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Rausio H, Cervera A, Heuser VD, West G, Oikkonen J, Pianfetti E, Lovino M, Ficarra E, Taimen P, Hynninen J, Lehtonen R, Hautaniemi S, Carpén O, Huhtinen K. PIK3R1 fusion drives chemoresistance in ovarian cancer by activating ERK1/2 and inducing rod and ring-like structures. Neoplasia 2024; 51:100987. [PMID: 38489912 PMCID: PMC10955102 DOI: 10.1016/j.neo.2024.100987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/17/2024]
Abstract
Gene fusions are common in high-grade serous ovarian cancer (HGSC). Such genetic lesions may promote tumorigenesis, but the pathogenic mechanisms are currently poorly understood. Here, we investigated the role of a PIK3R1-CCDC178 fusion identified from a patient with advanced HGSC. We show that the fusion induces HGSC cell migration by regulating ERK1/2 and increases resistance to platinum treatment. Platinum resistance was associated with rod and ring-like cellular structure formation. These structures contained, in addition to the fusion protein, CIN85, a key regulator of PI3K-AKT-mTOR signaling. Our data suggest that the fusion-driven structure formation induces a previously unrecognized cell survival and resistance mechanism, which depends on ERK1/2-activation.
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Affiliation(s)
- Heidi Rausio
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland; Drug Research Doctoral Programme (DRDP), University of Turku, Turku, Finland.
| | - Alejandra Cervera
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Vanina D Heuser
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland
| | - Gun West
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Elena Pianfetti
- Department of Engineering, Enzo Ferrari, University of Modena and Reggio Emilia, Modena, Italy
| | - Marta Lovino
- Department of Engineering, Enzo Ferrari, University of Modena and Reggio Emilia, Modena, Italy
| | - Elisa Ficarra
- Department of Engineering, Enzo Ferrari, University of Modena and Reggio Emilia, Modena, Italy
| | - Pekka Taimen
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland; Department of Pathology, Turku University Hospital, Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Rainer Lehtonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Pathology, University of Helsinki and HUSLAB, University Hospital, Helsinki, Finland
| | - Kaisa Huhtinen
- Institute of Biomedicine and FICAN West Cancer Centre, Faculty of Medicine, University of Turku, Turku, Finland; Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Aljedani SS, Aldehaiman A, Sandholu A, Alharbi S, Mak VCY, Wu H, Lugari A, Jaremko M, Morelli X, Backer JW, Ladbury JE, Nowakowski M, Cheung LWT, Arold ST. Functional selection in SH3-mediated activation of the PI3 kinase. bioRxiv 2024:2024.04.30.591319. [PMID: 38746413 PMCID: PMC11092569 DOI: 10.1101/2024.04.30.591319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The phosphoinositide-3 kinase (PI3K), a heterodimeric enzyme, plays a pivotal role in cellular metabolism and survival. Its deregulation is associated with major human diseases, particularly cancer. The p85 regulatory subunit of PI3K binds to the catalytic p110 subunit via its C-terminal domains, stabilising it in an inhibited state. Certain Src homology 3 (SH3) domains can activate p110 by binding to the proline-rich (PR) 1 motif located at the N-terminus of p85. However, the mechanism by which this N-terminal interaction activates the C-terminally bound p110 remains elusive. Moreover, the intrinsically poor ligand selectivity of SH3 domains raises the question of how they can control PI3K. Combining structural, biophysical, and functional methods, we demonstrate that the answers to both these unknown issues are linked: PI3K-activating SH3 domains engage in additional "tertiary" interactions with the C-terminal domains of p85, thereby relieving their inhibition of p110. SH3 domains lacking these tertiary interactions may still bind to p85 but cannot activate PI3K. Thus, p85 uses a functional selection mechanism that precludes nonspecific activation rather than nonspecific binding. This separation of binding and activation may provide a general mechanism for how biological activities can be controlled by promiscuous protein-protein interaction domains.
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Cobleigh MA, Layng KV, Mauer E, Mahon B, Hockenberry AJ, Abukhdeir AM. Comparative genomic analysis of PIK3R1-mutated and wild-type breast cancers. Breast Cancer Res Treat 2024; 204:407-414. [PMID: 38153569 DOI: 10.1007/s10549-023-07196-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
PURPOSE The PIK3R1 gene encodes the regulatory subunit-p85a-of the PI3K signaling complex. Prior studies have found that pathogenic somatic alterations in PIK3R1 are enriched in human breast cancers but the genomic landscape of breast cancer patients harboring PIK3R1 mutations has not been extensively characterized. METHODS We retrospectively analyzed 6,009 patient records that underwent next-generation sequencing (NGS) using the Tempus xT solid tumor assay. All patients had breast cancer with known HER2 (+/-) and hormone receptor (HR; +/-) status and were classified according to the presence of PIK3R1 mutations including short variants and copy number alterations. RESULTS The frequency of PIK3R1 mutations varied according to subtype: 6% in triple negative (TNBC, 89/1,475), 2% in HER2-/HR+ (80/3,893) and 2.3% in HER2+ (15/641) (p < 0.001). Co-mutations in PTEN, TP53 and NF1 were significantly enriched, co-mutations in PIK3CA were significantly less prevalent, and tumor mutational burden was significantly higher in PIK3R1-mutated HER2- samples relative to PIK3R1 wild-type. At the transcriptional-level, PIK3R1 RNA expression in HER2- disease was significantly higher in PIK3R1-mutated (excluding copy number loss) samples, regardless of subtype. CONCLUSION This is the largest investigation of the PIK3R1 mutational landscape in breast cancer patients (n = 6,009). PIK3R1 mutations were more common in triple-negative breast cancer (~ 6%) than in HER2 + or HER2-/HR + disease (approximately 2%). While alterations in the PI3K/AKT pathway are often actionable in HER2-/HR + breast cancer, our study suggests that PIK3R1 could be an important target in TNBC as well.
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Affiliation(s)
- Melody A Cobleigh
- Rush University Medical Center, 1620 W Harrison St, Chicago, IL, 60612, USA.
| | | | | | - Brett Mahon
- Tempus Labs Inc, 600 W Chicago, Chicago, IL, 60654, USA
| | | | - Abde M Abukhdeir
- Rush University Medical Center, 1620 W Harrison St, Chicago, IL, 60612, USA
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Bajusz D, Pándy-Szekeres G, Takács Á, de Araujo ED, Keserű GM. SH2db, an information system for the SH2 domain. Nucleic Acids Res 2023:7173719. [PMID: 37207333 DOI: 10.1093/nar/gkad420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 05/21/2023] Open
Abstract
SH2 domains are key mediators of phosphotyrosine-based signalling, and therapeutic targets for diverse, mostly oncological, disease indications. They have a highly conserved structure with a central beta sheet that divides the binding surface of the protein into two main pockets, responsible for phosphotyrosine binding (pY pocket) and substrate specificity (pY + 3 pocket). In recent years, structural databases have proven to be invaluable resources for the drug discovery community, as they contain highly relevant and up-to-date information on important protein classes. Here, we present SH2db, a comprehensive structural database and webserver for SH2 domain structures. To organize these protein structures efficiently, we introduce (i) a generic residue numbering scheme to enhance the comparability of different SH2 domains, (ii) a structure-based multiple sequence alignment of all 120 human wild-type SH2 domain sequences and their PDB and AlphaFold structures. The aligned sequences and structures can be searched, browsed and downloaded from the online interface of SH2db (http://sh2db.ttk.hu), with functions to conveniently prepare multiple structures into a Pymol session, and to export simple charts on the contents of the database. Our hope is that SH2db can assist researchers in their day-to-day work by becoming a one-stop shop for SH2 domain related research.
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Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group and National Laboratory for Drug Researchand Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Gáspár Pándy-Szekeres
- Medicinal Chemistry Research Group and National Laboratory for Drug Researchand Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Ágnes Takács
- Medicinal Chemistry Research Group and National Laboratory for Drug Researchand Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Elvin D de Araujo
- Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - György M Keserű
- Medicinal Chemistry Research Group and National Laboratory for Drug Researchand Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
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Abstract
A vast effort has been invested in the identification of driver mutations of cancer. However, recent studies and observations call into question whether the activating mutations or the signal strength are the major determinant of tumor development. The data argue that signal strength determines cell fate, not the mutation that initiated it. In addition to activating mutations, factors that can impact signaling strength include (i) homeostatic mechanisms that can block or enhance the signal, (ii) the types and locations of additional mutations, and (iii) the expression levels of specific isoforms of genes and regulators of proteins in the pathway. Because signal levels are largely decided by chromatin structure, they vary across cell types, states, and time windows. A strong activating mutation can be restricted by low expression, whereas a weaker mutation can be strengthened by high expression. Strong signals can be associated with cell proliferation, but too strong a signal may result in oncogene-induced senescence. Beyond cancer, moderate signal strength in embryonic neural cells may be associated with neurodevelopmental disorders, and moderate signals in aging may be associated with neurodegenerative diseases, like Alzheimer's disease. The challenge for improving patient outcomes therefore lies in determining signaling thresholds and predicting signal strength.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, NCI, Frederick, Maryland
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, NCI, Frederick, Maryland
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, NCI, Frederick, Maryland
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Basant A, Way M. The relative binding position of Nck and Grb2 adaptors impacts actin-based motility of Vaccinia virus. eLife 2022; 11:74655. [PMID: 35796545 PMCID: PMC9333988 DOI: 10.7554/elife.74655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Phosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to assemble complex signalling networks. The concept of phase separation has recently changed our appreciation of multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now investigated this parameter in the operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3 complex-mediated actin polymerisation. Manipulating the position of pTyr motifs in A36 and the unrelated p14 from Orthoreovirus, we find that only specific spatial arrangements of Nck and Grb2 binding sites result in robust N-WASP recruitment, Arp2/3 complex driven actin polymerisation and viral spread. This suggests that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are frequently conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those undergoing phase transitions.
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Affiliation(s)
- Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
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Karagiannakos A, Adamaki M, Tsintarakis A, Vojtesek B, Fåhraeus R, Zoumpourlis V, Karakostis K. Targeting Oncogenic Pathways in the Era of Personalized Oncology: A Systemic Analysis Reveals Highly Mutated Signaling Pathways in Cancer Patients and Potential Therapeutic Targets. Cancers (Basel) 2022; 14:cancers14030664. [PMID: 35158934 PMCID: PMC8833388 DOI: 10.3390/cancers14030664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer is the second leading cause of death globally. One of the main hallmarks in cancer is the functional deregulation of crucial molecular pathways via driver genetic events that lead to abnormal gene expression, giving cells a selective growth advantage. Driver events are defined as mutations, fusions and copy number alterations that are causally implicated in oncogenesis. Molecular analysis on tissues that have originated from a wide range of anatomical areas has shown that mutations in different members of several pathways are implicated in different cancer types. In recent decades, significant efforts have been made to incorporate this knowledge into daily medical practice, providing substantial insight towards clinical diagnosis and personalized therapies. However, since there is still a strong need for more effective drug development, a deep understanding of the involved signaling mechanisms and the interconnections between these pathways is highly anticipated. Here, we perform a systemic analysis on cancer patients included in the Pan-Cancer Atlas project, with the aim to select the ten most highly mutated signaling pathways (p53, RTK-RAS, lipids metabolism, PI-3-Kinase/Akt, ubiquitination, b-catenin/Wnt, Notch, cell cycle, homology directed repair (HDR) and splicing) and to provide a detailed description of each pathway, along with the corresponding therapeutic applications currently being developed or applied. The ultimate scope is to review the current knowledge on highly mutated pathways and to address the attractive perspectives arising from ongoing experimental studies for the clinical implementation of personalized medicine.
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Affiliation(s)
- Alexandros Karagiannakos
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Avenue, 11635 Athens, Greece; (A.K.); (M.A.); (A.T.)
| | - Maria Adamaki
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Avenue, 11635 Athens, Greece; (A.K.); (M.A.); (A.T.)
| | - Antonis Tsintarakis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Avenue, 11635 Athens, Greece; (A.K.); (M.A.); (A.T.)
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 65653 Brno, Czech Republic; (B.V.); (R.F.)
| | - Robin Fåhraeus
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 65653 Brno, Czech Republic; (B.V.); (R.F.)
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
- International Centre for Cancer Vaccine Science, University of Gdansk, 80-822 Gdansk, Poland
| | - Vassilis Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Avenue, 11635 Athens, Greece; (A.K.); (M.A.); (A.T.)
- Correspondence: (V.Z.); (K.K.)
| | - Konstantinos Karakostis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Avenue, 11635 Athens, Greece; (A.K.); (M.A.); (A.T.)
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
- Correspondence: (V.Z.); (K.K.)
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