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Li X, Kirkpatrick RB, Wang X, Tucker CJ, Shukla A, Jessen HJ, Wang H, Shears SB, Gu C. Homeostatic coordination of cellular phosphate uptake and efflux requires an organelle-based receptor for the inositol pyrophosphate IP8. Cell Rep 2024; 43:114316. [PMID: 38833370 DOI: 10.1016/j.celrep.2024.114316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/16/2024] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
Phosphate (Pi) serves countless metabolic pathways and is involved in macromolecule synthesis, energy storage, cellular signaling, and bone maintenance. Herein, we describe the coordination of Pi uptake and efflux pathways to maintain mammalian cell Pi homeostasis. We discover that XPR1, the presumed Pi efflux transporter, separately supervises rates of Pi uptake. This direct, regulatory interplay arises from XPR1 being a binding partner for the Pi uptake transporter PiT1, involving a predicted transmembrane helix/extramembrane loop in XPR1, and its hitherto unknown localization in a subset of intracellular LAMP1-positive puncta (named "XLPVs"). A pharmacological mimic of Pi homeostatic challenge is sensed by the inositol pyrophosphate IP8, which functionalizes XPR1 to respond in a temporally hierarchal manner, initially adjusting the rate of Pi efflux, followed subsequently by independent modulation of PiT1 turnover to reset the rate of Pi uptake. These observations generate a unifying model of mammalian cellular Pi homeostasis, expanding opportunities for therapeutic intervention.
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Affiliation(s)
- Xingyao Li
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA
| | - Regan B Kirkpatrick
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles J Tucker
- Fluorescence Microscopy and Imaging Center, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Anuj Shukla
- Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, and CIBSS - the Center for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA; Nucleolar Integrity Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA
| | - Chunfang Gu
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA; Synaptic & Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA.
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2
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Krieg S, Rohde T, Rausch T, Butthof L, Wendler-Link L, Eckert C, Breuhahn K, Galy B, Korbel J, Billmann M, Breinig M, Tschaharganeh DF. Mitoferrin2 is a synthetic lethal target for chromosome 8p deleted cancers. Genome Med 2024; 16:83. [PMID: 38886830 PMCID: PMC11181659 DOI: 10.1186/s13073-024-01357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Somatic copy number alterations are a hallmark of cancer that offer unique opportunities for therapeutic exploitation. Here, we focused on the identification of specific vulnerabilities for tumors harboring chromosome 8p deletions. METHODS We developed and applied an integrative analysis of The Cancer Genome Atlas (TCGA), the Cancer Dependency Map (DepMap), and the Cancer Cell Line Encyclopedia to identify chromosome 8p-specific vulnerabilities. We employ orthogonal gene targeting strategies, both in vitro and in vivo, including short hairpin RNA-mediated gene knockdown and CRISPR/Cas9-mediated gene knockout to validate vulnerabilities. RESULTS We identified SLC25A28 (also known as MFRN2), as a specific vulnerability for tumors harboring chromosome 8p deletions. We demonstrate that vulnerability towards MFRN2 loss is dictated by the expression of its paralog, SLC25A37 (also known as MFRN1), which resides on chromosome 8p. In line with their function as mitochondrial iron transporters, MFRN1/2 paralog protein deficiency profoundly impaired mitochondrial respiration, induced global depletion of iron-sulfur cluster proteins, and resulted in DNA-damage and cell death. MFRN2 depletion in MFRN1-deficient tumors led to impaired growth and even tumor eradication in preclinical mouse xenograft experiments, highlighting its therapeutic potential. CONCLUSIONS Our data reveal MFRN2 as a therapeutic target of chromosome 8p deleted cancers and nominate MFNR1 as the complimentary biomarker for MFRN2-directed therapies.
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Affiliation(s)
- Stephan Krieg
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Rohde
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Luise Butthof
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lena Wendler-Link
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Eckert
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bruno Galy
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Maximilian Billmann
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.
| | - Marco Breinig
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
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3
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Yates J, Schaufelberger H, Steinacher R, Schär P, Truninger K, Boeva V. DNA-methylation variability in normal mucosa: a field cancerization marker in patients with adenomatous polyps. J Natl Cancer Inst 2024; 116:974-982. [PMID: 38273663 PMCID: PMC11160500 DOI: 10.1093/jnci/djae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/13/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The phenomenon of field cancerization reflects the transition of normal cells into those predisposed to cancer. Assessing the scope and intensity of this process in the colon may support risk prediction and colorectal cancer prevention. METHODS The Swiss Epigenetic Colorectal Cancer Study (SWEPIC) study, encompassing 1111 participants for DNA methylation analysis and a subset of 84 for RNA sequencing, was employed to detect field cancerization in individuals with adenomatous polyps (AP). Methylation variations were evaluated for their discriminative capability, including in external cohorts, genomic localization, clinical correlations, and associated RNA expression patterns. RESULTS Normal cecal tissue of individuals harboring an AP in the proximal colon manifested dysregulated DNA methylation compared to tissue from healthy individuals at 558 unique loci. Leveraging these adenoma-related differentially variable and methylated CpGs (aDVMCs), our classifier discerned between healthy and AP-adjacent tissues across SWEPIC datasets (cross-validated area under the receiver operating characteristic curve [ROC AUC] = 0.63-0.81), including within age-stratified cohorts. This discriminative capacity was validated in 3 external sets, differentiating healthy from cancer-adjacent tissue (ROC AUC = 0.82-0.88). Notably, aDVMC dysregulation correlated with polyp multiplicity. More than 50% of aDVMCs were significantly associated with age. These aDVMCs were enriched in active regions of the genome (P < .001), and associated genes exhibited altered expression in AP-adjacent tissues. CONCLUSIONS Our findings underscore the early onset of field cancerization in the right colon during the neoplastic transformation process. A more extensive validation of aDVMC dysregulation as a stratification tool could pave the way for enhanced surveillance approaches, especially given its linkage to adenoma emergence.
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Affiliation(s)
- Josephine Yates
- Department of Computer Science, Institute for Machine Learning, ETH Zürich, Zurich, Switzerland
- ETH AI Center, ETH Zürich, Zurich, Switzerland
- Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
| | | | | | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Kaspar Truninger
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Valentina Boeva
- Department of Computer Science, Institute for Machine Learning, ETH Zürich, Zurich, Switzerland
- ETH AI Center, ETH Zürich, Zurich, Switzerland
- Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
- Cochin Institute, Inserm U1016, National Centre for Scientific Research (CNRS) UMR 8104, Paris Descartes University UMR-S1016, Paris, France
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4
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Malone CF, Mabe NW, Forman AB, Alexe G, Engel KL, Chen YJC, Soeung M, Salhotra S, Basanthakumar A, Liu B, Dent SYR, Stegmaier K. The KAT module of the SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma. SCIENCE ADVANCES 2024; 10:eadm9449. [PMID: 38820154 PMCID: PMC11141635 DOI: 10.1126/sciadv.adm9449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
Pediatric cancers are frequently driven by genomic alterations that result in aberrant transcription factor activity. Here, we used functional genomic screens to identify multiple genes within the transcriptional coactivator Spt-Ada-Gcn5-acetyltransferase (SAGA) complex as selective dependencies for MYCN-amplified neuroblastoma, a disease of dysregulated development driven by an aberrant oncogenic transcriptional program. We characterized the DNA recruitment sites of the SAGA complex in neuroblastoma and the consequences of loss of SAGA complex lysine acetyltransferase (KAT) activity on histone acetylation and gene expression. We demonstrate that loss of SAGA complex KAT activity is associated with reduced MYCN binding on chromatin, suppression of MYC/MYCN gene expression programs, and impaired cell cycle progression. Further, we showed that the SAGA complex is pharmacologically targetable in vitro and in vivo with a KAT2A/KAT2B proteolysis targeting chimeric. Our findings expand our understanding of the histone-modifying complexes that maintain the oncogenic transcriptional state in this disease and suggest therapeutic potential for inhibitors of SAGA KAT activity in MYCN-amplified neuroblastoma.
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Affiliation(s)
- Clare F. Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nathaniel W. Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Alexandra B. Forman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kathleen L. Engel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ying-Jiun C. Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melinda Soeung
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Silvi Salhotra
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Allen Basanthakumar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon Y. R. Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
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5
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Burns D, Berlinguer-Palmini R, Werner A. XPR1: a regulator of cellular phosphate homeostasis rather than a Pi exporter. Pflugers Arch 2024; 476:861-869. [PMID: 38507112 PMCID: PMC11033234 DOI: 10.1007/s00424-024-02941-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Phosphate (Pi) is an essential nutrient, and its plasma levels are under tight hormonal control. Uphill transport of Pi into cells is mediated by the two Na-dependent Pi transporter families SLC34 and SLC20. The molecular identity of a potential Pi export pathway is controversial, though XPR1 has recently been suggested by Giovannini and coworkers to mediate Pi export. We expressed XPR1 in Xenopus oocytes to determine its functional characteristics. Xenopus isoforms of proteins were used to avoid species incompatibility. Protein tagging confirmed the localization of XPR1 at the plasma membrane. Efflux experiments, however, failed to detect translocation of Pi attributable to XPR1. We tested various counter ions and export medium compositions (pH, plasma) as well as potential protein co-factors that could stimulate the activity of XPR1, though without success. Expression of truncated XPR1 constructs and individual domains of XPR1 (SPX, transmembrane core, C-terminus) demonstrated downregulation of the uptake of Pi mediated by the C-terminal domain of XPR1. Tethering the C-terminus to the transmembrane core changed the kinetics of the inhibition and the presence of the SPX domain blunted the inhibitory effect. Our observations suggest a regulatory role of XPR1 in cellular Pi handling rather than a function as Pi exporter. Accordingly, XPR1 senses intracellular Pi levels via its SPX domain and downregulates cellular Pi uptake via the C-terminal domain. The molecular identity of a potential Pi export protein remains therefore elusive.
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Affiliation(s)
- David Burns
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | | | - Andreas Werner
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.
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6
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Hernando N. Is XPR1 mediating phosphate efflux? Pflugers Arch 2024; 476:717-719. [PMID: 38512477 DOI: 10.1007/s00424-024-02946-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Affiliation(s)
- Nati Hernando
- Institute of Physiology, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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7
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Sannigrahi MK, Cao AC, Rajagopalan P, Sun L, Brody RM, Raghav L, Gimotty PA, Basu D. A novel pipeline for prioritizing cancer type-specific therapeutic vulnerabilities using DepMap identifies PAK2 as a target in head and neck squamous cell carcinomas. Mol Oncol 2024; 18:336-349. [PMID: 37997254 PMCID: PMC10850805 DOI: 10.1002/1878-0261.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/23/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
There is limited guidance on exploiting the genome-wide loss-of-function CRISPR screens in cancer Dependency Map (DepMap) to identify new targets for individual cancer types. This study integrated multiple tools to filter these data in order to seek new therapeutic targets specific to head and neck squamous cell carcinoma (HNSCC). The resulting pipeline prioritized 143 targetable dependencies that represented both well-studied targets and emerging target classes like mitochondrial carriers and RNA-binding proteins. In total, 14 targets had clinical inhibitors used for other cancers or nonmalignant diseases that hold near-term potential to repurpose for HNSCC therapy. Comparing inhibitor response data that were publicly available for 13 prioritized targets between the cell lines with high vs. low dependency on each target uncovered novel therapeutic potential for the PAK2 serine/threonine kinase. PAK2 gene dependency was found to be associated with wild-type p53, low PAK2 mRNA, and diploid status of the 3q amplicon containing PAK2. These findings establish a generalizable pipeline to prioritize clinically relevant targets for individual cancer types using DepMap. Its application to HNSCC highlights novel relevance for PAK2 inhibition and identifies biomarkers of PAK2 inhibitor response.
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Affiliation(s)
- Malay K. Sannigrahi
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Austin C. Cao
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Pavithra Rajagopalan
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lova Sun
- Department of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Robert M. Brody
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lovely Raghav
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Devraj Basu
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
- Ellen and Ronald Caplan Cancer CenterThe Wistar InstitutePhiladelphiaPAUSA
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8
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Cai S, Sun Z, Gao X, Ji KE, Ruge F, Shankla D, Liu X, Jiang WG, Ye L. Kinase D-interacting Substrate of 220 kDa Is Overexpressed in Gastric Cancer and Associated With Local Invasion. Cancer Genomics Proteomics 2023; 20:735-743. [PMID: 38035704 PMCID: PMC10687735 DOI: 10.21873/cgp.20420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND/AIM Kinase D-interacting substrate of 220 kDa (Kidins220), also known as ankyrin repeat-rich membrane spanning protein (ARMS), is a transmembrane scaffold protein. Deregulated Kidins220 has been observed in various malignancies including melanoma, glioma, neuroblastoma, prostate cancer, pancreatic cancer, and ovarian cancer. MATERIALS AND METHODS In the current study, Kidins220 expression was determined at transcript and protein levels. A Kidins220 knockdown cell model was established to identify its role in cellular functions including cell cycle, proliferation, and invasion. Cell signalling was analysed by protein array and the TCGA gastric cancer cohort. RESULTS Kidins220 transcript levels were significantly increased in gastric tumours, compared with adjacent normal tissues. More advanced tumours (TNMIII and TNMIV) exhibited higher protein levels of Kidins220 compared with early-stage tumours (TNMI and TNMII). Increased expression of Kidins220 in gastric cancer was associated with poorer overall survival. Loss of Kidins220 promoted cell invasion and adhesion of gastric cancer and correlated to epithelial-mesenchymal transition (EMT) and matrix metalloproteinase (MMP) signalling. Knockdown of Kidins220 promoted proliferation of gastric cancer cells with an increased population at the G2/M phase. CONCLUSION Our study identified increased expression of Kidins220 in gastric cancer, which is associated with disease progression and poor prognosis. However, Kidins220 presented an inhibitory effect on the proliferation, invasion, and adhesion through a regulation of EMT, MMP and cell cycle.
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Affiliation(s)
- Shuo Cai
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K
- Department of Endoscopy Centre, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, P.R. China
| | - Zhiwei Sun
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K
- VIP-II Division of Medical Department, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, P.R. China
| | - Xiangyu Gao
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Gastrointestinal Tumour Centre, Peking University Cancer Hospital & Institute, Beijing, P.R. China
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - K E Ji
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Gastrointestinal Tumour Centre, Peking University Cancer Hospital & Institute, Beijing, P.R. China
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, P.R. China
| | - Fiona Ruge
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K
| | - Deepa Shankla
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K
| | - Xiangyi Liu
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K
| | - Lin Ye
- Cardiff China Medical Research Collaborative, Cardiff University School of Medicine, Cardiff, U.K.;
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9
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Maheshwari U, Mateos JM, Weber‐Stadlbauer U, Ni R, Tamatey V, Sridhar S, Restrepo A, de Jong PA, Huang S, Schaffenrath J, Stifter SA, Szeri F, Greter M, Koek HL, Keller A. Inorganic phosphate exporter heterozygosity in mice leads to brain vascular calcification, microangiopathy, and microgliosis. Brain Pathol 2023; 33:e13189. [PMID: 37505935 PMCID: PMC10580014 DOI: 10.1111/bpa.13189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Calcification of the cerebral microvessels in the basal ganglia in the absence of systemic calcium and phosphate imbalance is a hallmark of primary familial brain calcification (PFBC), a rare neurodegenerative disorder. Mutation in genes encoding for sodium-dependent phosphate transporter 2 (SLC20A2), xenotropic and polytropic retrovirus receptor 1 (XPR1), platelet-derived growth factor B (PDGFB), platelet-derived growth factor receptor beta (PDGFRB), myogenesis regulating glycosidase (MYORG), and junctional adhesion molecule 2 (JAM2) are known to cause PFBC. Loss-of-function mutations in XPR1, the only known inorganic phosphate exporter in metazoans, causing dominantly inherited PFBC was first reported in 2015 but until now no studies in the brain have addressed whether loss of one functional allele leads to pathological alterations in mice, a commonly used organism to model human diseases. Here we show that mice heterozygous for Xpr1 (Xpr1WT/lacZ ) present with reduced inorganic phosphate levels in the cerebrospinal fluid and age- and sex-dependent growth of vascular calcifications in the thalamus. Vascular calcifications are surrounded by vascular basement membrane and are located at arterioles in the smooth muscle layer. Similar to previously characterized PFBC mouse models, vascular calcifications in Xpr1WT/lacZ mice contain bone matrix proteins and are surrounded by reactive astrocytes and microglia. However, microglial activation is not confined to calcified vessels but shows a widespread presence. In addition to vascular calcifications, we observed vessel tortuosity and transmission electron microscopy analysis revealed microangiopathy-endothelial swelling, phenotypic alterations in vascular smooth muscle cells, and thickening of the basement membrane.
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Affiliation(s)
- Upasana Maheshwari
- Department of Neurosurgery, Clinical Neuroscience CenterUniversity Hospital Zurich, University of ZurichZurichSwitzerland
| | - José M. Mateos
- Center for Microscopy and Image analysisUniversity of ZurichZurichSwitzerland
| | - Ulrike Weber‐Stadlbauer
- Institute of Veterinary Pharmacology and ToxicologyUniversity of Zurich‐Vetsuisse, University of ZurichZurichSwitzerland
- Neuroscience Center ZurichUniversity of Zurich and ETH ZurichZurichSwitzerland
| | - Ruiqing Ni
- Neuroscience Center ZurichUniversity of Zurich and ETH ZurichZurichSwitzerland
- Institute for Biomedical EngineeringUniversity of Zurich and ETH ZurichZurichSwitzerland
| | - Virgil Tamatey
- Research Centre for Natural SciencesInstitute of EnzymologyBudapestHungary
- Doctoral School of BiologyELTE Eotvos Lorand UniversityBudapestHungary
| | - Sucheta Sridhar
- Department of Neurosurgery, Clinical Neuroscience CenterUniversity Hospital Zurich, University of ZurichZurichSwitzerland
- Neuroscience Center ZurichUniversity of Zurich and ETH ZurichZurichSwitzerland
| | - Alejandro Restrepo
- Department of Neurosurgery, Clinical Neuroscience CenterUniversity Hospital Zurich, University of ZurichZurichSwitzerland
| | - Pim A. de Jong
- Department of RadiologyUniversity Medical Center Utrecht, Utrecht UniversityUtrechtThe Netherlands
| | - Sheng‐Fu Huang
- Department of Neurosurgery, Clinical Neuroscience CenterUniversity Hospital Zurich, University of ZurichZurichSwitzerland
| | - Johanna Schaffenrath
- Department of Neurosurgery, Clinical Neuroscience CenterUniversity Hospital Zurich, University of ZurichZurichSwitzerland
| | | | - Flora Szeri
- Research Centre for Natural SciencesInstitute of EnzymologyBudapestHungary
| | - Melanie Greter
- Institute of Experimental ImmunologyUniversity of ZurichZurichSwitzerland
| | - Huiberdina L. Koek
- Department of Geriatric MedicineUniversity Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
| | - Annika Keller
- Department of Neurosurgery, Clinical Neuroscience CenterUniversity Hospital Zurich, University of ZurichZurichSwitzerland
- Neuroscience Center ZurichUniversity of Zurich and ETH ZurichZurichSwitzerland
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10
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Yao D, Binan L, Bezney J, Simonton B, Freedman J, Frangieh CJ, Dey K, Geiger-Schuller K, Eraslan B, Gusev A, Regev A, Cleary B. Scalable genetic screening for regulatory circuits using compressed Perturb-seq. Nat Biotechnol 2023:10.1038/s41587-023-01964-9. [PMID: 37872410 PMCID: PMC11035494 DOI: 10.1038/s41587-023-01964-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/22/2023] [Indexed: 10/25/2023]
Abstract
Pooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have emerged as a key technique in functional genomics, but they are limited in scale by cost and combinatorial complexity. In this study, we modified the design of Perturb-seq by incorporating algorithms applied to random, low-dimensional observations. Compressed Perturb-seq measures multiple random perturbations per cell or multiple cells per droplet and computationally decompresses these measurements by leveraging the sparse structure of regulatory circuits. Applied to 598 genes in the immune response to bacterial lipopolysaccharide, compressed Perturb-seq achieves the same accuracy as conventional Perturb-seq with an order of magnitude cost reduction and greater power to learn genetic interactions. We identified known and novel regulators of immune responses and uncovered evolutionarily constrained genes with downstream targets enriched for immune disease heritability, including many missed by existing genome-wide association studies. Our framework enables new scales of interrogation for a foundational method in functional genomics.
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Affiliation(s)
- Douglas Yao
- Program in Systems, Synthetic, and Quantitative Biology, Harvard University, Cambridge, MA, USA
| | - Loic Binan
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jon Bezney
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Brooke Simonton
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jahanara Freedman
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chris J Frangieh
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kushal Dey
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Alexander Gusev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Genentech, South San Francisco, CA, USA
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Program in Bioinformatics, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
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11
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Jia M, Liang J, Li Z, Qin Y, Li Q, Wang J, Lu X. Screening tumor stage-specific candidate neoantigens in thyroid adenocarcinoma using integrated exome and transcriptome sequencing. Front Immunol 2023; 14:1187160. [PMID: 37854594 PMCID: PMC10579579 DOI: 10.3389/fimmu.2023.1187160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
Background The incidence of thyroid carcinoma (THCA), the most common endocrine tumor, is continuously increasing worldwide. Although the overall prognosis of THCA is good, patients with distant metastases exhibit a mortality rate of 5-20%. Methods To improve the diagnosis and overall prognosis of patients with thyroid cancer, we screened specific candidate neoantigen genes in early- and late-stage THCA by analyzing the transcriptome and somatic cell mutations in this study. Results The top five early-stage neoantigen-related genes (NRGs) were G protein-coupled receptor 4 [GPR4], chondroitin sulfate proteoglycan 4 [CSPG4], teneurin transmembrane protein 1 [TENM1], protein S 1 [PROS1], and thymidine kinase 1 [TK1], whereas the top five late-stage NRGs were cadherin 6 [CDH6], semaphorin 6B [SEMA6B], dysferlin [DYSF], xenotropic and polytropic retrovirus receptor 1 [XPR1], and ABR activator of RhoGEF and GTPase [ABR]. Subsequently, we used machine learning models to verify their ability to screen NRGs and analyze the correlations among NRGs, immune cell types, and immune checkpoint regulators. The use of candidate antigen genes resulted in a better diagnostic model (the area under the curve [AUC] value of the early-stage group [0.979] was higher than that of the late-stage group [0.959]). Then, a prognostic model was constructed to predict NRG survival, and the 1-, 3- and 5-year AUC values were 0.83, 0.87, and 0.86, respectively, which were closely related to different immune cell types. Comparison of the expression trends and mutation frequencies of NRGs in multiple tumors revealed their potential for the development of broad spectrum therapeutic drugs. Conclusion In conclusion, the candidate NRGs identified in this study could potentially be used as therapeutic targets and diagnostic biomarkers for the development of novel broad spectrum therapeutic agents.
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Affiliation(s)
- Meng Jia
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiawen Liang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Zhuyao Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ye Qin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qianqian Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianwei Wang
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou, China
| | - Xiubo Lu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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12
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Dvorak V, Casiraghi A, Colas C, Koren A, Tomek T, Offensperger F, Rukavina A, Tin G, Hahn E, Dobner S, Frommelt F, Boeszoermenyi A, Bernada V, Hannich JT, Ecker GF, Winter GE, Kubicek S, Superti-Furga G. Paralog-dependent isogenic cell assay cascade generates highly selective SLC16A3 inhibitors. Cell Chem Biol 2023; 30:953-964.e9. [PMID: 37516113 PMCID: PMC10437005 DOI: 10.1016/j.chembiol.2023.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/02/2023] [Accepted: 06/30/2023] [Indexed: 07/31/2023]
Abstract
Despite being considered druggable and attractive therapeutic targets, most of the solute carrier (SLC) membrane transporters remain pharmacologically underexploited. One of the reasons for this is a lack of reliable chemical screening assays, made difficult by functional redundancies among SLCs. In this study we leveraged synthetic lethality between the lactate transporters SLC16A1 and SLC16A3 in a screening strategy that we call paralog-dependent isogenic cell assay (PARADISO). The system involves five isogenic cell lines, each dependent on various paralog genes for survival/fitness, arranged in a screening cascade tuned for the identification of SLC16A3 inhibitors. We screened a diversity-oriented library of ∼90,000 compounds and further developed our hits into slCeMM1, a paralog-selective and potent SLC16A3 inhibitor. By implementing chemoproteomics, we showed that slCeMM1 is selective also at the proteome-wide level, thus fulfilling an important criterion for chemical probes. This study represents a framework for the development of specific cell-based drug discovery assays.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andrea Casiraghi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Claire Colas
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fabian Offensperger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Viktoriia Bernada
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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13
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Bi QC, Deng ZQ, Lv YF, Liu Y, Xie CS, He YQ, Tang Q. Low Pi stress enhances the sensitivity of hepatocellular carcinoma to sorafenib. Biochem Pharmacol 2023; 213:115593. [PMID: 37196682 DOI: 10.1016/j.bcp.2023.115593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
Sorafenib is a tyrosine kinase inhibitor for the treatment of advanced-stage HCC; however, clinical trials of sorafenib failed to demonstrate long-term survival benefits due to drug resistance. Low Pi stress has been shown to inhibit tumor growth and the expression of multidrug resistance-associated proteins. In this study, we investigated the sensitivity of HCC to sorafenib under conditions of low Pi stress. As a result, we found that low Pi stress facilitated sorafenib-mediated suppression of migration and invasion of HepG-2 and Hepa1-6 cells by decreasing the phosphorylation or expression of AKT, Erk and MMP-9. Angiogenesis was inhibited due to decreased expression of PDGFR under low Pi stress. Low Pi stress also decreased the viability of sorafenib-resistant cells by directly regulating the expression of AKT, HIF-1a and P62. In vivo drug sensitivity analysis in the four animal models showed a similar tendency that low Pi stress enhances sorafenib sensitivity in both the normal and drug-resistant models. Altogether, low Pi stress enhances the sensitivity of hepatocellular carcinoma to sorafenib and expands the indications for sevelamer.
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Affiliation(s)
- Qiu-Chen Bi
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, China; Institute for Advanced Study, Nanchang University, Nanchang, China
| | - Zhi-Qiang Deng
- Department of Oncology, The First People's Hospital of Fuzhou, Fuzhou, China
| | - Yang-Feng Lv
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, China; Institute for Advanced Study, Nanchang University, Nanchang, China
| | - Yue Liu
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, China
| | - Chuan-Sheng Xie
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, China
| | - Yuan-Qiao He
- Department of Laboratory Animal Science, Nanchang University, Nanchang, China
| | - Qun Tang
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, China; Institute for Advanced Study, Nanchang University, Nanchang, China.
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14
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Vredevoogd DW, Peeper DS. Heterogeneity in functional genetic screens: friend or foe? Front Immunol 2023; 14:1162706. [PMID: 37398651 PMCID: PMC10312307 DOI: 10.3389/fimmu.2023.1162706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Functional genetic screens to uncover tumor-intrinsic nodes of immune resistance have uncovered numerous mechanisms by which tumors evade our immune system. However, due to technical limitations, tumor heterogeneity is imperfectly captured with many of these analyses. Here, we provide an overview of the nature and sources of heterogeneity that are relevant for tumor-immune interactions. We argue that this heterogeneity may actually contribute to the discovery of novel mechanisms of immune evasion, given a sufficiently large and heterogeneous set of input data. Taking advantage of tumor cell heterogeneity, we provide proof-of-concept analyses of mechanisms of TNF resistance. Thus, consideration of tumor heterogeneity is imperative to increase our understanding of immune resistance mechanisms.
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15
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Weiskittel TM, Cao A, Meng-Lin K, Lehmann Z, Feng B, Correia C, Zhang C, Wisniewski P, Zhu S, Yong Ung C, Li H. Network Biology-Inspired Machine Learning Features Predict Cancer Gene Targets and Reveal Target Coordinating Mechanisms. Pharmaceuticals (Basel) 2023; 16:752. [PMID: 37242535 PMCID: PMC10223789 DOI: 10.3390/ph16050752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Anticipating and understanding cancers' need for specific gene activities is key for novel therapeutic development. Here we utilized DepMap, a cancer gene dependency screen, to demonstrate that machine learning combined with network biology can produce robust algorithms that both predict what genes a cancer is dependent on and what network features coordinate such gene dependencies. Using network topology and biological annotations, we constructed four groups of novel engineered machine learning features that produced high accuracies when predicting binary gene dependencies. We found that in all examined cancer types, F1 scores were greater than 0.90, and model accuracy remained robust under multiple hyperparameter tests. We then deconstructed these models to identify tumor type-specific coordinators of gene dependency and identified that in certain cancers, such as thyroid and kidney, tumors' dependencies are highly predicted by gene connectivity. In contrast, other histologies relied on pathway-based features such as lung, where gene dependencies were highly predictive by associations with cell death pathway genes. In sum, we show that biologically informed network features can be a valuable and robust addition to predictive pharmacology models while simultaneously providing mechanistic insights.
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Affiliation(s)
- Taylor M. Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
- Mayo Clinic Alix School of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Andrew Cao
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Kevin Meng-Lin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Zachary Lehmann
- Department of Chemistry, Biochemistry and Physics, South Dakota State University, Brookings, SD 57006, USA
| | - Benjamin Feng
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Philip Wisniewski
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
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16
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Pipercevic J, Kohl B, Gerasimaite R, Comte-Miserez V, Hostachy S, Müntener T, Agustoni E, Jessen HJ, Fiedler D, Mayer A, Hiller S. Inositol pyrophosphates activate the vacuolar transport chaperone complex in yeast by disrupting a homotypic SPX domain interaction. Nat Commun 2023; 14:2645. [PMID: 37156835 PMCID: PMC10167327 DOI: 10.1038/s41467-023-38315-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
Many proteins involved in eukaryotic phosphate homeostasis are regulated by SPX domains. In yeast, the vacuolar transporter chaperone (VTC) complex contains two such domains, but mechanistic details of its regulation are not well understood. Here, we show at the atomic level how inositol pyrophosphates interact with SPX domains of subunits Vtc2 and Vtc3 to control the activity of the VTC complex. Vtc2 inhibits the catalytically active VTC subunit Vtc4 by homotypic SPX-SPX interactions via the conserved helix α1 and the previously undescribed helix α7. Binding of inositol pyrophosphates to Vtc2 abrogates this interaction, thus activating the VTC complex. Accordingly, VTC activation is also achieved by site-specific point mutations that disrupt the SPX-SPX interface. Structural data suggest that ligand binding induces reorientation of helix α1 and exposes the modifiable helix α7, which might facilitate its post-translational modification in vivo. The variable composition of these regions within the SPX domain family might contribute to the diversified SPX functions in eukaryotic phosphate homeostasis.
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Affiliation(s)
- Joka Pipercevic
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Bastian Kohl
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Ruta Gerasimaite
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
- Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Véronique Comte-Miserez
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
| | - Sarah Hostachy
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Elia Agustoni
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Henning Jacob Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Dorothea Fiedler
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, CP51 1066, Epalinges, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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17
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Jennings ML. Role of transporters in regulating mammalian intracellular inorganic phosphate. Front Pharmacol 2023; 14:1163442. [PMID: 37063296 PMCID: PMC10097972 DOI: 10.3389/fphar.2023.1163442] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
This review summarizes the current understanding of the role of plasma membrane transporters in regulating intracellular inorganic phosphate ([Pi]In) in mammals. Pi influx is mediated by SLC34 and SLC20 Na+-Pi cotransporters. In non-epithelial cells other than erythrocytes, Pi influx via SLC20 transporters PiT1 and/or PiT2 is balanced by efflux through XPR1 (xenotropic and polytropic retrovirus receptor 1). Two new pathways for mammalian Pi transport regulation have been described recently: 1) in the presence of adequate Pi, cells continuously internalize and degrade PiT1. Pi starvation causes recycling of PiT1 from early endosomes to the plasma membrane and thereby increases the capacity for Pi influx; and 2) binding of inositol pyrophosphate InsP8 to the SPX domain of XPR1 increases Pi efflux. InsP8 is degraded by a phosphatase that is strongly inhibited by Pi. Therefore, an increase in [Pi]In decreases InsP8 degradation, increases InsP8 binding to SPX, and increases Pi efflux, completing a feedback loop for [Pi]In homeostasis. Published data on [Pi]In by magnetic resonance spectroscopy indicate that the steady state [Pi]In of skeletal muscle, heart, and brain is normally in the range of 1–5 mM, but it is not yet known whether PiT1 recycling or XPR1 activation by InsP8 contributes to Pi homeostasis in these organs. Data on [Pi]In in cultured cells are variable and suggest that some cells can regulate [Pi] better than others, following a change in [Pi]Ex. More measurements of [Pi]In, influx, and efflux are needed to determine how closely, and how rapidly, mammalian [Pi]In is regulated during either hyper- or hypophosphatemia.
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18
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Golgi damage caused by dysfunction of PiT-2 in primary familial brain calcification. Biochem Biophys Res Commun 2023; 642:167-174. [PMID: 36584480 DOI: 10.1016/j.bbrc.2022.12.050] [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: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022]
Abstract
The Golgi apparatus is vital for protein modification and molecular trafficking. It is essential for nerve development and activity, and damage thereof is implicated in many neurological diseases. Primary familial brain calcification (PFBC) is a rare inherited neurodegenerative disease characterized by multiple brain calcifications. SLC20A2, which encodes the inorganic phosphate transporter 2 (PiT-2) protein, is the main pathogenic gene in PFBC. The PiT-2 protein is a sodium-dependent phosphate type III transporter, and dysfunction leads to a deficit in the cellular intake of inorganic phosphate (Pi) and calcium deposits. Whether the impaired Golgi apparatus is involved in the PFBC procession requires elucidation. In this study, we constructed induced pluripotent stem cells (iPSCs) derived from two PFBC patients with different SLC20A2 gene mutations (c.613G > A or del exon10) and two healthy volunteers as dependable cell models for research on pathogenic mechanism. To study the mechanism, we differentiated iPSCs into neurons and astrocytes in vitro. Our study found disruptive Golgi structure and damaged autophagy in PFBC neurons with increased activity of mTOR. We also found damaged mitochondria and increased apoptosis in the PFBC dopaminergic neurons and astrocytes. In this study, we prove that dysfunctional PiT-2 leads to an imbalance of cellular Pi, which may disrupt the Golgi apparatus with impaired autophagy, mitochondria and apoptosis in PFBC. Our study provides a new avenue for understanding nerve damage and pathogenic mechanism in brain calcifications.
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19
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Functional genomics of complex cancer genomes. Nat Commun 2022; 13:5908. [PMID: 36207330 PMCID: PMC9547052 DOI: 10.1038/s41467-022-33717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 09/29/2022] [Indexed: 02/01/2023] Open
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20
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Systematic profiling of conditional degron tag technologies for target validation studies. Nat Commun 2022; 13:5495. [PMID: 36127368 PMCID: PMC9489723 DOI: 10.1038/s41467-022-33246-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/08/2022] [Indexed: 12/03/2022] Open
Abstract
Conditional degron tags (CDTs) are a powerful tool for target validation that combines the kinetics and reversible action of pharmacological agents with the generalizability of genetic manipulation. However, successful design of a CDT fusion protein often requires a prolonged, ad hoc cycle of construct design, failure, and re-design. To address this limitation, we report here a system to rapidly compare the activity of five unique CDTs: AID/AID2, IKZF3d, dTAG, HaloTag, and SMASh. We demonstrate the utility of this system against 16 unique protein targets. We find that expression and degradation are highly dependent on the specific CDT, the construct design, and the target. None of the CDTs leads to efficient expression and/or degradation across all targets; however, our systematic approach enables the identification of at least one optimal CDT fusion for each target. To enable the adoption of CDT strategies more broadly, we have made these reagents, and a detailed protocol, available as a community resource. Conditional Degron Tags are a valuable tool to validate and study novel therapeutic targets. Here, the authors compared 5 orthogonal tags across 16 unique proteins and provide a panel of vectors for users to systematically screen the tags with their own protein of interest.
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21
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Nguyen Trung M, Furkert D, Fiedler D. Versatile signaling mechanisms of inositol pyrophosphates. Curr Opin Chem Biol 2022; 70:102177. [PMID: 35780751 DOI: 10.1016/j.cbpa.2022.102177] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 01/03/2023]
Abstract
Inositol pyrophosphates (PP-InsPs) constitute a group of highly charged messengers, which regulate central biological processes in health and disease, such as cellular phosphate and general energy homeostasis. Deciphering the molecular mechanisms underlying PP-InsP-mediated signaling remains a challenge due to the unique properties of these molecules, the different modes of action they can access, and a somewhat limited chemical and analytical toolset. Herein, we summarize the most recent mechanistic insights into PP-InsP signaling, which illustrate our progress in connecting mechanism and function of PP-InsPs.
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Affiliation(s)
- Minh Nguyen Trung
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - David Furkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany.
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