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Pabon A, Bhupana JN, Wong CO. Crosstalk between degradation and bioenergetics: how autophagy and endolysosomal processes regulate energy production. Neural Regen Res 2025; 20:671-681. [PMID: 38886933 DOI: 10.4103/nrr.nrr-d-23-02095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/30/2024] [Indexed: 06/20/2024] Open
Abstract
Cells undergo metabolic reprogramming to adapt to changes in nutrient availability, cellular activity, and transitions in cell states. The balance between glycolysis and mitochondrial respiration is crucial for energy production, and metabolic reprogramming stipulates a shift in such balance to optimize both bioenergetic efficiency and anabolic requirements. Failure in switching bioenergetic dependence can lead to maladaptation and pathogenesis. While cellular degradation is known to recycle precursor molecules for anabolism, its potential role in regulating energy production remains less explored. The bioenergetic switch between glycolysis and mitochondrial respiration involves transcription factors and organelle homeostasis, which are both regulated by the cellular degradation pathways. A growing body of studies has demonstrated that both stem cells and differentiated cells exhibit bioenergetic switch upon perturbations of autophagic activity or endolysosomal processes. Here, we highlighted the current understanding of the interplay between degradation processes, specifically autophagy and endolysosomes, transcription factors, endolysosomal signaling, and mitochondrial homeostasis in shaping cellular bioenergetics. This review aims to summarize the relationship between degradation processes and bioenergetics, providing a foundation for future research to unveil deeper mechanistic insights into bioenergetic regulation.
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Affiliation(s)
- Angelid Pabon
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
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2
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Yang D, Chen H, Zhou Z, Guo J. ANXA5 predicts prognosis and immune response and mediates proliferation and migration in head and neck squamous cell carcinoma. Gene 2024; 931:148867. [PMID: 39168258 DOI: 10.1016/j.gene.2024.148867] [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: 01/04/2024] [Revised: 08/03/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is a common malignancy that often develops unnoticed. Typically, these tumors are identified at advanced stages, resulting in a relatively low chance of successful treatment. Anoikis serves as a natural defense against the spread of tumor cells, meaning circumventing anoikis can effectively inhibit tumor metastasis. Nonetheless, studies focusing on anoikis in the context of HNSCC remain scarce. METHODS Anoikis-related genes (ARGs) were identified by using the GeneCards and Harmonizome databases. Expression data of these genes and relevant clinical features were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A LASSO regression and a prognostic risk score model were developed to determine their prognostic significance. The analysis included the use of the CIBERSORT algorithm to quantify immune and stromal cell presence. Furthermore, in vitro and in vivo, we confirmed the expression and functional roles of proteins and mRNA of genes independently predictive of prognosis. RESULTS The study identified eight genes linked to prognosis (ANXA5, BAK1, CDKN2A, PPARG, CCR7, MAPK11, CRYAB, CRYBA1) and developed a prognostic model that effectively forecasts the survival outcomes for patients with HNSCC. A higher survival likelihood is associated with lower risk scores. In addition, a significant relationship was found between immune and risk score, and ANXA5 deletion promoted the killing of HNSCC cells by activated CD8+ T cells. During the screening process, 65 different chemotherapeutic drugs were found to have significant differences in IC50 values when comparing high- and low-risk categories. ANXA5 emerged as a gene with independent prognostic significance, exhibiting notably elevated protein and mRNA levels in HNSCC tissue compared to non-tumorous tissue. The suppression of ANXA5 gene activity resulted in a substantial decrease in both the growth and mobility of HNSCC cells. Animal model experiments demonstrated that inhibiting ANXA5 suppressed HNSCC growth and migration in vivo. CONCLUSION Through bioinformatics, a prognostic risk model of high precision was developed, offering valuable insights into the survival rates and immune responses in patients with HNSCC. ANXA5 is highlighted as a significant prognostic factor among the identified genes, indicating its promise as a potential therapeutic target for those with HNSCC.
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Affiliation(s)
- Donghui Yang
- Department of Otorhinolaryngology, Gaozhou People's Hospital, Gaozhou, China.
| | - Huikuan Chen
- Department of Otorhinolaryngology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zheng Zhou
- Department of Otolaryngology Head and Neck Surgery, Hunan Children's Hospital, Changsha, China
| | - Jinfei Guo
- Department of Otorhinolaryngology, Gaozhou People's Hospital, Gaozhou, China
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3
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Wu X, Chen M, Liu K, Wu Y, Feng Y, Fu S, Xu H, Zhao Y, Lin F, Lin L, Ye S, Lin J, Xiao T, Li W, Lou M, Lv H, Qiu Y, Yu R, Chen W, Li M, Feng X, Luo Z, Guo L, Ke H, Zhao L. Molecular classification of geriatric breast cancer displays distinct senescent subgroups of prognostic significance. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102309. [PMID: 39296329 PMCID: PMC11408383 DOI: 10.1016/j.omtn.2024.102309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/12/2024] [Indexed: 09/21/2024]
Abstract
Breast cancer in the elderly presents distinct biological characteristics and clinical treatment responses compared with cancer in younger patients. Comprehensive Geriatric Assessment is recommended for evaluating treatment efficacy in elderly cancer patients based on physiological classification. However, research on molecular classification in older cancer patients remains insufficient. In this study, we identified two subgroups with distinct senescent clusters among geriatric breast cancer patients through multi-omics analysis. Using various machine learning algorithms, we developed a comprehensive scoring model called "Sene_Signature," which more accurately distinguished elderly breast cancer patients compared with existing methods and better predicted their prognosis. The Sene_Signature was correlated with tumor immune cell infiltration, as supported by single-cell transcriptomics, RNA sequencing, and pathological data. Furthermore, we observed increased drug responsiveness in patients with a high Sene_Signature to treatments targeting the epidermal growth factor receptor and cell-cycle pathways. We also established a user-friendly web platform to assist investigators in assessing Sene_Signature scores and predicting treatment responses for elderly breast cancer patients. In conclusion, we developed a novel model for evaluating prognosis and therapeutic responses, providing a potential molecular classification that assists in the pre-treatment assessment of geriatric breast cancer.
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Affiliation(s)
- Xia Wu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
- Ningbo Clinical Pathology Diagnosis Center, Ningbo, Zhejiang 315021, China
| | - Mengxin Chen
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Kang Liu
- Ganzhou People's Hospital, Ganzhou 341000, China
| | - Yixin Wu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Yun Feng
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Shiting Fu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Huaimeng Xu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Yongqi Zhao
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Feilong Lin
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Liang Lin
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Shihui Ye
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Junqiang Lin
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Taiping Xiao
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Wenhao Li
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Meng Lou
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Hongyu Lv
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Ye Qiu
- Huankui Academy, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Ruifan Yu
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
| | - Wenyan Chen
- Department of Medical Oncology, Nanchang People's Hospital, Nanchang 330008, China
| | - Mengyuan Li
- Department of Gynaecology and Obstetrics, Chongqing General Hospital, Chongqing 401147, China
| | - Xu Feng
- Xianlin High School, Weinan 714000, China
| | | | - Lu Guo
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310000, China
| | - Hao Ke
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Limin Zhao
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China
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Jornayvaz FR, Gariani K, Somm E, Jaquet V, Bouzakri K, Szanto I. NADPH oxidases in healthy white adipose tissue and in obesity: function, regulation, and clinical implications. Obesity (Silver Spring) 2024; 32:1799-1811. [PMID: 39315402 DOI: 10.1002/oby.24113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/19/2024] [Accepted: 06/11/2024] [Indexed: 09/25/2024]
Abstract
Reactive oxygen species, when produced in a controlled manner, are physiological modulators of healthy white adipose tissue (WAT) expansion and metabolic function. By contrast, unbridled production of oxidants is associated with pathological WAT expansion and the establishment of metabolic dysfunctions, most notably insulin resistance and type 2 diabetes mellitus. NADPH oxidases (NOXs) produce oxidants in an orderly fashion and are present in adipocytes and in other diverse WAT-constituent cell types. Recent studies have established several links between aberrant NOX-derived oxidant production, adiposity, and metabolic homeostasis. The objective of this review is to highlight the physiological roles attributed to diverse NOX isoforms in healthy WAT and summarize current knowledge of the metabolic consequences related to perturbations in their adequate oxidant production. We detail WAT-related alterations in preclinical investigations conducted in NOX-deficient murine models. In addition, we review clinical studies that have employed NOX inhibitors and currently available data related to human NOX mutations in metabolic disturbances. Future investigations aimed at understanding the integration of NOX-derived oxidants in the regulation of the WAT cellular redox network are essential for designing successful redox-related precision therapies to curb obesity and attenuate obesity-associated metabolic pathologies.
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Affiliation(s)
- François R Jornayvaz
- Service of Endocrinology, Diabetes, Nutrition and Patient Therapeutic Education, Department of Internal Medicine, Geneva University Hospitals and University of Geneva Medical School, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
- Diabetes Center of the Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Karim Gariani
- Service of Endocrinology, Diabetes, Nutrition and Patient Therapeutic Education, Department of Internal Medicine, Geneva University Hospitals and University of Geneva Medical School, Geneva, Switzerland
- Diabetes Center of the Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Emmanuel Somm
- Service of Endocrinology, Diabetes, Nutrition and Patient Therapeutic Education, Department of Internal Medicine, Geneva University Hospitals and University of Geneva Medical School, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
- Diabetes Center of the Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Vincent Jaquet
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
- RE.A.D.S. Unit (Readers, Assay Development and Screening Unit), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karim Bouzakri
- UMR DIATHEC, EA 7294, Centre Européen d'Etude du Diabète, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Ildiko Szanto
- Service of Endocrinology, Diabetes, Nutrition and Patient Therapeutic Education, Department of Internal Medicine, Geneva University Hospitals and University of Geneva Medical School, Geneva, Switzerland
- Diabetes Center of the Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
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5
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Courtemanche N, Henty-Ridilla JL. Actin filament dynamics at barbed ends: New structures, new insights. Curr Opin Cell Biol 2024; 90:102419. [PMID: 39178734 DOI: 10.1016/j.ceb.2024.102419] [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: 05/01/2024] [Revised: 06/30/2024] [Accepted: 07/31/2024] [Indexed: 08/26/2024]
Abstract
The dynamic actin cytoskeleton contributes to many critical biological processes by providing the structural support underlying the morphology of most cells, facilitating intracellular transport, and generating forces required for cell motility and division. To execute many of these functions, actin monomers polymerize into polarized filaments that display different structural and biochemical properties at each end. Filament dynamics are regulated by diverse regulatory proteins which collaborate to dictate rates of elongation and disassembly, particularly at the fast-growing barbed (plus) end. This review highlights the biochemical mechanisms of six barbed end regulatory proteins: formin, profilin, capping protein, IQGAP1, cyclase-associated protein, and twinfilin. We discuss how individual proteins influence actin dynamics and how several intriguing complex assemblies influence the polymerization fate of actin filaments. Understanding these mechanisms offers insights into how actin is regulated in essential cell processes and dysregulated in disease.
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Affiliation(s)
- Naomi Courtemanche
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jessica L Henty-Ridilla
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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6
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Martisova A, Faktor J, Sosolikova T, Klemesova I, Kolarova T, Holcakova J, Hrstka R. Characterization of the AGR2-NPM3 axis uncovers the AGR2 involvement in PD-L1 regulation in colorectal cancer. Sci Rep 2024; 14:21926. [PMID: 39300184 PMCID: PMC11413233 DOI: 10.1038/s41598-024-72990-z] [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: 06/04/2024] [Accepted: 09/12/2024] [Indexed: 09/22/2024] Open
Abstract
Despite extensive research, the molecular role of AGR2 in the progression and metastasis of colorectal cancer (CRC) has not been fully characterized. We used quantitative mass spectrometry (SWATH MS) to identify differentially expressed proteins in paired CRC cell models of the SW480 and SW620 cell lines in response to AGR2 protein level manipulation. Relying on the results from SWATH MS and subsequent immunochemical validation, we selected NMP3 as the top candidate protein associated with AGR2 in CRC tumour cells in our screen. RT‒qPCR and immunochemical analysis confirmed the involvement of AGR2-mediated regulation of NPM3 at the transcriptional and posttranscriptional levels. Since PD-L1 is a constituent of the NPM3 regulatory axis, we aimed to correlate the changes in PD-L1 to the differential expression of AGR2 in our cell models. We found that AGR2 positively regulates PD-L1 levels in both SW480 and SW620 cell lines; additionally, several different CRC patient transcriptome cohorts confirmed the association of AGR2 with PD-L1. Our work reveals a new AGR2-NPM3 regulatory axis and the involvement of AGR2 in the regulation of PD-L1, which paves the way for the association of AGR2 with immune evasion in CRC cells.
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Affiliation(s)
- Andrea Martisova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, Brno, 65653, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, Gdansk, 80-822, Poland
| | - Tereza Sosolikova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, Brno, 65653, Czech Republic
- Department of Experimental Biology, Faculty of Science, 117204 Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Iveta Klemesova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, Brno, 65653, Czech Republic
| | - Tamara Kolarova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, Brno, 65653, Czech Republic
| | - Jitka Holcakova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, Brno, 65653, Czech Republic
| | - Roman Hrstka
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty Kopec 7, Brno, 65653, Czech Republic.
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7
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Messa L, Testa C, Carelli S, Rey F, Jacchetti E, Cereda C, Raimondi MT, Ceri S, Pinoli P. Non-Negative Matrix Tri-Factorization for Representation Learning in Multi-Omics Datasets with Applications to Drug Repurposing and Selection. Int J Mol Sci 2024; 25:9576. [PMID: 39273521 PMCID: PMC11394968 DOI: 10.3390/ijms25179576] [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: 07/12/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
The vast corpus of heterogeneous biomedical data stored in databases, ontologies, and terminologies presents a unique opportunity for drug design. Integrating and fusing these sources is essential to develop data representations that can be analyzed using artificial intelligence methods to generate novel drug candidates or hypotheses. Here, we propose Non-Negative Matrix Tri-Factorization as an invaluable tool for integrating and fusing data, as well as for representation learning. Additionally, we demonstrate how representations learned by Non-Negative Matrix Tri-Factorization can effectively be utilized by traditional artificial intelligence methods. While this approach is domain-agnostic and applicable to any field with vast amounts of structured and semi-structured data, we apply it specifically to computational pharmacology and drug repurposing. This field is poised to benefit significantly from artificial intelligence, particularly in personalized medicine. We conducted extensive experiments to evaluate the performance of the proposed method, yielding exciting results, particularly compared to traditional methods. Novel drug-target predictions have also been validated in the literature, further confirming their validity. Additionally, we tested our method to predict drug synergism, where constructing a classical matrix dataset is challenging. The method demonstrated great flexibility, suggesting its applicability to a wide range of tasks in drug design and discovery.
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Affiliation(s)
- Letizia Messa
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milan, Italy
| | - Carolina Testa
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milan, Italy
| | - Stephana Carelli
- Center of Functional Genomics and Rare Diseases, Buzzi Children's Hospital, 20154 Milan, Italy
- Pediatric Clinical Research Center "Fondazione Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20157 Milan, Italy
| | - Federica Rey
- Pediatric Clinical Research Center "Fondazione Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20157 Milan, Italy
| | - Emanuela Jacchetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20133 Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20133 Milan, Italy
| | - Stefano Ceri
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milan, Italy
| | - Pietro Pinoli
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milan, Italy
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8
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Ranti D, Yu H, Wang YA, Bieber C, Strandgaard T, Salomé B, Houghton S, Kim J, Ravichandran H, Okulate I, Merritt E, Bang S, Demetriou A, Li Z, Lindskrog SV, Ruan DF, Daza J, Rai R, Hegewisch-Solloa E, Mace EM, Fernandez-Rodriguez R, Izadmehr S, Doherty G, Narasimhan A, Farkas AM, Cruz-Encarnacion P, Shroff S, Patel F, Tran M, Park SJ, Qi J, Patel M, Geanon D, Kelly G, de Real RM, Lee B, Nie K, Miake-Iye S, Angeliadis K, Radkevich E, Thin TH, Garcia-Barros M, Brown H, Martin B, Mateo A, Soto A, Sussman R, Shiwlani S, Francisco-Simon S, Beaumont KG, Hu Y, Wang YC, Wang L, Sebra RP, Smith S, Skobe M, Clancy-Thompson E, Palmer D, Hammond S, Hopkins BD, Wiklund P, Zhu J, Bravo-Cordero JJ, Brody R, Hopkins B, Chen Z, Kim-Schulze S, Dyrskjøt L, Elemento O, Tocheva A, Song WM, Bhardwaj N, Galsky MD, Sfakianos JP, Horowitz A. HLA-E and NKG2A Mediate Resistance to M. bovis BCG Immunotherapy in Non-Muscle-Invasive Bladder Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.02.610816. [PMID: 39282294 PMCID: PMC11398371 DOI: 10.1101/2024.09.02.610816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Mycobacterium bovis Bacillus Calmette-Guerin (BCG) is the primary treatment for non-muscle-invasive bladder cancer (NMIBC), known to stimulate inflammatory cytokines, notably interferon (IFN)-γ. We observed that prolonged IFN-γ exposure fosters adaptive resistance in recurrent tumors, aiding immune evasion and tumor proliferation. We identify HLA-E and NKG2A, part of a novel NK and T cell checkpoint pathway, as key mediators of resistance in BCG-unresponsive NMIBC. IFN-γ enhances HLA-E and PD-L1 expression in recurrent tumors, with an enrichment of intra-tumoral NKG2A-expressing NK and CD8 T cells. CXCL9+ macrophages and dendritic cells and CXCL12-expressing stromal cells likely recruit CXCR3/CXCR4-expressing NK and T cells and CXCR7+ HLA-EHIGH tumor cells. NK and CD8 T cells remain functional within BCG-unresponsive tumors but are inhibited by HLA-E and PD-L1, providing a framework for combined NKG2A and PD-L1 blockade strategy for bladder-sparing treatment of BCG-unresponsive NMIBC.
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Affiliation(s)
- D Ranti
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - H Yu
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Y A Wang
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - C Bieber
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - T Strandgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - B Salomé
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean Houghton
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - J Kim
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - H Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - I Okulate
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - E Merritt
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Bang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A Demetriou
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Z Li
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S V Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - D F Ruan
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Daza
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Rai
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - E Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York NY, USA
| | - E M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York NY, USA
| | - R Fernandez-Rodriguez
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Izadmehr
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - G Doherty
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Microscopy and Advanced Bioimaging Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A Narasimhan
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Microscopy and Advanced Bioimaging Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A M Farkas
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P Cruz-Encarnacion
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Shroff
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - F Patel
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Tran
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S J Park
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Qi
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D Geanon
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - G Kelly
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R M de Real
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - B Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - K Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Miake-Iye
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - K Angeliadis
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - E Radkevich
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - T H Thin
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - M Garcia-Barros
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - H Brown
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - B Martin
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - A Mateo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - A Soto
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - R Sussman
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - S Shiwlani
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - S Francisco-Simon
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - K G Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Y Hu
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Y-C Wang
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - L Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Smith
- Center for Inflammation research and Translational Medicine, Brunel University London, London, UK
| | - M Skobe
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - D Palmer
- AstraZeneca, Oncology R & D Unit, Gaithersburg, Maryland, USA
| | - S Hammond
- AstraZeneca, Oncology R & D Unit, Gaithersburg, Maryland, USA
| | - B D Hopkins
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P Wiklund
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J J Bravo-Cordero
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Microscopy and Advanced Bioimaging Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Brody
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - B Hopkins
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Microscopy and Advanced Bioimaging Core, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Inflammation research and Translational Medicine, Brunel University London, London, UK
- AstraZeneca, Oncology R & D Unit, Gaithersburg, Maryland, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Z Chen
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Kim-Schulze
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - L Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - O Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - A Tocheva
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - W-M Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - N Bhardwaj
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M D Galsky
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J P Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A Horowitz
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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9
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Bukhari Z, Gu L, Nederstigt AE, Cope LJ, Bolhuis DL, Harvey K, Allen T, Hill S, Yang Y, Lawson G, Lu C, Tran T, Pineda L, Low L, Chiang A, Song J, Fong MV, Rangel VM, Chan WK, Kleiger G, Goldfarb D, Vierra CA, Brown NG, Harrison JS. Design of linked-domain protein inhibitors of UBE2D as tools to study cellular ubiquitination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.02.610852. [PMID: 39282319 PMCID: PMC11398408 DOI: 10.1101/2024.09.02.610852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Ubiquitin (Ub) is a post-translational modification that largely controls proteostasis through mechanisms spanning transcription, translation, and notably, protein degradation. Ub conjugation occurs through a hierarchical cascade of three enzyme classes (E1, E2, and E3s) involving >1000 proteins that regulate the ubiquitination of proteins. The E2 Ub-conjugating enzymes are the midpoint, yet their cellular roles remain under-characterized, partly due to a lack of inhibitors. For example, the cellular roles of the promiscuous E2 UBE2D/UBCH5 are not well described. Here, we develop a highly selective, multivalent, engineered protein inhibitor for the UBE2D family that simultaneously targets the RING- and backside-binding sites. In HeLa cells, these inhibitors phenocopy knockdown of UBE2D by reducing the IC 50 to cisplatin and whole-cell proteomics reveal an increased abundance of ∼20% of the identified proteins, consistent with reduced Ub degradation and proteotoxic stress. These precision tools will enable new studies probing UBE2D's central role in proteome management.
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10
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Young CA, Burt E, Munnamalai V. A cochlear progenitor pool influences patterning of the mammalian sensory epithelium via MYBL2. Development 2024; 151:dev202635. [PMID: 39254648 DOI: 10.1242/dev.202635] [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: 12/18/2023] [Accepted: 08/01/2024] [Indexed: 09/11/2024]
Abstract
During embryonic development, Wnt signaling influences both proliferation and sensory formation in the cochlea. How this dual nature of Wnt signaling is coordinated is unknown. In this study, we define a novel role for a Wnt-regulated gene, Mybl2, which was already known to be important for proliferation, in determining the size and patterning of the sensory epithelium in the murine cochlea. Using a quantitative spatial analysis approach and analyzing Mybl2 loss-of-function, we show that Mybl2 promoted proliferation in the inner sulcus domain but limited the size of the sensory domain by influencing their adjoining boundary position via Jag1 regulation during development. Mybl2 loss-of-function simultaneously decreased proliferation in the inner sulcus and increased the size of the sensory domain, resulting in a wider sensory epithelium with ectopic inner hair cell formation during late embryonic stages. These data suggest that progenitor cells in the inner sulcus determine boundary formation and pattern the sensory epithelium via MYBL2.
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Affiliation(s)
- Caryl A Young
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Emily Burt
- Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Vidhya Munnamalai
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
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11
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Koch RL, Stanton JB, McClatchy S, Churchill GA, Craig SW, Williams DN, Johns ME, Chase KR, Thiesfeldt DL, Flynt JC, Pazdro R. Discovery of genomic loci for liver health and steatosis reveals overlap with glutathione redox genetics. Redox Biol 2024; 75:103248. [PMID: 38917671 PMCID: PMC11254179 DOI: 10.1016/j.redox.2024.103248] [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: 03/08/2024] [Revised: 05/27/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver condition in the United States, encompassing a wide spectrum of liver pathologies including steatosis, steatohepatitis, fibrosis, and cirrhosis. Despite its high prevalence, there are no medications currently approved by the Food and Drug Administration for the treatment of NAFLD. Recent work has suggested that NAFLD has a strong genetic component and identifying causative genes will improve our understanding of the molecular mechanisms contributing to NAFLD and yield targets for future therapeutic investigations. Oxidative stress is known to play an important role in NAFLD pathogenesis, yet the underlying mechanisms accounting for disturbances in redox status are not entirely understood. To better understand the relationship between the glutathione redox system and signs of NAFLD in a genetically-diverse population, we measured liver weight, serum biomarkers aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and graded liver pathology in a large cohort of Diversity Outbred mice. We compared hepatic endpoints to those of the glutathione redox system previously measured in the livers and kidneys of the same mice, and we screened for statistical and genetic associations using the R/qtl2 software. We discovered several novel genetic loci associated with markers of liver health, including loci that were associated with both liver steatosis and glutathione redox status. Candidate genes within each locus point to possible new mechanisms underlying the complex relationship between NAFLD and the glutathione redox system, which could have translational implications for future studies targeting NAFLD pathology.
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Affiliation(s)
- Rebecca L Koch
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - James B Stanton
- Department of Pathology, University of Georgia, Athens, GA, USA, 30602
| | | | | | - Steven W Craig
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Darian N Williams
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Mallory E Johns
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Kylah R Chase
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Dana L Thiesfeldt
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Jessica C Flynt
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Robert Pazdro
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602.
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12
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Wang RH, Thakar J. Comparative analysis of single-cell pathway scoring methods and a novel approach. NAR Genom Bioinform 2024; 6:lqae124. [PMID: 39318507 PMCID: PMC11420841 DOI: 10.1093/nargab/lqae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/22/2024] [Accepted: 09/03/2024] [Indexed: 09/26/2024] Open
Abstract
Single-cell gene set analysis (scGSA) provides a useful approach for quantifying molecular functions and pathways in high-throughput transcriptomic data, facilitating the biological interpretation of complex human datasets. However, various factors such as gene set size, quality of the gene sets and the dropouts impact the performance of scGSA. To address these limitations, we present a single-cell Pathway Score (scPS) method to measure gene set activity at single-cell resolution. Furthermore, we benchmark our method with six other methods: AUCell, AddModuleScore, JASMINE, UCell, SCSE and ssGSEA. The comparison across all the methods using two different simulation approaches highlights the effect of cell count, gene set size, noise, condition-specific genes and zero imputation on their performance. The results of our study indicate that the scPS is comparable with other single-cell scoring methods and detects fewer false positives. Importantly, this work reveals critical variables in the scGSA.
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Affiliation(s)
- Ruoqiao H Wang
- Department of Biomedical Genetics, University of Rochester, 601 Elmwood Ave, NY 14642, USA
| | - Juilee Thakar
- Department of Biomedical Genetics, University of Rochester, 601 Elmwood Ave, NY 14642, USA
- Department of Microbiology and Immunology, University of Rochester, 601 Elmwood Ave, NY 14642, USA
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13
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Chen K, Yu Q, Sha Q, Wang J, Fang J, Li X, Shen X, Fu B, Guo C. Single-cell transcriptomic analysis of immune cell dynamics in the healthy human endometrium. Biochem Biophys Rep 2024; 39:101802. [PMID: 39161579 PMCID: PMC11332207 DOI: 10.1016/j.bbrep.2024.101802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/25/2024] [Accepted: 07/23/2024] [Indexed: 08/21/2024] Open
Abstract
The microenvironment of the endometrial immune system is crucial to the success of placental implantation and healthy pregnancy. However, the functionalities of immune cells across various stages of the reproductive cycle have yet to be fully comprehended. To address this, we conducted advanced bioinformatic analysis on 230,049 high-quality single-cell transcriptomes from healthy endometrial samples obtained during the proliferative, secretory, early pregnancy, and late pregnancy stages. Our investigation has unveiled that proliferative natural killer (NK) cells, a potential source of endometrial NK cells, exhibit the most robust proliferative and differentiation potential during non-pregnant stages. We have also identified similar differentiation trajectories of NK cells originating from proliferative NK cells across four stages. Notably, during early pregnancy, NK cells demonstrate the highest oxidative phosphorylation metabolism activity, and, in conjunction with macrophages and T cells, exhibit the strongest type II interferon response. With spatial transcriptome data, we have discerned that the most robust immune-non-immune interactions are associated with the promotion and inhibition of cell proliferation, differentiation and migration during four stages. Furthermore, we have compiled lists of stage-specific risk genes implicated in reproductive diseases, which hold promise as potential disease biomarkers. Our study provides insights into the dynamics of the endometrial immune microenvironment during different reproductive cycle stages, thus serving as a reference for detecting pathological changes during pregnancy.
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Affiliation(s)
- Kaixing Chen
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
- CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Qiaoni Yu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
| | - Qing Sha
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
| | - Junyu Wang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
| | - Jingwen Fang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang, 311200, China
| | - Xin Li
- Department of Rheumatology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121001, China
| | - Xiaokun Shen
- Department of Immunology, School of Basic Medical Science, Jinzhou Medical University, Jinzhou, 121001, China
| | - Binqing Fu
- CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Chuang Guo
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China
- CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, 230027, Hefei, Anhui, China
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14
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Greenwood M, Gillard BT, Murphy D, Greenwood MP. Dimerization of hub protein DYNLL1 and bZIP transcription factor CREB3L1 enhances transcriptional activation of CREB3L1 target genes like arginine vasopressin. Peptides 2024; 179:171269. [PMID: 38960286 DOI: 10.1016/j.peptides.2024.171269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024]
Abstract
bZIP transcription factors can function as homodimers or heterodimers through interactions with their disordered coiled-coil domain. Such dimer assemblies are known to influence DNA-binding specificity and/or the recruitment of binding partners, which can cause a functional switch of a transcription factor from being an activator to a repressor. We recently identified the genomic targets of a bZIP transcription factor called CREB3L1 in rat hypothalamic supraoptic nucleus by ChIP-seq. The objective of this study was to investigate the CREB3L1 protein-to-protein interactome of which little is known. For this approach, we created and screened a rat supraoptic nucleus yeast two-hybrid prey library with the bZIP region of rat CREB3L1 as the bait. Our yeast two-hybrid approach captured five putative CREB3L1 interacting prey proteins in the supraoptic nucleus. One interactor was selected by bioinformatic analyses for more detailed investigation by co-immunoprecipitation, immunofluorescent cellular localisation, and reporter assays in vitro. Here we identify dimerisation hub protein Dynein Light Chain LC8-Type 1 as a CREB3L1 interacting protein that in vitro enhances CREB3L1 activation of target genes.
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Affiliation(s)
- Mingkwan Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom
| | - Benjamin T Gillard
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom
| | - David Murphy
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom
| | - Michael P Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School: Translational Health Sciences, University of Bristol, Dorothy Hodgkin Building, Bristol, United Kingdom.
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15
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Jain L, Jardim CA, Yulo R, Bolam SM, Monk AP, Munro JT, Pitto R, Tamatea J, Dalbeth N, Poulsen RC. Phenotype and energy metabolism differ between osteoarthritic chondrocytes from male compared to female patients: Implications for sexual dimorphism in osteoarthritis development? Osteoarthritis Cartilage 2024; 32:1084-1096. [PMID: 37935325 DOI: 10.1016/j.joca.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/28/2023] [Accepted: 09/15/2023] [Indexed: 11/09/2023]
Abstract
OBJECTIVES The prevalence and severity of knee osteoarthritis (OA) are greater in females than males. The purpose of this study was to determine whether there is an underlying difference in the biology of OA chondrocytes between males and females. METHODS Chondrocytes were obtained following knee arthroplasty from male and female patients with primary OA. Phenotype marker expression, glucose and fat consumption, and rates of glycolysis and oxidative phosphorylation were compared between females and males. RNAi was used to determine the consequences of differential expression of Sry-box transcription factor 9 (SOX9) and PGC1α between males and females. RESULTS OA chondrocytes from male donors showed elevated ribonucleic acid (RNA) and protein levels of SOX9, elevated COL2A1 protein synthesis, higher glucose consumption, and higher usage of glycolysis compared to females. OA chondrocytes from females had higher PGC1α protein levels, higher fat consumption, and higher oxidative energy metabolism than males. Knockdown of SOX9 reduced expression of COL2A1 to a greater extent in male OA chondrocytes than females whereas knockdown of PGC1α reduced COL2A1 expression in females but not males. Expression of ACAN and the glycolytic enzyme PGK1 was also reduced in males but not females following SOX9 knockdown. CONCLUSIONS OA chondrocyte phenotype and energy metabolism differ between males and females. Our results indicate transcriptional control of COL2A1 differs between the two. Differences in chondrocyte biology between males and females imply the underlying mechanisms involved in OA may also differ, highlighting the need to consider sex and gender when investigating pathogenesis and potential treatments for OA.
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Affiliation(s)
- Lekha Jain
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand.
| | - Caitlin A Jardim
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand.
| | - Richard Yulo
- Biomedical Imaging Research Unit, University of Auckland, Auckland, New Zealand.
| | - Scott M Bolam
- Department of Surgery, University of Auckland, Auckland, New Zealand; Department of Medicine, University of Auckland, Auckland, New Zealand.
| | - A Paul Monk
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.
| | - Jacob T Munro
- Department of Surgery, University of Auckland, Auckland, New Zealand.
| | - Rocco Pitto
- Department of Surgery, University of Auckland, Auckland, New Zealand.
| | - Jade Tamatea
- Te Kupenga Hauora Māori, University of Auckland, Auckland, New Zealand.
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand.
| | - Raewyn C Poulsen
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand.
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16
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Shen X, Xie J, Liu S, Cai Y, Yuan S, Uehara Y, Zhu D, Zheng M. Anoikis-related subtype and prognosis analyses based on bioinformatics, and an expression verification of ANGPTL4 based on experiments of lung adenocarcinoma. J Thorac Dis 2024; 16:5361-5378. [PMID: 39268091 PMCID: PMC11388259 DOI: 10.21037/jtd-24-1123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024]
Abstract
Background Lung adenocarcinoma (LUAD) is one of the most common malignant tumors with high mortality. Anoikis resistance is an important mechanism of tumor cell proliferation and migration. Our research is devoted to exploring the role of anoikis in the diagnosis, classification, and prognosis of LUAD. Methods We downloaded the expression profile, mutation, and clinical data of LUAD from The Cancer Genome Atlas (TCGA) database. The "ConsensusClusterPlus" package was then used for the cluster analysis, and least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analyses were used to establish the prognostic model. We verified the reliability of the model using a Gene Expression Omnibus (GEO) data set. A gene set variation analysis (GSVA) was conducted to investigate the functional enrichment differences in the different clusters and risk groups. The CIBERSORT algorithm and a single-sample gene set enrichment analysis (ssGSEA) were used to analyze immune cell infiltration. The tumor mutation burden (TMB) and Tumor Immune Dysfunction and Exclusion (TIDE) scores were used to evaluate the patients' sensitivity to immunotherapy. Immunohistochemical staining of tissue microarrays was used to verify the correlation between ANGPTL4 expression and the clinicopathological characteristics and prognosis of LUAD patients. Results First, we screened 135 differentially expressed anoikis-related genes (ARGs) and 23 prognosis-related ARGs from TCGA-LUAD data set. Next, 494 LUAD samples were allocated to cluster A and cluster B based on the 23 prognosis-related ARGs. The Kaplan-Meier (K-M) analysis showed the overall survival (OS) of cluster B was better than that of cluster A. The clinicopathological characteristics and functional enrichment analyses revealed significant differences between clusters A and B. The tumor microenvironment (TME) analysis showed that cluster B had more immune cell infiltration and a higher TME score than cluster A. Subsequently, a LASSO Cox regression model of LUAD was constructed with ten ARGs. The K-M analysis showed that the low-risk patients had longer OS than the high-risk patients. The receiver operating characteristic curve, nomogram, and GEO data set verification results showed that the model had high accuracy and reliability. The level of immune cell infiltration and TME score were higher in the low-risk group than the high-risk group. The high-risk group had stronger sensitivity to immune checkpoint block therapy and weaker sensitivity to chemotherapy drugs than the low-risk group. ANGPTL4 expression was correlated with stage, tumor differentiation, tumor size, lymph node metastasis, and OS. Conclusions We discovered novel molecular subtypes and constructed a novel prognostic model of LUAD. Our findings provide important insights into subtype classification and the accurate survival prediction of LUAD. We also identified ANGPTL4 as a prognostic indicator of LUAD.
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Affiliation(s)
- Xiaojian Shen
- Department of Pathology, The People's Hospital of Rugao, Rugao Hospital Affiliated to Nantong University, Rugao, China
| | - Jing Xie
- Department of Pathology, The People's Hospital of Rugao, Rugao Hospital Affiliated to Nantong University, Rugao, China
| | - Shu Liu
- Department of Pathology, The People's Hospital of Rugao, Rugao Hospital Affiliated to Nantong University, Rugao, China
| | - Yun Cai
- Department of Pathology, The People's Hospital of Rugao, Rugao Hospital Affiliated to Nantong University, Rugao, China
| | - Shen Yuan
- Department of Pathology, The People's Hospital of Rugao, Rugao Hospital Affiliated to Nantong University, Rugao, China
| | - Yuji Uehara
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Honkomagoame, Tokyo, Japan
- Division of Cancer Evolution, National Cancer Center Japan Research Institute, Tokyo, Japan
| | - Dongbing Zhu
- Department of Pathology, The People's Hospital of Rugao, Rugao Hospital Affiliated to Nantong University, Rugao, China
| | - Miaosen Zheng
- Department of Pathology, The People's Hospital of Rugao, Rugao Hospital Affiliated to Nantong University, Rugao, China
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Ohnuki Y, Akiyama M, Sakakibara Y. Deep learning of multimodal networks with topological regularization for drug repositioning. J Cheminform 2024; 16:103. [PMID: 39180095 PMCID: PMC11342530 DOI: 10.1186/s13321-024-00897-y] [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: 01/14/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024] Open
Abstract
MOTIVATION Computational techniques for drug-disease prediction are essential in enhancing drug discovery and repositioning. While many methods utilize multimodal networks from various biological databases, few integrate comprehensive multi-omics data, including transcriptomes, proteomes, and metabolomes. We introduce STRGNN, a novel graph deep learning approach that predicts drug-disease relationships using extensive multimodal networks comprising proteins, RNAs, metabolites, and compounds. We have constructed a detailed dataset incorporating multi-omics data and developed a learning algorithm with topological regularization. This algorithm selectively leverages informative modalities while filtering out redundancies. RESULTS STRGNN demonstrates superior accuracy compared to existing methods and has identified several novel drug effects, corroborating existing literature. STRGNN emerges as a powerful tool for drug prediction and discovery. The source code for STRGNN, along with the dataset for performance evaluation, is available at https://github.com/yuto-ohnuki/STRGNN.git .
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Affiliation(s)
- Yuto Ohnuki
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Manato Akiyama
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan.
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18
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Mohajeri Khorasani A, Raghibi A, Haj Mohammad Hassani B, Bolbolizadeh P, Amali A, Sadeghi M, Farshidi N, Dehghani A, Mousavi P. Decoding the Role of NEIL1 Gene in DNA Repair and Lifespan: A Literature Review with Bioinformatics Analysis. Adv Biol (Weinh) 2024:e2300708. [PMID: 39164210 DOI: 10.1002/adbi.202300708] [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: 12/22/2023] [Revised: 06/21/2024] [Indexed: 08/22/2024]
Abstract
Longevity, the length of an organism's lifespan, is impacted by environmental factors, metabolic processes, and genetic determinants. The base excision repair (BER) pathway is crucial for maintaining genomic integrity by repairing oxidatively modified base lesions. Nei-like DNA Glycosylase 1 (NEIL1), part of the BER pathway, is vital in repairing oxidative bases in G-rich DNA regions, such as telomeres and promoters. Hence, in this comprehensive review, it have undertaken a meticulous investigation of the intricate association between NEIL1 and longevity. The analysis delves into the multifaceted aspects of the NEIL1 gene, its various RNA transcripts, and the diverse protein isoforms. In addition, a combination of bioinformatic analysis is conducted to identify NEIL1 mutations, transcription factors, and epigenetic modifications, as well as its lncRNA/pseudogene/circRNA-miRNA-mRNA regulatory network. The findings suggest that the normal function of NEIL1 is a significant factor in human health and longevity, with defects in NEIL1 potentially leading to various cancers and related syndromes, Alzheimer's disease, obesity, and diabetes.
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Affiliation(s)
- Amirhossein Mohajeri Khorasani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Alireza Raghibi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, 1416634793, Iran
| | - Behzad Haj Mohammad Hassani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Pedram Bolbolizadeh
- Student Research Committee, Faculty of Para-Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Arian Amali
- School of Infection & Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mahboubeh Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Narges Farshidi
- Department of Pharmaceutics, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- USERN Office, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Aghdas Dehghani
- Endocrinology and Metabolism Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
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19
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Bhatt IS, Garay JAR, Torkamani A, Dias R. DNA Methylation Patterns Associated with Tinnitus in Young Adults-A Pilot Study. J Assoc Res Otolaryngol 2024:10.1007/s10162-024-00961-2. [PMID: 39147981 DOI: 10.1007/s10162-024-00961-2] [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: 12/01/2023] [Accepted: 07/31/2024] [Indexed: 08/17/2024] Open
Abstract
PURPOSE Tinnitus, the perception of sound without any external sound source, is a prevalent hearing health concern. Mounting evidence suggests that a confluence of genetic, environmental, and lifestyle factors can influence the pathogenesis of tinnitus. We hypothesized that alteration in DNA methylation, an epigenetic modification that occurs at cytosines of cytosine-phosphate-guanine (CpG) dinucleotide sites, where a methyl group from S-adenyl methionine gets transferred to the fifth carbon of the cytosine, could contribute to tinnitus. DNA methylation patterns are tissue-specific, but the tissues involved in tinnitus are not easily accessible in humans. This pilot study used saliva as a surrogate tissue to identify differentially methylated CpG regions (DMRs) associated with tinnitus. The study was conducted on healthy young adults reporting bilateral continuous chronic tinnitus to limit the influence of age-related confounding factors and health-related comorbidities. METHODS The present study evaluated the genome-wide methylation levels from saliva-derived DNA samples from 24 healthy young adults with bilateral continuous chronic tinnitus (> 1 year) and 24 age, sex, and ethnicity-matched controls with no tinnitus. Genome-wide DNA methylation was evaluated for > 850,000 CpG sites using the Infinium Human Methylation EPIC BeadChip. The association analysis used the Bumphunter algorithm on 23 cases and 20 controls meeting the quality control standards. The methylation level was expressed as the area under the curve of CpG sites within DMRs.The FDR-adjusted p-value threshold of 0.05 was used to identify statistically significant DMRs associated with tinnitus. RESULTS We obtained 25 differentially methylated regions (DMRs) associated with tinnitus. Genes within or in the proximity of the hypermethylated DMRs related to tinnitus included LCLAT1, RUNX1, RUFY1, NUDT12, TTC23, SLC43A2, C4orf27 (STPG2), and EFCAB4B. Genes within or in the proximity of hypomethylated DMRs associated with tinnitus included HLA-DPB2, PM20D1, TMEM18, SNTG2, MUC4, MIR886, MIR596, TXNRD1, EID3, SDHAP3, HLA-DPB2, LASS3 (CERS3), C10orf11 (LRMDA), HLA-DQB1, NADK, SZRD1, MFAP2, NUP210L, TPM3, INTS9, and SLC2A14. The burden of genetic variation could explain the differences in the methylation levels for DMRs involving HLA-DPB2, HLA-DQB1, and MUC4, indicating the need for replication in large independent cohorts. CONCLUSION Consistent with the literature on comorbidities associated with tinnitus, we identified genes within or close to DMRs involved in auditory functions, chemical dependency, cardiovascular diseases, psychiatric conditions, immune disorders, and metabolic syndromes. These results indicate that epigenetic mechanisms could influence tinnitus, and saliva can be a good surrogate for identifying the epigenetic underpinnings of tinnitus in humans. Further research with a larger sample size is needed to identify epigenetic biomarkers and investigate their influence on the phenotypic expression of tinnitus.
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Affiliation(s)
- Ishan Sunilkumar Bhatt
- Department of Communication Sciences & Disorders, University of Iowa, Iowa City, IA, 52242, USA.
| | - Juan Antonio Raygoza Garay
- Department of Communication Sciences & Disorders, University of Iowa, Iowa City, IA, 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Science Institute, La Jolla, CA, 92037, USA
| | - Raquel Dias
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32608, USA
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20
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Li E, Benitez C, Boggess SC, Koontz M, Rose IVL, Martinez D, Draeger N, Teter OM, Samelson AJ, Na'im P, Ullian EM, Kampmann M. CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.26.538498. [PMID: 37163077 PMCID: PMC10168378 DOI: 10.1101/2023.04.26.538498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The sheer complexity of the brain has complicated our ability to understand the cellular and molecular mechanisms underlying its function in health and disease. Genome-wide association studies have uncovered genetic variants associated with specific neurological phenotypes and diseases. In addition, single-cell transcriptomics have provided molecular descriptions of specific brain cell types and the changes they undergo during disease. Although these approaches provide a giant leap forward towards understanding how genetic variation can lead to functional changes in the brain, they do not establish molecular mechanisms. To address this need, we developed a 3D co-culture system termed iAssembloids (induced multi-lineage assembloids) that enables the rapid generation of homogenous neuron-glia spheroids. We characterize these iAssembloids with immunohistochemistry and single-cell transcriptomics and combine them with large-scale CRISPRi-based screens. In our first application, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response in the presence of reactive oxygen species elicited by high neuronal activity, which was not previously found in 2D monoculture neuron screens. We also apply the platform to investigate the role of APOE-ɛ4, a risk variant for Alzheimer's Disease, in its effect on neuronal survival. We find that APOE-ɛ4-expressing astrocytes may promote more neuronal activity as compared to APOE-ɛ3-expressing astrocytes. This platform expands the toolbox for the unbiased identification of mechanisms of cell-cell interactions in brain health and disease.
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21
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Starr AL, Nishimura T, Igarashi KJ, Funamoto C, Nakauchi H, Fraser HB. Disentangling cell-intrinsic and extrinsic factors underlying evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592777. [PMID: 38798687 PMCID: PMC11118348 DOI: 10.1101/2024.05.06.592777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
A key goal of developmental biology is to determine the extent to which cells and organs develop autonomously, as opposed to requiring interactions with other cells or environmental factors. Chimeras have played a foundational role in this by enabling qualitative classification of cell-intrinsically vs. extrinsically driven processes. Here, we extend this framework to precisely decompose evolutionary divergence in any quantitative trait into cell-intrinsic, extrinsic, and intrinsic-extrinsic interaction components. Applying this framework to thousands of gene expression levels in reciprocal rat-mouse chimeras, we found that the majority of their divergence is attributable to cell-intrinsic factors, though extrinsic factors also play an integral role. For example, a rat-like extracellular environment extrinsically up-regulates the expression of a key transcriptional regulator of the endoplasmic reticulum (ER) stress response in some but not all cell types, which in turn strongly predicts extrinsic up-regulation of its target genes and of the ER stress response pathway as a whole. This effect is also seen at the protein level, suggesting propagation through multiple regulatory levels. Applying our framework to a cellular trait, neuronal differentiation, revealed a complex interaction of intrinsic and extrinsic factors. Finally, we show that imprinted genes are dramatically mis-expressed in species-mismatched environments, suggesting that mismatch between rapidly evolving intrinsic and extrinsic mechanisms controlling gene imprinting may contribute to barriers to interspecies chimerism. Overall, our conceptual framework opens new avenues to investigate the mechanistic basis of developmental processes and evolutionary divergence across myriad quantitative traits in any multicellular organism.
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Affiliation(s)
| | - Toshiya Nishimura
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- WPI Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Osaka, 565-0871, Japan (current address for T.N.)
- Division of Stem Cell and Organoid Medicine, Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Kyomi J. Igarashi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chihiro Funamoto
- Division of Stem Cell and Organoid Medicine, Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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22
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Lysenkova Wiklander M, Arvidsson G, Bunikis I, Lundmark A, Raine A, Marincevic-Zuniga Y, Gezelius H, Bremer A, Feuk L, Ameur A, Nordlund J. A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing. Life Sci Alliance 2024; 7:e202302481. [PMID: 38777370 PMCID: PMC11111970 DOI: 10.26508/lsa.202302481] [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: 11/14/2023] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.
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Affiliation(s)
- Mariya Lysenkova Wiklander
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Gustav Arvidsson
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Henrik Gezelius
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Anna Bremer
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/01apvbh93 Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden
- https://ror.org/048a87296 National Genomics Infrastructure, Uppsala University, Uppsala, Sweden
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23
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Ning C, Wu X, Zhao X, Lu Z, Yao X, Zhou T, Yi L, Sun Y, Wu S, Liu Z, Huang X, Gao L, Liu J. Epigenomic landscapes during prefrontal cortex development and aging in rhesus. Natl Sci Rev 2024; 11:nwae213. [PMID: 39183748 PMCID: PMC11342245 DOI: 10.1093/nsr/nwae213] [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: 09/08/2023] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 08/27/2024] Open
Abstract
The prefrontal cortex (PFC) is essential for higher-level cognitive functions. How epigenetic dynamics participates in PFC development and aging is largely unknown. Here, we profiled epigenomic landscapes of rhesus monkey PFCs from prenatal to aging stages. The dynamics of chromatin states, including higher-order chromatin structure, chromatin interaction and histone modifications are coordinated to regulate stage-specific gene transcription, participating in distinct processes of neurodevelopment. Dramatic changes of epigenetic signals occur around the birth stage. Notably, genes involved in neuronal cell differentiation and layer specification are pre-configured by bivalent promoters. We identified a cis-regulatory module and the transcription factors (TFs) associated with basal radial glia development, which was associated with large brain size in primates. These TFs include GLI3, CREB5 and SOX9. Interestingly, the genes associated with the basal radial glia (bRG)-associated cis-element module, such as SRY and SOX9, are enriched in sex differentiation. Schizophrenia-associated single nucleotide polymorphisms are more enriched in super enhancers (SEs) than typical enhancers, suggesting that SEs play an important role in neural network wiring. A cis-regulatory element of DBN1 is identified, which is critical for neuronal cell proliferation and synaptic neuron differentiation. Notably, the loss of distal chromatin interaction and H3K27me3 signal are hallmarks of PFC aging, which are associated with abnormal expression of aging-related genes and transposon activation, respectively. Collectively, our findings shed light on epigenetic mechanisms underlying primate brain development and aging.
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Affiliation(s)
- Chao Ning
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), State Key Laboratory of Drug Regulatory Science, Beijing 102629, China
| | - Xudong Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Zongyang Lu
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Xuelong Yao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- GuangzhouNvwa Life Technology Co., Ltd, Guangzhou 510535, China
| | - Tao Zhou
- Shenzhen Neher Neural Plasticity Laboratory, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lizhi Yi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoyu Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuaishuai Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenbo Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingxu Huang
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lei Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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24
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Metzner E, Southard KM, Norman TM. Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605307. [PMID: 39091800 PMCID: PMC11291144 DOI: 10.1101/2024.07.26.605307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes to their regulatory foundations are limited. Here we introduce Multiome Perturb-seq, extending single-cell CRISPR screens to simultaneously measure perturbation-induced changes in gene expression and chromatin accessibility. We apply Multiome Perturb-seq in a CRISPRi screen of 13 chromatin remodelers in human RPE-1 cells, achieving efficient assignment of sgRNA identities to single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. We organize expression and accessibility measurements into coherent programs describing the integrated effects of perturbations on cell state, finding that ARID1A and SUZ12 knockdowns induce programs enriched for developmental features. Pseudotime analysis of perturbations connects accessibility changes to changes in gene expression, highlighting the value of multimodal profiling. Overall, our method provides a scalable and simply implemented system to dissect the regulatory logic underpinning cell state.
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Affiliation(s)
- Eli Metzner
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Kaden M. Southard
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas M. Norman
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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25
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Li F, Wang J, Li M, Zhang X, Tang Y, Song X, Zhang Y, Pei L, Liu J, Zhang C, Li X, Xu Y, Zhang Y. Identifying cell type-specific transcription factor-mediated activity immune modules reveal implications for immunotherapy and molecular classification of pan-cancer. Brief Bioinform 2024; 25:bbae368. [PMID: 39082649 PMCID: PMC11289680 DOI: 10.1093/bib/bbae368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 06/11/2024] [Accepted: 07/15/2024] [Indexed: 08/03/2024] Open
Abstract
Systematic investigation of tumor-infiltrating immune (TII) cells is important to the development of immunotherapies, and the clinical response prediction in cancers. There exists complex transcriptional regulation within TII cells, and different immune cell types display specific regulation patterns. To dissect transcriptional regulation in TII cells, we first integrated the gene expression profiles from single-cell datasets, and proposed a computational pipeline to identify TII cell type-specific transcription factor (TF) mediated activity immune modules (TF-AIMs). Our analysis revealed key TFs, such as BACH2 and NFKB1 play important roles in B and NK cells, respectively. We also found some of these TF-AIMs may contribute to tumor pathogenesis. Based on TII cell type-specific TF-AIMs, we identified eight CD8+ T cell subtypes. In particular, we found the PD1 + CD8+ T cell subset and its specific TF-AIMs associated with immunotherapy response. Furthermore, the TII cell type-specific TF-AIMs displayed the potential to be used as predictive markers for immunotherapy response of cancer patients. At the pan-cancer level, we also identified and characterized six molecular subtypes across 9680 samples based on the activation status of TII cell type-specific TF-AIMs. Finally, we constructed a user-friendly web interface CellTF-AIMs (http://bio-bigdata.hrbmu.edu.cn/CellTF-AIMs/) for exploring transcriptional regulatory pattern in various TII cell types. Our study provides valuable implications and a rich resource for understanding the mechanisms involved in cancer microenvironment and immunotherapy.
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Affiliation(s)
- Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Jingwen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Mengyue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Xiaomeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Yongjuan Tang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Xinyu Song
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Yifang Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Liying Pei
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Jiaqi Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 157 Baojian Road, Harbin, China
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26
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Li Y, Ma A, Wang Y, Guo Q, Wang C, Fu H, Liu B, Ma Q. Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. Brief Bioinform 2024; 25:bbae369. [PMID: 39082647 PMCID: PMC11289686 DOI: 10.1093/bib/bbae369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/19/2024] [Accepted: 07/15/2024] [Indexed: 08/03/2024] Open
Abstract
Deciphering the intricate relationships between transcription factors (TFs), enhancers, and genes through the inference of enhancer-driven gene regulatory networks (eGRNs) is crucial in understanding gene regulatory programs in a complex biological system. This study introduces STREAM, a novel method that leverages a Steiner forest problem model, a hybrid biclustering pipeline, and submodular optimization to infer eGRNs from jointly profiled single-cell transcriptome and chromatin accessibility data. Compared to existing methods, STREAM demonstrates enhanced performance in terms of TF recovery, TF-enhancer linkage prediction, and enhancer-gene relation discovery. Application of STREAM to an Alzheimer's disease dataset and a diffuse small lymphocytic lymphoma dataset reveals its ability to identify TF-enhancer-gene relations associated with pseudotime, as well as key TF-enhancer-gene relations and TF cooperation underlying tumor cells.
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Affiliation(s)
- Yang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, United States
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, United States
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Yizhong Wang
- School of Mathematics, Shandong University, Jinan, Shandong 250100, China
| | - Qi Guo
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, United States
| | - Cankun Wang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, United States
| | - Hongjun Fu
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, OH 43210, United States
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, Shandong 250100, China
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, United States
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
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27
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Tang L, Xu S, Wei R, Fan G, Zhou J, Wei X, Xu X. Transcription factor 7 like 2 promotes metastasis in hepatocellular carcinoma via NEDD9-mediated activation of AKT/mTOR signaling pathway. Mol Med 2024; 30:108. [PMID: 39060928 PMCID: PMC11282612 DOI: 10.1186/s10020-024-00878-9] [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: 12/26/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common malignant tumors of the digestive system, and the exact mechanism of HCC is still unclear. Transcription factor 7 like 2 (TCF7L2) plays a pivotal role in cell proliferation and stemness maintenance. However, the exact mechanism of TCF7L2 in HCC remains unclear. METHODS Clinical samples and public databases were used to analyze the expression and prognosis of TCF7L2 in HCC. The function of TCF7L2 in HCC was studied in vitro and in vivo. ChIP and luciferase assays were used to explore the molecular mechanism of TCF7L2. The relationship between TCF7L2 and NEDD9 was verified in HCC clinical samples by tissue microarrays. RESULTS The expression of TCF7L2 was upregulated in HCC, and high expression of TCF7L2 was associated with poor prognosis of HCC patients. Overexpression of TCF7L2 promoted the metastasis of HCC in vitro and in vivo, while Knockdown of TCF7L2 showed the opposite effect. Mechanically, TCF7L2 activated neural precursor cell expressed developmentally downregulated protein 9 (NEDD9) transcription by binding to the -1522/-1509 site of the NEDD9 promoter region, thereby increasing the phosphorylation levels of AKT and mTOR. The combination of TCF7L2 and NEDD9 could distinguish the survival of HCC patients. CONCLUSIONS This study demonstrated that TCF7L2 promotes HCC metastasis by activating AKT/mTOR pathway in a NEDD9-dependent manner, suggesting that potential of TCF7L2 and NEDD9 as prognostic markers and therapeutic targets for HCC.
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Affiliation(s)
- Linsong Tang
- Department of Urology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, Zhejiang, China
| | - Shengjun Xu
- Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, Zhejiang, China
| | - Rongli Wei
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Guanghan Fan
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Junbin Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Lishui People's Hospital, Lishui, Zhejiang, China
| | - Xuyong Wei
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, Zhejiang, China
| | - Xiao Xu
- Institute of Translational Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
- Department of Hepatobiliary & Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), School of Clinical Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China.
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, Zhejiang, China.
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28
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Lam YC, Hamchand R, Mucci NC, Kauffman SJ, Dudkina N, Reagle EV, Casanova-Torres ÁM, DeCuyper J, Chen H, Song D, Thomas MG, Palm NW, Goodrich-Blair H, Crawford JM. The Xenorhabdus nematophila LrhA transcriptional regulator modulates production of γ-keto- N-acyl amides with inhibitory activity against mutualistic host nematode egg hatching. Appl Environ Microbiol 2024; 90:e0052824. [PMID: 38916293 PMCID: PMC11267870 DOI: 10.1128/aem.00528-24] [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: 03/21/2024] [Accepted: 06/01/2024] [Indexed: 06/26/2024] Open
Abstract
Xenorhabdus nematophila is a symbiotic Gammaproteobacterium that produces diverse natural products that facilitate mutualistic and pathogenic interactions in their nematode and insect hosts, respectively. The interplay between X. nematophila secondary metabolism and symbiosis stage is tuned by various global regulators. An example of such a regulator is the LysR-type protein transcription factor LrhA, which regulates amino acid metabolism and is necessary for virulence in insects and normal nematode progeny production. Here, we utilized comparative metabolomics and molecular networking to identify small molecule factors regulated by LrhA and characterized a rare γ-ketoacid (GKA) and two new N-acyl amides, GKA-Arg (1) and GKA-Pro (2) which harbor a γ-keto acyl appendage. A lrhA null mutant produced elevated levels of compound 1 and reduced levels of compound 2 relative to wild type. N-acyl amides 1 and 2 were shown to be selective agonists for the human G-protein-coupled receptors (GPCRs) C3AR1 and CHRM2, respectively. The CHRM2 agonist 2 deleteriously affected the hatch rate and length of Steinernema nematodes. This work further highlights the utility of exploiting regulators of host-bacteria interactions for the identification of the bioactive small molecule signals that they control. IMPORTANCE Xenorhabdus bacteria are of interest due to their symbiotic relationship with Steinernema nematodes and their ability to produce a variety of natural bioactive compounds. Despite their importance, the regulatory hierarchy connecting specific natural products and their regulators is poorly understood. In this study, comparative metabolomic profiling was utilized to identify the secondary metabolites modulated by the X. nematophila global regulator LrhA. This analysis led to the discovery of three metabolites, including an N-acyl amide that inhibited the egg hatching rate and length of Steinernema carpocapsae nematodes. These findings support the notion that X. nematophila LrhA influences the symbiosis between X. nematophila and S. carpocapsae through N-acyl amide signaling. A deeper understanding of the regulatory hierarchy of these natural products could contribute to a better comprehension of the symbiotic relationship between X. nematophila and S. carpocapsae.
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Affiliation(s)
- Yick Chong Lam
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Randy Hamchand
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Nicholas C. Mucci
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Sarah J. Kauffman
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Natavan Dudkina
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Emily V. Reagle
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jessica DeCuyper
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Haiwei Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deguang Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael G. Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah W. Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Heidi Goodrich-Blair
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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29
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Zhang Y, Fong KW, Mao F, Wang R, Allison DB, Napier D, He D, Liu J, Zhang Y, Chen J, Kong Y, Li C, Li G, Liu J, Li Z, Zhu H, Wang C, Liu X. Elevating PLK1 overcomes BETi resistance in prostate cancer via triggering BRD4 phosphorylation-dependent degradation in mitosis. Cell Rep 2024; 43:114431. [PMID: 38968071 PMCID: PMC11334074 DOI: 10.1016/j.celrep.2024.114431] [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: 10/20/2023] [Revised: 04/20/2024] [Accepted: 06/18/2024] [Indexed: 07/07/2024] Open
Abstract
Bromodomain-containing protein 4 (BRD4) has emerged as a promising therapeutic target in prostate cancer (PCa). Understanding the mechanisms of BRD4 stability could enhance the clinical response to BRD4-targeted therapy. In this study, we report that BRD4 protein levels are significantly decreased during mitosis in a PLK1-dependent manner. Mechanistically, we show that BRD4 is primarily phosphorylated at T1186 by the CDK1/cyclin B complex, recruiting PLK1 to phosphorylate BRD4 at S24/S1100, which are recognized by the APC/CCdh1 complex for proteasome pathway degradation. We find that PLK1 overexpression lowers SPOP mutation-stabilized BRD4, consequently rendering PCa cells re-sensitized to BRD4 inhibitors. Intriguingly, we report that sequential treatment of docetaxel and JQ1 resulted in significant inhibition of PCa. Collectively, the results support that PLK1-phosphorylated BRD4 triggers its degradation at M phase. Sequential treatment of docetaxel and JQ1 overcomes BRD4 accumulation-associated bromodomain and extra-terminal inhibitor (BETi) resistance, which may shed light on the development of strategies to treat PCa.
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Affiliation(s)
- Yanquan Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
| | - Ka-Wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Fengyi Mao
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Ruixin Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Derek B Allison
- Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY 40508, USA
| | - Dana Napier
- Biospecimen Procurement & Translational Pathology Shared Resource Facility, University of Kentucky, Lexington, KY 40536, USA
| | - Daheng He
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Jinpeng Liu
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Yeqing Zhang
- Department of Biology, College of Arts & Sciences, University of Kentucky, Lexington, KY 40506, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Yifan Kong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Chaohao Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Guangbing Li
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghui Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Zhiguo Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
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30
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Koljonen L, Salonen P, Rusanen S, Mäyränpää MK, Pekkinen M, Mäkitie O. A de novo PRPF8 Pathogenic Variant in Transient Severe Hypophosphatemia with Delayed Puberty and Growth Failure. Horm Res Paediatr 2024:1-11. [PMID: 38976971 DOI: 10.1159/000540249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024] Open
Abstract
INTRODUCTION Childhood hypophosphatemia is a rare condition and may be caused by malabsorption, malignancies, or genetic factors. Prolonged hypophosphatemia leads to impaired growth and radiographic signs of rickets. METHODS We performed a detailed clinical and genetic evaluation of an adolescent boy with repeatedly low plasma phosphate concentrations (below 0.60 mmol/L) and growth failure. RESULTS At 14 years, the patient presented with decelerating growth and delayed puberty. Biochemistry showed hypophosphatemia due to increased urinary phosphate loss; kidney function and vitamin D status were normal. Radiographs showed mild metaphyseal changes. A gene panel for known genetic hypophosphatemia was negative. Trio exome analysis followed by Sanger sequencing identified a pathogenic heterozygous de novo stop-gain variant in PRPF8 gene, c.5548C>T p.(Arg1850*), in the conserved RNase H homology domain. PRPF8 encodes the pre-RNA protein 8, which has a role in RNA processing. Heterozygous PRPF8 variants have been associated with retinitis pigmentosa and neurodevelopmental disorders but not with phosphate metabolism. The patient underwent growth hormone (GH) stimulation tests which confirmed GH deficiency. Head MRI indicated partially empty sella. GH treatment was started at 15 years. Surprisingly, phosphate metabolism normalized during GH treatment, suggesting that hypophosphatemia was at least partly secondary to GH deficiency. CONCLUSION The evaluation of an adolescent with profound long-term hypophosphatemia revealed a pituitary developmental defect associated with a stop-gain variant in PRPF8. Hypophosphatemia alleviated with GH treatment. The pathological PRPF8 variant may contribute to abnormal pituitary development; however, its role in phosphate metabolism remains uncertain.
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Affiliation(s)
- Laura Koljonen
- Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pia Salonen
- Department of Pediatrics, Central Hospital of Päijät-Häme, Lahti, Finland
| | | | - Mervi K Mäyränpää
- Department of Radiology, HUS Diagnostic Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Minna Pekkinen
- Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
| | - Outi Mäkitie
- Folkhälsan Research Center, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Department of Molecular Medicine and Surgery, Karolinska Institutet, and Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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31
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Delvenne A, Vandendriessche C, Gobom J, Burgelman M, Dujardin P, De Nolf C, Tijms BM, Teunissen CE, Schindler SE, Verhey F, Ramakers I, Martinez-Lage P, Tainta M, Vandenberghe R, Schaeverbeke J, Engelborghs S, De Roeck E, Popp J, Peyratout G, Tsolaki M, Freund-Levi Y, Lovestone S, Streffer J, Bertram L, Blennow K, Zetterberg H, Visser PJ, Vandenbroucke RE, Vos SJB. Involvement of the choroid plexus in Alzheimer's disease pathophysiology: findings from mouse and human proteomic studies. Fluids Barriers CNS 2024; 21:58. [PMID: 39020361 PMCID: PMC11256635 DOI: 10.1186/s12987-024-00555-3] [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: 04/15/2024] [Accepted: 06/03/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Structural and functional changes of the choroid plexus (ChP) have been reported in Alzheimer's disease (AD). Nonetheless, the role of the ChP in the pathogenesis of AD remains largely unknown. We aim to unravel the relation between ChP functioning and core AD pathogenesis using a unique proteomic approach in mice and humans. METHODS We used an APP knock-in mouse model, APPNL-G-F, exhibiting amyloid pathology, to study the association between AD brain pathology and protein changes in mouse ChP tissue and CSF using liquid chromatography mass spectrometry. Mouse proteomes were investigated at the age of 7 weeks (n = 5) and 40 weeks (n = 5). Results were compared with previously published human AD CSF proteomic data (n = 496) to identify key proteins and pathways associated with ChP changes in AD. RESULTS ChP tissue proteome was dysregulated in APPNL-G-F mice relative to wild-type mice at both 7 and 40 weeks. At both ages, ChP tissue proteomic changes were associated with epithelial cells, mitochondria, protein modification, extracellular matrix and lipids. Nonetheless, some ChP tissue proteomic changes were different across the disease trajectory; pathways related to lysosomal function, endocytosis, protein formation, actin and complement were uniquely dysregulated at 7 weeks, while pathways associated with nervous system, immune system, protein degradation and vascular system were uniquely dysregulated at 40 weeks. CSF proteomics in both mice and humans showed similar ChP-related dysregulated pathways. CONCLUSIONS Together, our findings support the hypothesis of ChP dysfunction in AD. These ChP changes were related to amyloid pathology. Therefore, the ChP could become a novel promising therapeutic target for AD.
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Affiliation(s)
- Aurore Delvenne
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands.
| | - Charysse Vandendriessche
- VIB Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Marlies Burgelman
- VIB Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Pieter Dujardin
- VIB Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Clint De Nolf
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam University Medical Centers (AUMC), Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Suzanne E Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, USA
| | - Frans Verhey
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
| | - Inez Ramakers
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
| | | | - Mikel Tainta
- Fundación CITA-Alzhéimer Fundazioa, San Sebastian, Spain
| | - Rik Vandenberghe
- Neurology Service, University Hospitals Leuven, Louvain, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Louvain, Belgium
| | - Jolien Schaeverbeke
- Neurology Service, University Hospitals Leuven, Louvain, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Louvain, Belgium
| | - Sebastiaan Engelborghs
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Bru-BRAIN, Universitair Ziekenhuis Brussel, Brussels, Belgium
- NEUR Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel, Brussels, Belgium
| | - Ellen De Roeck
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Julius Popp
- Old Age Psychiatry, University Hospital Lausanne, Lausanne, Switzerland
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatry University Hospital Zürich, Zurich, Switzerland
| | | | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Makedonia, Thessaloniki, Greece
| | - Yvonne Freund-Levi
- Department of Neurobiology, Caring Sciences and Society (NVS), Division of Clinical Geriatrics, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatry in Region Örebro County and School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Old Age Psychiatry, Psychology & Neuroscience, King's College, London, UK
| | - Simon Lovestone
- University of Oxford, Oxford, UK
- Johnson and Johnson Medical Ltd., Wokingham, UK
| | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- H. Lundbeck A/S, Valby, Denmark
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, and Department of Neurology, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, People's Republic of China
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Roosmarijn E Vandenbroucke
- VIB Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, P.O. Box 616, Maastricht, 6200 MD, The Netherlands
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Choza JI, Virani M, Kuhn NC, Adams M, Kochmanski J, Bernstein AI. Parkinson's disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain in PD-related genes, including PARK19 (DNAJC6) and PTPRN2 (IA-2β). RESEARCH SQUARE 2024:rs.3.rs-4572401. [PMID: 39070644 PMCID: PMC11275970 DOI: 10.21203/rs.3.rs-4572401/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background The majority of Parkinson's disease (PD) cases are due to a complex interaction between aging, genetics, and environmental factors; epigenetic mechanisms are thought to act as important mediators of these risk factors. While multiple studies to date have explored the role of DNA modifications in PD, few focus on 5-hydroxymethylcytosine (5hmC). Because 5hmC occurs at its highest levels in the brain and is thought to be particularly important in the central nervous system, particularly in the response to neurotoxicants, it is important to explore the potential role of 5hmC in PD. This study expands on our previously published epigenome-wide association study (EWAS) performed on DNA isolated from neuron-enriched nuclei from human postmortem parietal cortex from the Banner Sun Health Research Institute Brain Bank. The study aimed to identify paired changes in 5hmC and 5mC in PD in enriched neuronal nuclei isolated from PD post-mortem parietal cortex and age- and sex-matched controls. We performed oxidative bisulfite (oxBS) conversion and paired it with our previously published bisulfite (BS)-based EWAS on the same samples to identify cytosines with significant shifts between these two related epigenetic marks. Interaction differentially modified cytosines (iDMCs) were identified using our recently published mixed-effects model for co-analyzing βmC and βhmC data. Results We identified 1,030 iDMCs with paired changes in 5mC and 5hmC (FDR < 0.05) that map to 695 genes, including PARK19 (DNAJC6), a familial PD gene, and PTPRN2 (IA-2), which has been previously implicated in PD in both epigenetic and mechanistic studies. The majority of iDMC-containing genes have not previously been implicated in PD and were not identified in our previous BS-based EWAS. Conclusions These data potentially link epigenetic regulation of the PARK19 and PTPRN2 loci in the pathogenesis of idiopathic PD. In addition, iDMC-containing genes have known functions in synaptic formation and function, cell cycle and senescence, neuroinflammation, and epigenetic regulation. These data suggest that there are significant shifts between 5mC and 5hmC associated with PD in genes relevant to PD pathogenesis that are not captured by analyzing BS-based data alone or by analyzing each mark as a distinct dataset.
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Garcia SA, Wilson K, Tang N, Tian H, Oichi T, Gunawardena AT, Chorny M, Alferiev IS, Herzenberg JE, Ng VY, Iwamoto M, Enomoto-Iwamoto M. Analysis of the Actions of RARγ Agonists on Growing Osteochondromas in a Mouse Model. Int J Mol Sci 2024; 25:7610. [PMID: 39062860 PMCID: PMC11277217 DOI: 10.3390/ijms25147610] [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: 06/13/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
The actions of the retinoic acid nuclear receptor gamma (RARγ) agonist, palovarotene, on pre-existing osteochondromas were investigated using a mouse multiple osteochondroma model. This approach was based on the knowledge that patients often present to the clinic after realizing the existence of osteochondroma masses, and the findings from preclinical investigations are the effects of drugs on the initial formation of osteochondromas. Systemic administration of palovarotene, with increased doses (from 1.76 to 4.0 mg/kg) over time, fully inhibited tumor growth, keeping the tumor size (0.31 ± 0.049 mm3) similar to the initial size (0.27 ± 0.031 mm3, p = 0.66) while the control group tumor grew (1.03 ± 0.23 mm3, p = 0.023 to the drug-treated group). Nanoparticle (NP)-based local delivery of the RARγ agonist also inhibited the growth of osteochondromas at an early stage (Control: 0.52 ± 0.11 mm3; NP: 0.26 ± 0.10, p = 0.008). Transcriptome analysis revealed that the osteoarthritis pathway was activated in cultured chondrocytes treated with palovarotene (Z-score = 2.29), with the upregulation of matrix catabolic genes and the downregulation of matrix anabolic genes, consistent with the histology of palovarotene-treated osteochondromas. A reporter assay performed in cultured chondrocytes demonstrated that the Stat3 pathway, but not the Stat1/2 pathway, was stimulated by RARγ agonists. The activation of Stat3 by palovarotene was confirmed using immunoblotting and immunohistochemistry. These findings suggest that palovarotene treatment is effective against pre-existing osteochondromas and that the Stat3 pathway is involved in the antitumor actions of palovarotene.
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Affiliation(s)
- Sonia A. Garcia
- Department of Orthopaedics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (S.A.G.); (K.W.); (N.T.); (H.T.); (T.O.); (V.Y.N.); (M.I.)
| | - Kimberly Wilson
- Department of Orthopaedics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (S.A.G.); (K.W.); (N.T.); (H.T.); (T.O.); (V.Y.N.); (M.I.)
| | - Ningfeng Tang
- Department of Orthopaedics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (S.A.G.); (K.W.); (N.T.); (H.T.); (T.O.); (V.Y.N.); (M.I.)
| | - Hongying Tian
- Department of Orthopaedics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (S.A.G.); (K.W.); (N.T.); (H.T.); (T.O.); (V.Y.N.); (M.I.)
| | - Takeshi Oichi
- Department of Orthopaedics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (S.A.G.); (K.W.); (N.T.); (H.T.); (T.O.); (V.Y.N.); (M.I.)
- Department of Orthopedics, Teikyo University School of Medicine, Tokyo 1738608, Japan
| | - Aruni T. Gunawardena
- Department of Biomechanics, Northeast College of Health Sciences, Seneca Falls, NY 13148, USA;
| | - Michael Chorny
- Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (M.C.); (I.S.A.)
| | - Ivan S. Alferiev
- Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (M.C.); (I.S.A.)
| | - John E. Herzenberg
- International Center for Limb Lengthening, Rubin Institute for Advanced Orthopedics, Sinai Hospital of Baltimore, Baltimore, MD 21215, USA;
| | - Vincent Y. Ng
- Department of Orthopaedics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (S.A.G.); (K.W.); (N.T.); (H.T.); (T.O.); (V.Y.N.); (M.I.)
| | - Masahiro Iwamoto
- Department of Orthopaedics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (S.A.G.); (K.W.); (N.T.); (H.T.); (T.O.); (V.Y.N.); (M.I.)
| | - Motomi Enomoto-Iwamoto
- Department of Orthopaedics, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (S.A.G.); (K.W.); (N.T.); (H.T.); (T.O.); (V.Y.N.); (M.I.)
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Delvenne A, Gobom J, Schindler SE, Kate MT, Reus LM, Dobricic V, Tijms BM, Benzinger TLS, Cruchaga C, Teunissen CE, Ramakers I, Martinez-Lage P, Tainta M, Vandenberghe R, Schaeverbeke J, Engelborghs S, Roeck ED, Popp J, Peyratout G, Tsolaki M, Freund-Levi Y, Lovestone S, Streffer J, Barkhof F, Bertram L, Blennow K, Zetterberg H, Visser PJ, Vos SJB. CSF proteomic profiles of neurodegeneration biomarkers in Alzheimer's disease. Alzheimers Dement 2024. [PMID: 38970402 DOI: 10.1002/alz.14103] [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: 04/03/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 07/08/2024]
Abstract
INTRODUCTION We aimed to unravel the underlying pathophysiology of the neurodegeneration (N) markers neurogranin (Ng), neurofilament light (NfL), and hippocampal volume (HCV), in Alzheimer's disease (AD) using cerebrospinal fluid (CSF) proteomics. METHODS Individuals without dementia were classified as A+ (CSF amyloid beta [Aβ]42), T+ (CSF phosphorylated tau181), and N+ or N- based on Ng, NfL, or HCV separately. CSF proteomics were generated and compared between groups using analysis of covariance. RESULTS Only a few individuals were A+T+Ng-. A+T+Ng+ and A+T+NfL+ showed different proteomic profiles compared to A+T+Ng- and A+T+NfL-, respectively. Both Ng+ and NfL+ were associated with neuroplasticity, though in opposite directions. Compared to A+T+HCV-, A+T+HCV+ showed few proteomic changes, associated with oxidative stress. DISCUSSION Different N markers are associated with distinct neurodegenerative processes and should not be equated. N markers may differentially complement disease staging beyond amyloid and tau. Our findings suggest that Ng may not be an optimal N marker, given its low incongruency with tau pathophysiology. HIGHLIGHTS In Alzheimer's disease, neurogranin (Ng)+, neurofilament light (NfL)+, and hippocampal volume (HCV)+ showed differential protein expression in cerebrospinal fluid. Ng+ and NfL+ were associated with neuroplasticity, although in opposite directions. HCV+ showed few proteomic changes, related to oxidative stress. Neurodegeneration (N) markers may differentially refine disease staging beyond amyloid and tau. Ng might not be an optimal N marker, as it relates more closely to tau.
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Affiliation(s)
- Aurore Delvenne
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Suzanne E Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mara Ten Kate
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Lianne M Reus
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Tammie L S Benzinger
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam University Medical Centers (AUMC), Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Inez Ramakers
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
| | | | - Mikel Tainta
- Fundación CITA-Alzhéimer Fundazioa, Donostia, Spain
| | - Rik Vandenberghe
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Jolien Schaeverbeke
- Neurology Service, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sebastiaan Engelborghs
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Bru-BRAIN, Universitair Ziekenhuis Brussel and NEUR Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel, Brussels, Belgium
| | - Ellen De Roeck
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Julius Popp
- Old Age Psychiatry, University Hospital Lausanne, Lausanne, Switzerland
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatry University Hospital Zürich, Zürich, Switzerland
| | | | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Makedonia, Thessaloniki, Greece
| | - Yvonne Freund-Levi
- Department of Neurobiology, Caring Sciences and Society (NVS), Division of Clinical Geriatrics, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Department of Psychiatry in Region Örebro County and School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Old Age Psychiatry, Psychology & Neuroscience, King's College, London, UK
| | - Simon Lovestone
- University of Oxford, United Kingdom (currently at Johnson and Johnson Medical Ltd., Oxford, UK
| | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- H. Lundbeck A/S, Valby, Denmark
| | - Frederik Barkhof
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, and Department of Neurology, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, P.R. China
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Stephanie J B Vos
- Department of Psychiatry and Neuropsychology, Alzheimer Centrum Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
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Bosch M, Kallin N, Donakonda S, Zhang JD, Wintersteller H, Hegenbarth S, Heim K, Ramirez C, Fürst A, Lattouf EI, Feuerherd M, Chattopadhyay S, Kumpesa N, Griesser V, Hoflack JC, Siebourg-Polster J, Mogler C, Swadling L, Pallett LJ, Meiser P, Manske K, de Almeida GP, Kosinska AD, Sandu I, Schneider A, Steinbacher V, Teng Y, Schnabel J, Theis F, Gehring AJ, Boonstra A, Janssen HLA, Vandenbosch M, Cuypers E, Öllinger R, Engleitner T, Rad R, Steiger K, Oxenius A, Lo WL, Klepsch V, Baier G, Holzmann B, Maini MK, Heeren R, Murray PJ, Thimme R, Herrmann C, Protzer U, Böttcher JP, Zehn D, Wohlleber D, Lauer GM, Hofmann M, Luangsay S, Knolle PA. A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection. Nature 2024; 631:867-875. [PMID: 38987588 PMCID: PMC11269190 DOI: 10.1038/s41586-024-07630-7] [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: 09/19/2022] [Accepted: 05/30/2024] [Indexed: 07/12/2024]
Abstract
Chronic hepatitis B virus (HBV) infection affects 300 million patients worldwide1,2, in whom virus-specific CD8 T cells by still ill-defined mechanisms lose their function and cannot eliminate HBV-infected hepatocytes3-7. Here we demonstrate that a liver immune rheostat renders virus-specific CD8 T cells refractory to activation and leads to their loss of effector functions. In preclinical models of persistent infection with hepatotropic viruses such as HBV, dysfunctional virus-specific CXCR6+ CD8 T cells accumulated in the liver and, as a characteristic hallmark, showed enhanced transcriptional activity of cAMP-responsive element modulator (CREM) distinct from T cell exhaustion. In patients with chronic hepatitis B, circulating and intrahepatic HBV-specific CXCR6+ CD8 T cells with enhanced CREM expression and transcriptional activity were detected at a frequency of 12-22% of HBV-specific CD8 T cells. Knocking out the inhibitory CREM/ICER isoform in T cells, however, failed to rescue T cell immunity. This indicates that CREM activity was a consequence, rather than the cause, of loss in T cell function, further supported by the observation of enhanced phosphorylation of protein kinase A (PKA) which is upstream of CREM. Indeed, we found that enhanced cAMP-PKA-signalling from increased T cell adenylyl cyclase activity augmented CREM activity and curbed T cell activation and effector function in persistent hepatic infection. Mechanistically, CD8 T cells recognizing their antigen on hepatocytes established close and extensive contact with liver sinusoidal endothelial cells, thereby enhancing adenylyl cyclase-cAMP-PKA signalling in T cells. In these hepatic CD8 T cells, which recognize their antigen on hepatocytes, phosphorylation of key signalling kinases of the T cell receptor signalling pathway was impaired, which rendered them refractory to activation. Thus, close contact with liver sinusoidal endothelial cells curbs the activation and effector function of HBV-specific CD8 T cells that target hepatocytes expressing viral antigens by means of the adenylyl cyclase-cAMP-PKA axis in an immune rheostat-like fashion.
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Affiliation(s)
- Miriam Bosch
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Nina Kallin
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Sainitin Donakonda
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Jitao David Zhang
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
| | - Hannah Wintersteller
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Silke Hegenbarth
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Kathrin Heim
- Third Department of Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Carlos Ramirez
- Health Data Science Unit, Biomedical Genomics Group, Bioquant, Faculty of Medicine Heidelberg, Heidelberg, Germany
| | - Anna Fürst
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Elias Isaac Lattouf
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Feuerherd
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sutirtha Chattopadhyay
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Nadine Kumpesa
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
| | - Vera Griesser
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
| | - Jean-Christophe Hoflack
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
| | - Juliane Siebourg-Polster
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
| | - Carolin Mogler
- Institute of Pathology, School of Medicine and Health, TUM, Munich, Germany
| | - Leo Swadling
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | - Laura J Pallett
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
| | - Philippa Meiser
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Katrin Manske
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Gustavo P de Almeida
- Institute of Immunology and Animal Physiology, School of Life Science, TUM, Munich, Germany
| | - Anna D Kosinska
- Institute of Virology, School of Medicine and Health, TUM, Munich, Germany
- Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research, Munich site, Munich, Germany
| | - Ioana Sandu
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Annika Schneider
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Vincent Steinbacher
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Yan Teng
- Institute of Virology, School of Medicine and Health, TUM, Munich, Germany
| | - Julia Schnabel
- Institute of Machine Learning and Biomedical Imaging, Helmholtz Zentrum Munich, Munich, Germany
| | - Fabian Theis
- Institute of Computational Biology, TUM, Munich, Germany
| | - Adam J Gehring
- Toronto Centre for Liver Disease and Toronto General Hospital Research Institute, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Andre Boonstra
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Harry L A Janssen
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Toronto General Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Michiel Vandenbosch
- Institute of Multimodal Imaging, University of Maastricht, Maastricht, The Netherlands
| | - Eva Cuypers
- Institute of Multimodal Imaging, University of Maastricht, Maastricht, The Netherlands
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine and Health, TUM, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine and Health, TUM, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine and Health, TUM, Munich, Germany
| | - Katja Steiger
- Comparative Experimental Pathology, School of Medicine and Health, TUM, Munich, Germany
| | | | - Wan-Lin Lo
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Victoria Klepsch
- Institute of Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Gottfried Baier
- Institute of Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Bernhard Holzmann
- Department of Surgery, School of Medicine and Health, TUM, Munich, Germany
| | - Mala K Maini
- Institute of Pathology, School of Medicine and Health, TUM, Munich, Germany
| | - Ron Heeren
- Institute of Multimodal Imaging, University of Maastricht, Maastricht, The Netherlands
| | - Peter J Murray
- Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | - Robert Thimme
- Third Department of Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Carl Herrmann
- Health Data Science Unit, Biomedical Genomics Group, Bioquant, Faculty of Medicine Heidelberg, Heidelberg, Germany
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ulrike Protzer
- Institute of Immunology and Animal Physiology, School of Life Science, TUM, Munich, Germany
- Institute of Virology, School of Medicine and Health, TUM, Munich, Germany
- Helmholtz Zentrum München, Munich, Germany
| | - Jan P Böttcher
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Dietmar Zehn
- Institute of Immunology and Animal Physiology, School of Life Science, TUM, Munich, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Georg M Lauer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Maike Hofmann
- Third Department of Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Souphalone Luangsay
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
| | - Percy A Knolle
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany.
- German Center for Infection Research, Munich site, Munich, Germany.
- Institute of Molecular Immunology, School of Life Science, TUM, Munich, Germany.
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36
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Wang Y, Zhou F, Guan J. SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network. Bioinformatics 2024; 40:btae433. [PMID: 38950180 PMCID: PMC11236097 DOI: 10.1093/bioinformatics/btae433] [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: 02/06/2024] [Revised: 06/18/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024] Open
Abstract
MOTIVATION The rise of single-cell RNA sequencing (scRNA-seq) technology presents new opportunities for constructing detailed cell type-specific gene regulatory networks (GRNs) to study cell heterogeneity. However, challenges caused by noises, technical errors, and dropout phenomena in scRNA-seq data pose significant obstacles to GRN inference, making the design of accurate GRN inference algorithms still essential. The recent growth of both single-cell and spatial transcriptomic sequencing data enables the development of supervised deep learning methods to infer GRNs on these diverse single-cell datasets. RESULTS In this study, we introduce a novel deep learning framework based on shared factor neighborhood and integrated neural network (SFINN) for inferring potential interactions and causalities between transcription factors and target genes from single-cell and spatial transcriptomic data. SFINN utilizes shared factor neighborhood to construct cellular neighborhood network based on gene expression data and additionally integrates cellular network generated from spatial location information. Subsequently, the cell adjacency matrix and gene pair expression are fed into an integrated neural network framework consisting of a graph convolutional neural network and a fully-connected neural network to determine whether the genes interact. Performance evaluation in the tasks of gene interaction and causality prediction against the existing GRN reconstruction algorithms demonstrates the usability and competitiveness of SFINN across different kinds of data. SFINN can be applied to infer GRNs from conventional single-cell sequencing data and spatial transcriptomic data. AVAILABILITY AND IMPLEMENTATION SFINN can be accessed at GitHub: https://github.com/JGuan-lab/SFINN.
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Affiliation(s)
- Yongjie Wang
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
| | - Fengfan Zhou
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
| | - Jinting Guan
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
- Key Laboratory of System Control and Information Processing, Ministry of Education, Shanghai 200240, China
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361102, China
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37
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Deng C, Li HD, Zhang LS, Liu Y, Li Y, Wang J. Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks. Bioinformatics 2024; 40:i511-i520. [PMID: 38940121 PMCID: PMC11211849 DOI: 10.1093/bioinformatics/btae257] [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] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited. RESULTS Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of employing hypergraphs for representing annotated gene sets. Second, we validate the accuracy of DISHyper-predicted cancer genes using functional validation results and multiple independent functional genomics data. Third, our model predicts 44 novel cancer genes, and subsequent analysis shows their significant associations with multiple types of cancers. Overall, our study provides a new perspective for discovering cancer genes and reveals previously undiscovered cancer genes. AVAILABILITY AND IMPLEMENTATION DISHyper is freely available for download at https://github.com/genemine/DISHyper.
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Affiliation(s)
- Chao Deng
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Hong-Dong Li
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Li-Shen Zhang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Yiwei Liu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Yaohang Li
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529-0001, United States
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
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38
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Wang M, Ying Q, Ding R, Xing Y, Wang J, Pan Y, Pan B, Xiang G, Liu Z. Elucidating prognosis in cervical squamous cell carcinoma and endocervical adenocarcinoma: a novel anoikis-related gene signature model. Front Oncol 2024; 14:1352638. [PMID: 38988712 PMCID: PMC11234598 DOI: 10.3389/fonc.2024.1352638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
Background Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) are among the most prevalent gynecologic malignancies globally. The prognosis is abysmal once cervical cancer progresses to lymphatic metastasis. Anoikis, a specialized form of apoptosis induced by loss of cell adhesion to the extracellular matrix, plays a critical role. The prediction model based on anoikis-related genes (ARGs) expression and clinical data could greatly aid clinical decision-making. However, the relationship between ARGs and CESC remains unclear. Methods ARGs curated from the GeneCards and Harmonizome portals were instrumental in delineating CESC subtypes and in developing a prognostic framework for patients afflicted with this condition. We further delved into the intricacies of the immune microenvironment and pathway enrichment across the identified subtypes. Finally, our efforts culminated in the creation of an innovative nomogram that integrates ARGs. The utility of this prognostic tool was underscored by Decision Curve Analysis (DCA), which illuminate its prospective benefits in guiding clinical interventions. Results In our study, We discerned a set of 17 survival-pertinent, anoikis-related differentially expressed genes (DEGs) in CESC, from which nine were meticulously selected for the construction of prognostic models. The derived prognostic risk score was subsequently validated as an autonomous prognostic determinant. Through comprehensive functional analyses, we observed distinct immune profiles and drug response patterns among divergent prognostic stratifications. Further, we integrated the risk scores with the clinicopathological characteristics of CESC to develop a robust nomogram. DCA corroborated the utility of our model, demonstrating its potential to enhance patient outcomes through tailored clinical treatment strategies. Conclusion The predictive signature, encompassing nine pivotal genes, alongside the meticulously constructed nomogram developed in this research, furnishes clinicians with a sophisticated tool for tailoring treatment strategies to individual patients diagnosed with CESC.
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Affiliation(s)
- Mingwei- Wang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Qiaohui- Ying
- Institute of Oral Basic Research, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ru Ding
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, China
| | - Yuncan- Xing
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jue Wang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Yiming- Pan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Bo Pan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Guifen- Xiang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
- School of Public Health, Anhui Medical University, Hefei, China
| | - Zhong Liu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
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Karasik A, Lorenzi HA, DePass AV, Guydosh NR. Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response. Cell Rep 2024; 43:114287. [PMID: 38823018 PMCID: PMC11251458 DOI: 10.1016/j.celrep.2024.114287] [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: 09/30/2023] [Revised: 04/05/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024] Open
Abstract
Viral infection triggers several double-stranded RNA (dsRNA) sensors that lead to changes in gene expression in the cell. One of these sensors activates an endonuclease, ribonuclease L (RNase L), that cleaves single-stranded RNA. However, how the resultant widespread RNA fragmentation affects gene expression is not fully understood. Here, we show that this fragmentation induces the ribotoxic stress response via ZAKα, potentially through stalled ribosomes and/or ribosome collisions. The p38 and JNK pathways that are activated as part of this response promote outcomes that inhibit the virus, such as programmed cell death. We also show that RNase L limits the translation of stress-responsive genes. Intriguingly, we found that the activity of the generic endonuclease, RNase A, recapitulates many of the same molecular phenotypes as activated RNase L, demonstrating how widespread RNA cleavage can evoke an antiviral program.
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Affiliation(s)
- Agnes Karasik
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hernan A Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew V DePass
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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40
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Chen YJ, Tseng SC, Chen PT, Hwang E. The non-mitotic role of HMMR in regulating the localization of TPX2 and the dynamics of microtubules in neurons. eLife 2024; 13:RP94547. [PMID: 38904660 PMCID: PMC11192530 DOI: 10.7554/elife.94547] [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] [Indexed: 06/22/2024] Open
Abstract
A functional nervous system is built upon the proper morphogenesis of neurons to establish the intricate connection between them. The microtubule cytoskeleton is known to play various essential roles in this morphogenetic process. While many microtubule-associated proteins (MAPs) have been demonstrated to participate in neuronal morphogenesis, the function of many more remains to be determined. This study focuses on a MAP called HMMR in mice, which was originally identified as a hyaluronan binding protein and later found to possess microtubule and centrosome binding capacity. HMMR exhibits high abundance on neuronal microtubules and altering the level of HMMR significantly affects the morphology of neurons. Instead of confining to the centrosome(s) like cells in mitosis, HMMR localizes to microtubules along axons and dendrites. Furthermore, transiently expressing HMMR enhances the stability of neuronal microtubules and increases the formation frequency of growing microtubules along the neurites. HMMR regulates the microtubule localization of a non-centrosomal microtubule nucleator TPX2 along the neurite, offering an explanation for how HMMR contributes to the promotion of growing microtubules. This study sheds light on how cells utilize proteins involved in mitosis for non-mitotic functions.
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Affiliation(s)
- Yi-Ju Chen
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
| | - Shun-Cheng Tseng
- Department of Orthopedic Surgery, Changhua Christian HospitalChanghuaTaiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
| | - Peng-Tzu Chen
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
| | - Eric Hwang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung UniversityHsinchuTaiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung UniversityHsinchuTaiwan
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Adeoye T, Shah SI, Ullah G. Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer's Disease. Aging Dis 2024:AD.2024.0429. [PMID: 38913039 DOI: 10.14336/ad.2024.0429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/12/2024] [Indexed: 06/25/2024] Open
Abstract
Alzheimer's disease (AD) manifests as a complex systems pathology with intricate interplay among various genes and biological processes. Traditional differential gene expression (DEG) analysis, while commonly employed to characterize AD-driven perturbations, does not sufficiently capture the full spectrum of underlying biological processes. Utilizing single-nucleus RNA-sequencing data from postmortem brain samples across key regions-middle temporal gyrus, superior frontal gyrus, and entorhinal cortex-we provide a comprehensive systematic analysis of disrupted processes in AD. We go beyond the DEG-centric analysis by integrating pathway activity analysis with weighted gene co-expression patterns to comprehensively map gene interconnectivity, identifying region- and cell-type-specific drivers of biological processes associated with AD. Our analysis reveals profound modular heterogeneity in neurons and glia as well as extensive AD-related functional disruptions. Co-expression networks highlighted the extended involvement of astrocytes and microglia in biological processes beyond neuroinflammation, such as calcium homeostasis, glutamate regulation, lipid metabolism, vesicle-mediated transport, and TOR signaling. We find limited representation of DEGs within dysregulated pathways across neurons and glial cells, suggesting that differential gene expression alone may not adequately represent the disease complexity. Further dissection of inferred gene modules revealed distinct dynamics of hub DEGs in neurons versus glia, suggesting that DEGs exert more impact on neurons compared to glial cells in driving modular dysregulations underlying perturbed biological processes. Interestingly, we observe an overall downregulation of astrocyte and microglia modules across all brain regions in AD, indicating a prevailing trend of functional repression in glial cells across these regions. Notable genes from the CALM and HSP90 families emerged as hub genes across neuronal modules in all brain regions, suggesting conserved roles as drivers of synaptic dysfunction in AD. Our findings demonstrate the importance of an integrated, systems-oriented approach combining pathway and network analysis to comprehensively understand the cell-type-specific roles of genes in AD-related biological processes.
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42
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Pan Y, Wang C, Zhou W, Shi Y, Meng X, Muhammad Y, Hammer RD, Jia B, Zheng H, Li DP, Liu Z, Hildebrandt G, Kang X. Inhibiting AGTR1 reduces AML burden and protects the heart from cardiotoxicity in mouse models. Sci Transl Med 2024; 16:eadl5931. [PMID: 38896605 PMCID: PMC11250918 DOI: 10.1126/scitranslmed.adl5931] [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: 10/26/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Clinical treatment of acute myeloid leukemia (AML) largely relies on intensive chemotherapy. However, the application of chemotherapy is often hindered by cardiotoxicity. Patient sequence data revealed that angiotensin II receptor type 1 (AGTR1) is a shared target between AML and cardiovascular disease (CVD). We found that inhibiting AGTR1 sensitized AML to chemotherapy and protected the heart against chemotherapy-induced cardiotoxicity in a human AML cell-transplanted mouse model. These effects were regulated by the AGTR1-Notch1 axis in AML cells and cardiomyocytes from mice. In mouse cardiomyocytes, AGTR1 was hyperactivated by AML and chemotherapy. AML leukemogenesis increased the expression of the angiotensin-converting enzyme and led to increased production of angiotensin II, the ligand of AGTR1, in an MLL-AF9-driven AML mouse model. In this model, the AGTR1-Notch1 axis regulated a variety of genes involved with cell stemness and chemotherapy resistance. AML cell stemness was reduced after Agtr1a deletion in the mouse AML cell transplant model. Mechanistically, Agtr1a deletion decreased γ-secretase formation, which is required for transmembrane Notch1 cleavage and release of the Notch1 intracellular domain into the nucleus. Using multiomics, we identified AGTR1-Notch1 signaling downstream genes and found decreased binding between these gene sequences with Notch1 and chromatin enhancers, as well as increased binding with silencers. These findings describe an AML/CVD association that may be used to improve AML treatment.
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MESH Headings
- Animals
- Humans
- Mice
- Amyloid Precursor Protein Secretases/metabolism
- Cardiotoxicity/metabolism
- Cardiotoxicity/pathology
- Cell Line, Tumor
- Disease Models, Animal
- Heart/drug effects
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/drug effects
- Myocytes, Cardiac/pathology
- Receptor, Angiotensin, Type 1/metabolism
- Receptor, Angiotensin, Type 1/genetics
- Receptor, Notch1/metabolism
- Signal Transduction/drug effects
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Affiliation(s)
- Yi Pan
- Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA
| | - Chen Wang
- Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA
| | - WenXuan Zhou
- Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA
| | - Yao Shi
- Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA
| | - XiaDuo Meng
- Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA
| | - Yasir Muhammad
- Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA
- Division of Hematology and Oncology, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Richard D Hammer
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Bei Jia
- Division of Hematology/Oncology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Hong Zheng
- Division of Hematology/Oncology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - De-Pei Li
- Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Zhenguo Liu
- Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Gerhard Hildebrandt
- Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA
- Division of Hematology and Oncology, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - XunLei Kang
- Center for Precision Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center at MU Health Care, University of Missouri, Columbia, MO 65212, USA
- Division of Hematology and Oncology, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA
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Karlin H, Sooda M, Larson M, Rong J, Huan T, Mens MMJ, van Rooij FJA, Ikram MA, Courchesne P, Freedman JE, Joehanes R, Mueller GP, Kavousi M, Ghanbari M, Levy D. Plasma Extracellular MicroRNAs Associated With Cardiovascular Disease Risk Factors in Middle-Aged and Older Adults. J Am Heart Assoc 2024; 13:e033674. [PMID: 38860398 PMCID: PMC11255734 DOI: 10.1161/jaha.123.033674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/01/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Extracellular microRNAs (miRNAs) are a class of noncoding RNAs that remain stable in the extracellular milieu, where they contribute to various physiological and pathological processes by facilitating intercellular signaling. Previous studies have reported associations between miRNAs and cardiovascular diseases (CVDs); however, the plasma miRNA signatures of CVD and its risk factors have not been fully elucidated at the population level. METHODS AND RESULTS Plasma miRNA levels were measured in 4440 FHS (Framingham Heart Study) participants. Linear regression analyses were conducted to test the cross-sectional associations of each miRNA with 8 CVD risk factors. Prospective analyses of the associations of miRNAs with new-onset obesity, hypertension, type 2 diabetes, CVD, and all-cause mortality were conducted using proportional hazards regression. Replication was carried out in 1999 RS (Rotterdam Study) participants. Pathway enrichment analyses were conducted and target genes were predicted for miRNAs associated with ≥5 risk factors in the FHS. In the FHS, 6 miRNAs (miR-193b-3p, miR-122-5p, miR-365a-3p, miR-194-5p, miR-192-5p, and miR-193a-5p) were associated with ≥5 risk factors. This miRNA signature was enriched for pathways associated with CVD and several genes annotated to these pathways were predicted targets of the identified miRNAs. Furthermore, miR-193b-3p, miR-194-5p, and miR-193a-5p were each associated with ≥2 risk factors in the RS. Prospective analysis revealed 8 miRNAs associated with all-cause mortality in the FHS. CONCLUSIONS These findings highlight associations between miRNAs and CVD risk factors that may provide valuable insights into the underlying pathogenesis of CVD.
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Affiliation(s)
- Hannah Karlin
- Framingham Heart StudyFraminghamMAUSA
- Population Sciences BranchNational Heart, Lung, and Blood InstituteBethesdaMDUSA
| | - Meera Sooda
- Framingham Heart StudyFraminghamMAUSA
- Population Sciences BranchNational Heart, Lung, and Blood InstituteBethesdaMDUSA
| | - Martin Larson
- Framingham Heart StudyFraminghamMAUSA
- Department of BiostatisticsBoston University School of Public HealthBostonMAUSA
| | - Jian Rong
- Framingham Heart StudyFraminghamMAUSA
- Department of NeurologyBoston University Chobanian & Avedisian School of MedicineBostonMAUSA
| | - Tianxiao Huan
- Framingham Heart StudyFraminghamMAUSA
- Population Sciences BranchNational Heart, Lung, and Blood InstituteBethesdaMDUSA
- Ophthalmology and Visual SciencesUniversity of Massachusetts Medical SchoolWorcesterMAUSA
| | - Michelle M. J. Mens
- Department of EpidemiologyErasmus MC University Medical CenterRotterdamThe Netherlands
- Department of Social and Behavioral SciencesHarvard T.H Chan School of Public HealthBostonMAUSA
| | - Frank J. A. van Rooij
- Department of EpidemiologyErasmus MC University Medical CenterRotterdamThe Netherlands
| | - M. Arfan Ikram
- Department of EpidemiologyErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Paul Courchesne
- Framingham Heart StudyFraminghamMAUSA
- Population Sciences BranchNational Heart, Lung, and Blood InstituteBethesdaMDUSA
| | - Jane E. Freedman
- Department of Medicine, Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Roby Joehanes
- Framingham Heart StudyFraminghamMAUSA
- Population Sciences BranchNational Heart, Lung, and Blood InstituteBethesdaMDUSA
| | - Gregory P. Mueller
- Department of Anatomy, Physiology, and Genetics, F. Edward Hebert School of MedicineUniformed Services University of the Health SciencesBethesdaMDUSA
| | - Maryam Kavousi
- Department of EpidemiologyErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Mohsen Ghanbari
- Department of EpidemiologyErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Daniel Levy
- Framingham Heart StudyFraminghamMAUSA
- Population Sciences BranchNational Heart, Lung, and Blood InstituteBethesdaMDUSA
- Boston University School of MedicineBostonMAUSA
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Xue Y, Friedl V, Ding H, Wong CK, Stuart JM. Single-cell signatures identify microenvironment factors in tumors associated with patient outcomes. CELL REPORTS METHODS 2024; 4:100799. [PMID: 38889686 PMCID: PMC11228369 DOI: 10.1016/j.crmeth.2024.100799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
The cellular components of tumors and their microenvironment play pivotal roles in tumor progression, patient survival, and the response to cancer treatments. Unveiling a comprehensive cellular profile within bulk tumors via single-cell RNA sequencing (scRNA-seq) data is crucial, as it unveils intrinsic tumor cellular traits that elude identification through conventional cancer subtyping methods. Our contribution, scBeacon, is a tool that derives cell-type signatures by integrating and clustering multiple scRNA-seq datasets to extract signatures for deconvolving unrelated tumor datasets on bulk samples. Through the employment of scBeacon on the The Cancer Genome Atlas (TCGA) cohort, we find cellular and molecular attributes within specific tumor categories, many with patient outcome relevance. We developed a tumor cell-type map to visually depict the relationships among TCGA samples based on the cell-type inferences.
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Affiliation(s)
- Yuanqing Xue
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA
| | - Verena Friedl
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA
| | - Hongxu Ding
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA
| | - Christopher K Wong
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA
| | - Joshua M Stuart
- UC Santa Cruz Department, Biomolecular Engineering, Genomics Institute, Santa Cruz, CA, USA.
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Bai H, Liu X, Lin M, Meng Y, Tang R, Guo Y, Li N, Clarke MF, Cai S. Progressive senescence programs induce intrinsic vulnerability to aging-related female breast cancer. Nat Commun 2024; 15:5154. [PMID: 38886378 PMCID: PMC11183265 DOI: 10.1038/s41467-024-49106-2] [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: 06/16/2023] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Cancer incidence escalates exponentially with advancing age; however, the underlying mechanism remains unclear. In this study, we build a chronological molecular clock at single-cell transcription level with a mammary stem cell-enriched population to depict physiological aging dynamics in female mice. We find that the mammary aging process is asynchronous and progressive, initiated by an early senescence program, succeeded by an entropic late senescence program with elevated cancer associated pathways, vulnerable to cancer predisposition. The transition towards senescence program is governed by a stem cell factor Bcl11b, loss of which accelerates mammary ageing with enhanced DMBA-induced tumor formation. We have identified a drug TPCA-1 that can rejuvenate mammary cells and significantly reduce aging-related cancer incidence. Our findings establish a molecular portrait of progressive mammary cell aging and elucidate the transcriptional regulatory network bridging mammary aging and cancer predisposition, which has potential implications for the management of cancer prevalence in the aged.
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Affiliation(s)
- Huiru Bai
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaoqin Liu
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Meizhen Lin
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Yuan Meng
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Ruolan Tang
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Yajing Guo
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Li
- Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang, China
| | - Michael F Clarke
- Institute of Stem Cell and Regenerative Medicine, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Shang Cai
- Westlake Disease Modeling lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China.
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Frusciante L, Geminiani M, Olmastroni T, Mastroeni P, Trezza A, Salvini L, Lamponi S, Spiga O, Santucci A. Repurposing Castanea sativa Spiny Burr By-Products Extract as a Potentially Effective Anti-Inflammatory Agent for Novel Future Biotechnological Applications. Life (Basel) 2024; 14:763. [PMID: 38929746 PMCID: PMC11205080 DOI: 10.3390/life14060763] [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: 05/16/2024] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The concept of a "circular bioeconomy" holds great promise for the health, cosmetic, and nutrition sectors by re-using Castanea sativa (Mill.) by-products. This sustainable resource is rich in bioactive secondary metabolites with antioxidant and anti-inflammatory properties. By transforming these by-products into high-value products for human health, we can promote sustainable economic growth and reduce the environmental impact of traditional waste disposal, adding value to previously underutilized resources. In the present study, we investigated the antioxidant capacity, phytochemical composition, and in vitro antioxidant and anti-inflammatory activity of C. sativa burr (CSB) aqueous extract. The spectrophotometric study revealed high total phenolic content (TPC) values with significant antioxidant and anti-radical properties. Using UPLC-MS/MS techniques, the phytochemical investigation identified 56 metabolites, confirming the presence of phenolic compounds in CSBs. In addition, CSBs significantly downregulated pro-inflammatory mediators in LPS-stimulated RAW 264.7 macrophage cells without significant cell toxicity. Lastly, in silico studies pinpointed three kinases from RAW 264.7 cells as binding partners with ellagic acid, the predominant compound found in our extract. These findings strongly advocate for the recycling and valorization of C. sativa by-products, challenging their conventional classification as mere "waste".
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Affiliation(s)
- Luisa Frusciante
- Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (T.O.); (P.M.); (A.T.); (S.L.); (O.S.); (A.S.)
| | - Michela Geminiani
- Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (T.O.); (P.M.); (A.T.); (S.L.); (O.S.); (A.S.)
- SienabioACTIVE, Università di Siena, Via Aldo Moro, 53100 Siena, Italy
| | - Tommaso Olmastroni
- Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (T.O.); (P.M.); (A.T.); (S.L.); (O.S.); (A.S.)
| | - Pierfrancesco Mastroeni
- Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (T.O.); (P.M.); (A.T.); (S.L.); (O.S.); (A.S.)
| | - Alfonso Trezza
- Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (T.O.); (P.M.); (A.T.); (S.L.); (O.S.); (A.S.)
| | - Laura Salvini
- Fondazione Toscana Life Sciences, Strada del Petriccio e Belriguardo, 53100 Siena, Italy;
| | - Stefania Lamponi
- Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (T.O.); (P.M.); (A.T.); (S.L.); (O.S.); (A.S.)
- SienabioACTIVE, Università di Siena, Via Aldo Moro, 53100 Siena, Italy
| | - Ottavia Spiga
- Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (T.O.); (P.M.); (A.T.); (S.L.); (O.S.); (A.S.)
- ARTES 4.0, Viale Rinaldo Piaggio, 34, 56025 Pontedera, Italy
| | - Annalisa Santucci
- Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro, 53100 Siena, Italy; (L.F.); (T.O.); (P.M.); (A.T.); (S.L.); (O.S.); (A.S.)
- SienabioACTIVE, Università di Siena, Via Aldo Moro, 53100 Siena, Italy
- ARTES 4.0, Viale Rinaldo Piaggio, 34, 56025 Pontedera, Italy
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Khorani K, Burkart S, Weusthof C, Han R, Liang S, Stögbauer F, Hess J. Context-Dependent Regulation of Peripheral Nerve Abundance by the PI3K Pathway in the Tumor Microenvironment of Head and Neck Squamous Cell Carcinoma. Cells 2024; 13:1033. [PMID: 38920662 PMCID: PMC11202044 DOI: 10.3390/cells13121033] [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: 03/23/2024] [Revised: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
Recent studies have highlighted neurons and their associated Schwann cells (SCs) as key regulators of cancer development. However, the mode of their interaction with tumor cells or other components of the tumor microenvironment (TME) remains elusive. We established an SC-related 43-gene set as a surrogate for peripheral nerves in the TME. Head and neck squamous cell carcinoma (HNSCC) from The Cancer Genome Atlas (TCGA) were classified into low, intermediate and high SC score groups based on the expression of this gene set. Perineural invasion (PNI) and TGF-β signaling were hallmarks of SChigh tumors, whereas SClow tumors were enriched for HPV16-positive OPSCC and higher PI3K-MTOR activity. The latter activity was partially explained by a higher frequency of PTEN mutation and PIK3CA copy number gain. The inverse association between PI3K-MTOR activity and peripheral nerve abundance was context-dependent and influenced by the TP53 mutation status. An in silico drug screening approach highlighted the potential vulnerabilities of HNSCC with variable SC scores and predicted a higher sensitivity of SClow tumors to DNA topoisomerase inhibitors. In conclusion, we have established a tool for assessing peripheral nerve abundance in the TME and provided new clinical and biological insights into their regulation. This knowledge may pave the way for new therapeutic strategies and impart proof of concept in appropriate preclinical models.
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Affiliation(s)
- Karam Khorani
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.B.); (C.W.); (R.H.); (S.L.)
| | - Sebastian Burkart
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.B.); (C.W.); (R.H.); (S.L.)
| | - Christopher Weusthof
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.B.); (C.W.); (R.H.); (S.L.)
| | - Rui Han
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.B.); (C.W.); (R.H.); (S.L.)
| | - Siyuan Liang
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.B.); (C.W.); (R.H.); (S.L.)
| | - Fabian Stögbauer
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Germany and Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany;
- Institute of Pathology, School of Medicine, Technical University of Munich (TUM), 80337 Munich, Germany
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.B.); (C.W.); (R.H.); (S.L.)
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48
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Wu Z, Yu J, Han T, Tu Y, Su F, Li S, Huang Y. System analysis based on Anoikis-related genes identifies MAPK1 as a novel therapy target for osteosarcoma with neoadjuvant chemotherapy. BMC Musculoskelet Disord 2024; 25:437. [PMID: 38835052 PMCID: PMC11149263 DOI: 10.1186/s12891-024-07547-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/27/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Osteosarcoma (OS) is the most common bone malignant tumor in children, and its prognosis is often poor. Anoikis is a unique mode of cell death.However, the effects of Anoikis in OS remain unexplored. METHOD Differential analysis of Anoikis-related genes was performed based on the metastatic and non-metastatic groups. Then LASSO logistic regression and SVM-RFE algorithms were applied to screen out the characteristic genes. Later, Univariate and multivariate Cox regression was conducted to identify prognostic genes and further develop the Anoikis-based risk score. In addition, correlation analysis was performed to analyze the relationship between tumor microenvironment, drug sensitivity, and prognostic models. RESULTS We established novel Anoikis-related subgroups and developed a prognostic model based on three Anoikis-related genes (MAPK1, MYC, and EDIL3). The survival and ROC analysis results showed that the prognostic model was reliable. Besides, the results of single-cell sequencing analysis suggested that the three prognostic genes were closely related to immune cell infiltration. Subsequently, aberrant expression of two prognostic genes was identified in osteosarcoma cells. Nilotinib can promote the apoptosis of osteosarcoma cells and down-regulate the expression of MAPK1. CONCLUSIONS We developed a novel Anoikis-related risk score model, which can assist clinicians in evaluating the prognosis of osteosarcoma patients in clinical practice. Analysis of the tumor immune microenvironment and chemotherapeutic drug sensitivity can provide necessary insights into subsequent mechanisms. MAPK1 may be a valuable therapeutic target for neoadjuvant chemotherapy in osteosarcoma.
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Affiliation(s)
- Zhouwei Wu
- Department of Orthopedics, the Second Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou, 325000, China
| | - Jiapei Yu
- Department of Orthopedics, the Second Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou, 325000, China
| | - Tao Han
- Department of Orthopedics, the Shaoxing People's Hospital (Shaoxing Hospital of Zhejiang University), Shaoxing, 312000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou, 325000, China
| | - Yiting Tu
- Department of Orthopedics, the Second Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou, 325000, China
| | - Fang Su
- Department of Orthopedics, the Second Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Shi Li
- Department of Orthopedics, the Second Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou, 325000, China.
- Department of Orthopaedics, The Second Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, 109 West Xueyuan Road, Wenzhou, 325027, Zhejiang Province, China.
| | - Yixing Huang
- Department of Orthopedics, the Second Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
- Key Laboratory of Orthopedics of Zhejiang Province, Wenzhou, 325000, China.
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49
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Kruckow KL, Murray E, Shayhidin E, Rosenberg AF, Bowdish DME, Orihuela CJ. Chronic TNF exposure induces glucocorticoid-like immunosuppression in the alveolar macrophages of aged mice that enhances their susceptibility to pneumonia. Aging Cell 2024; 23:e14133. [PMID: 38459711 PMCID: PMC11296116 DOI: 10.1111/acel.14133] [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: 07/07/2023] [Revised: 01/22/2024] [Accepted: 02/12/2024] [Indexed: 03/10/2024] Open
Abstract
Chronic low-grade inflammation, particularly elevated tumor necrosis factor (TNF) levels, occurs due to advanced age and is associated with greater susceptibility to infection. One reason for this is age-dependent macrophage dysfunction (ADMD). Herein, we use the adoptive transfer of alveolar macrophages (AM) from aged mice into the airway of young mice to show that inherent age-related defects in AM were sufficient to increase the susceptibility to Streptococcus pneumoniae, a Gram-positive bacterium and the leading cause of community-acquired pneumonia. MAPK phosphorylation arrays using AM lysates from young and aged wild-type (WT) and TNF knockout (KO) mice revealed multilevel TNF-mediated suppression of kinase activity in aged mice. RNAseq analyses of AM validated the suppression of MAPK signaling as a consequence of TNF during aging. Two regulatory phosphatases that suppress MAPK signaling, Dusp1 and Ptprs, were confirmed to be upregulated with age and as a result of TNF exposure both ex vivo and in vitro. Dusp1 is known to be responsible for glucocorticoid-mediated immune suppression, and dexamethasone treatment increased Dusp1 and Ptprs expression in cells and recapitulated the ADMD phenotype. In young mice, treatment with dexamethasone increased the levels of Dusp1 and Ptprs and their susceptibility to infection. TNF-neutralizing antibody reduced Dusp1 and Ptprs levels in AM from aged mice and reduced pneumonia severity following bacterial challenge. We conclude that chronic exposure to TNF increases the expression of the glucocorticoid-associated MAPK signaling suppressors, Dusp1 and Ptprs, which inhibits AM activation and increases susceptibility to bacterial pneumonia in older adults.
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Affiliation(s)
- Katherine L. Kruckow
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Elizabeth Murray
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Elnur Shayhidin
- Firestone Institute for Respiratory HealthSt. Joseph's Healthcare HamiltonHamiltonOntarioCanada
- The M.G. DeGroote Institute for Infectious Disease ResearchMcMaster UniversityHamiltonOntarioCanada
| | - Alexander F. Rosenberg
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
- Informatics InstituteUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Dawn M. E. Bowdish
- Firestone Institute for Respiratory HealthSt. Joseph's Healthcare HamiltonHamiltonOntarioCanada
- The M.G. DeGroote Institute for Infectious Disease ResearchMcMaster UniversityHamiltonOntarioCanada
| | - Carlos J. Orihuela
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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50
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Cerda‐Troncoso C, Grünenwald F, Arias‐Muñoz E, Cavieres VA, Caceres‐Verschae A, Hernández S, Gaete‐Ramírez B, Álvarez‐Astudillo F, Acuña RA, Ostrowski M, Burgos PV, Varas‐Godoy M. Chemo-small extracellular vesicles released in cisplatin-resistance ovarian cancer cells are regulated by the lysosomal function. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e157. [PMID: 38947172 PMCID: PMC11212338 DOI: 10.1002/jex2.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 07/02/2024]
Abstract
Chemoresistance is a common problem in ovarian cancer (OvCa) treatment, where resistant cells, in response to chemotherapy, secrete small extracellular vesicles (sEVs), known as chemo-sEVs, that transfer resistance to recipient cells. sEVs are formed as intraluminal vesicles (ILVs) within multivesicular endosomes (MVEs), whose trafficking is regulated by Ras-associated binding (RAB) GTPases that mediate sEVs secretion or lysosomal degradation. A decrease in lysosomal function can promote sEVs secretion, but the relationship between MVEs trafficking pathways and sEVs secretion in OvCa chemoresistance is unclear. Here, we show that A2780cis cisplatin (CCDP) resistant OvCa cells had an increased number of MVEs and ILVs structures, higher levels of Endosomal Sorting Complex Required for Transport (ESCRTs) machinery components, and RAB27A compared to A2780 CDDP-sensitive OvCa cells. CDDP promoted the secretion of chemo-sEVs in A2780cis cells, enriched in DNA damage response proteins. A2780cis cells exhibited poor lysosomal function with reduced levels of RAB7, essential in MVEs-Lysosomal trafficking. The silencing of RAB27A in A2780cis cells prevents the Chemo-EVs secretion, reduces its chemoresistance and restores lysosomal function and levels of RAB7, switching them into an A2780-like cellular phenotype. Enhancing lysosomal function with rapamycin reduced chemo-sEVs secretion. Our results suggest that adjusting the balance between secretory MVEs and lysosomal MVEs trafficking could be a promising strategy for overcoming CDDP chemoresistance in OvCa.
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Affiliation(s)
- Cristóbal Cerda‐Troncoso
- Organelle Phagy Lab, CEBICEMFacultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
- Cancer Cell Biology Lab, CEBICEM, Facultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
- Centro Ciencia & VidaFundación Ciencia & VidaSantiagoChile
| | - Felipe Grünenwald
- Cancer Cell Biology Lab, CEBICEM, Facultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
| | - Eloísa Arias‐Muñoz
- Organelle Phagy Lab, CEBICEMFacultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
| | - Viviana A. Cavieres
- Organelle Phagy Lab, CEBICEMFacultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
- Departamento de Ciencias Biológicas y Químicas, Facultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
| | - Albano Caceres‐Verschae
- Cancer Cell Biology Lab, CEBICEM, Facultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
| | - Sergio Hernández
- Organelle Phagy Lab, CEBICEMFacultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
| | - Belén Gaete‐Ramírez
- Cancer Cell Biology Lab, CEBICEM, Facultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
| | | | - Rodrigo A. Acuña
- Centro de Medicina Regenerativa, Facultad de MedicinaClínica Alemana Universidad del DesarrolloSantiagoChile
| | - Matias Ostrowski
- Facultad de Medicina, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS)Universidad de Buenos Aires (UBA)Buenos AiresArgentina
| | - Patricia V. Burgos
- Organelle Phagy Lab, CEBICEMFacultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
- Centro Ciencia & VidaFundación Ciencia & VidaSantiagoChile
| | - Manuel Varas‐Godoy
- Cancer Cell Biology Lab, CEBICEM, Facultad de Medicina y CienciaUniversidad San SebastiánSantiagoChile
- Centro Ciencia & VidaFundación Ciencia & VidaSantiagoChile
- Advanced Center for Chronic DiseasesSantiagoChile
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