzone S, Ravera S, Nencioni A. SIRT6 enhances oxidative phosphorylation in breast cancer and promotes mammary tumorigenesis in mice. Cancer Metab 2021; 9:6. [PMID: 33482921 PMCID: PMC7821730 DOI: 10.1186/s40170-021-00240-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Sirtuin 6 (SIRT6) is a NAD+-dependent deacetylase with key roles in cell metabolism. High SIRT6 expression is associated with adverse prognosis in breast cancer (BC) patients. However, the mechanisms through which SIRT6 exerts its pro-oncogenic effects in BC remain unclear. Here, we sought to define the role of SIRT6 in BC cell metabolism and in mouse polyoma middle T antigen (PyMT)-driven mammary tumors. METHODS We evaluated the effect of a heterozygous deletion of Sirt6 on tumor latency and survival of mouse mammary tumor virus (MMTV)-PyMT mice. The effect of SIRT6 silencing on human BC cell growth was assessed in MDA-MB-231 xenografts. We also analyzed the effect of Sirt6 heterozygous deletion, of SIRT6 silencing, and of the overexpression of either wild-type (WT) or catalytically inactive (H133Y) SIRT6 on BC cell pyruvate dehydrogenase (PDH) expression and activity and oxidative phosphorylation (OXPHOS), including respiratory complex activity, ATP/AMP ratio, AMPK activation, and intracellular calcium concentration. RESULTS The heterozygous Sirt6 deletion extended tumor latency and mouse survival in the MMTV-PyMT mouse BC model, while SIRT6 silencing slowed the growth of MDA-MB-231 BC cell xenografts. WT, but not catalytically inactive, SIRT6 enhanced PDH expression and activity, OXPHOS, and ATP/AMP ratio in MDA-MB-231 and MCF7 BC cells. Opposite effects were obtained by SIRT6 silencing, which also blunted the expression of genes encoding for respiratory chain proteins, such as UQCRFS1, COX5B, NDUFB8, and UQCRC2, and increased AMPK activation in BC cells. In addition, SIRT6 overexpression increased, while SIRT6 silencing reduced, intracellular calcium concentration in MDA-MB-231 cells. Consistent with these findings, the heterozygous Sirt6 deletion reduced the expression of OXPHOS-related genes, the activity of respiratory complexes, and the ATP/AMP ratio in tumors isolated from MMTV-PyMT mice. CONCLUSIONS Via its enzymatic activity, SIRT6 enhances PDH expression and activity, OXPHOS, ATP/AMP ratio, and intracellular calcium concentration, while reducing AMPK activation, in BC cells. Thus, overall, SIRT6 inhibition appears as a viable strategy for preventing or treating BC.
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Affiliation(s)
- Pamela Becherini
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy.,Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Irene Caffa
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy.,Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Francesco Piacente
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy.,Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy.,Department of Experimental Medicine (DIMES), University of Genoa, V.le Benedetto XV 1, 16132, Genoa, Italy
| | - Patrizia Damonte
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Valerio G Vellone
- Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy.,Department of Integrated, Surgical and Diagnostic Sciences (DISC), University of Genoa, L.go Rosanna Benzi 8, 16132, Genoa, Italy
| | - Mario Passalacqua
- Department of Experimental Medicine (DIMES), University of Genoa, V.le Benedetto XV 1, 16132, Genoa, Italy
| | - Andrea Benzi
- Department of Experimental Medicine (DIMES), University of Genoa, V.le Benedetto XV 1, 16132, Genoa, Italy
| | - Tommaso Bonfiglio
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Daniele Reverberi
- Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Amr Khalifa
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Moustafa Ghanem
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Ana Guijarro
- Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Luca Tagliafico
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Marzia Sucameli
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Angelica Persia
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Fiammetta Monacelli
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy.,Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Michele Cea
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy.,Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Santina Bruzzone
- Department of Experimental Medicine (DIMES), University of Genoa, V.le Benedetto XV 1, 16132, Genoa, Italy
| | - Silvia Ravera
- Department of Experimental Medicine (DIMES), University of Genoa, V.le Benedetto XV 1, 16132, Genoa, Italy.
| | - Alessio Nencioni
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy. .,Ospedale Policlinico San Martino IRCCS, Largo Rosanna Benzi 10, 16132, Genoa, Italy.
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Nahálková J. Linking TPPII to the protein interaction and signalling networks. Comput Biol Chem 2020; 87:107291. [PMID: 32702546 DOI: 10.1016/j.compbiolchem.2020.107291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/21/2020] [Accepted: 05/22/2020] [Indexed: 01/18/2023]
Abstract
Tripeptidyl peptidase II (TPPII) is primarily considered a house-keeping exopeptidase, which contributes to the functions of the ubiquitin-proteasome system by the maintenance of the cellular amino acid homeostasis. Although functionally well-characterised in vitro and using the mammalian cell models, less is known about the molecular mechanisms of its involvement in the signalling and metabolic pathways, which mediate its cellular functions. The present protein-protein interaction network analysis identified these mechanisms involved in the adaptive and innate immunity, the metabolism of the glucose, cancer cell growth, apoptosis, cell cycle and DNA damage responses. The interaction network constructed based on the publicly available protein-protein interaction data was extended by the application GeneMania, which was further used for the pathway enrichment, the protein function prediction and the protein node prioritisation analysis. The analysis suggested that the molecular mechanisms linked to the adaptive and innate immunity (ID, Kit receptor, BCR, IL-2 and G-CSF signalling; the regulation of NFκB), the aerobic glycolysis (ID and IL-2 signalling), tumorigenesis (TGF-β and p53 signalling; the top priority nodes MAPKs, mTOR regulation), diabetes (Kit receptor signalling; the top priority node GSK3β) and neurodegeneration (the control of mTOR and Aβ peptide degradation) are controlling the resulting TPPII interaction network. The uncharacterized interactions with two lung cancer suppressors (DOK3, DENND2D), a protein involved in the increased risk of the lung cancer in smokers (CYP1A1) and a protein implicated in asthmatic reactions (CHIA) suggest potential roles of TPPII in the lung cancer pathology. The interactions with methyltransferase CARNMT1, which modifies di- and tripeptides and the xenobiotic processing enzyme CYP1A1, are additional candidates for the breakthrough in new functions discovery of TPPII.
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Affiliation(s)
- Jarmila Nahálková
- Biochemworld Co., Biochemistry, Molecular & Cell Biology Unit, Snickar-Anders väg 17, 74394, Skyttorp, Uppsala County, Sweden.
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Kober KM, Olshen A, Conley YP, Schumacher M, Topp K, Smoot B, Mazor M, Chesney M, Hammer M, Paul SM, Levine JD, Miaskowski C. Expression of mitochondrial dysfunction-related genes and pathways in paclitaxel-induced peripheral neuropathy in breast cancer survivors. Mol Pain 2018; 14:1744806918816462. [PMID: 30426838 PMCID: PMC6293373 DOI: 10.1177/1744806918816462] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Paclitaxel is one of the most commonly used drugs to treat breast cancer. Its
major dose-limiting toxicity is paclitaxel-induced peripheral neuropathy
(PIPN). PIPN persists into survivorship and has a negative impact on
patient’s mood, functional status, and quality of life. No interventions are
available to treat PIPN. A critical barrier to the development of
efficacious interventions is the lack of understanding of the mechanisms
that underlie PIPN. Mitochondrial dysfunction has been evaluated in
preclinical studies as a hypothesized mechanism for PIPN, but clinical data
to support this hypothesis are limited. The purpose of this pilot study was
to evaluate for differential gene expression and perturbed pathways between
breast cancer survivors with and without PIPN. Methods Gene expression in peripheral blood was assayed using RNA-seq. Differentially
expressed genes (DEG) and pathways associated with mitochondrial dysfunction
were identified between survivors who received paclitaxel and did (n = 25)
and did not (n = 25) develop PIPN. Results Breast cancer survivors with PIPN were significantly older; more likely to be
unemployed; reported lower alcohol use; had a higher body mass index and
poorer functional status; and had a higher number of lower extremity sites
with loss of light touch, cold, and pain sensations and higher vibration
thresholds. No between-group differences were found in the cumulative dose
of paclitaxel received or in the percentage of patients who had a dose
reduction or delay due to PIPN. Five DEGs and nine perturbed pathways were
associated with mitochondrial dysfunction related to oxidative stress, iron
homeostasis, mitochondrial fission, apoptosis, and autophagy. Conclusions This study is the first to provide molecular evidence that a number of
mitochondrial dysfunction mechanisms identified in preclinical models of
various types of neuropathic pain including chemotherapy-induced peripheral
neuropathy are found in breast cancer survivors with persistent PIPN and
suggest genes for validation and as potential therapeutic targets.
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Affiliation(s)
- Kord M Kober
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yvettte P Conley
- 3 School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark Schumacher
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kimberly Topp
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Betty Smoot
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Melissa Mazor
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Margaret Chesney
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Marilyn Hammer
- 4 Department of Nursing, Mount Sinai Medical Center, New York, NY, USA
| | - Steven M Paul
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Jon D Levine
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Christine Miaskowski
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
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