1
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Magaña-López G, Calzone L, Zinovyev A, Paulevé L. scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics. PLoS Comput Biol 2024; 20:e1011620. [PMID: 38976751 DOI: 10.1371/journal.pcbi.1011620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 06/24/2024] [Indexed: 07/10/2024] Open
Abstract
Boolean networks are largely employed to model the qualitative dynamics of cell fate processes by describing the change of binary activation states of genes and transcription factors with time. Being able to bridge such qualitative states with quantitative measurements of gene expressions in cells, as scRNA-seq, is a cornerstone for data-driven model construction and validation. On one hand, scRNA-seq binarisation is a key step for inferring and validating Boolean models. On the other hand, the generation of synthetic scRNA-seq data from baseline Boolean models provides an important asset to benchmark inference methods. However, linking characteristics of scRNA-seq datasets, including dropout events, with Boolean states is a challenging task. We present scBoolSeq, a method for the bidirectional linking of scRNA-seq data and Boolean activation state of genes. Given a reference scRNA-seq dataset, scBoolSeq computes statistical criteria to classify the empirical gene pseudocount distributions as either unimodal, bimodal, or zero-inflated, and fit a probabilistic model of dropouts, with gene-dependent parameters. From these learnt distributions, scBoolSeq can perform both binarisation of scRNA-seq datasets, and generate synthetic scRNA-seq datasets from Boolean traces, as issued from Boolean networks, using biased sampling and dropout simulation. We present a case study demonstrating the application of scBoolSeq's binarisation scheme in data-driven model inference. Furthermore, we compare synthetic scRNA-seq data generated by scBoolSeq with BoolODE's, data for the same Boolean Network model. The comparison shows that our method better reproduces the statistics of real scRNA-seq datasets, such as the mean-variance and mean-dropout relationships while exhibiting clearly defined trajectories in two-dimensional projections of the data.
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Affiliation(s)
| | - Laurence Calzone
- Institut Curie, Université PSL, Paris, France
- INSERM, U900, Paris, France
- Mines ParisTech, Université PSL, Paris, France
| | | | - Loïc Paulevé
- Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, Talence, France
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2
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Qian C, Yang Q, Rotinen M, Huang R, Kim H, Gallent B, Yan Y, Cadaneanu RM, Zhang B, Kaochar S, Freedland SJ, Posadas EM, Ellis L, Di Vizio D, Morrissey C, Nelson PS, Brady L, Murali R, Campbell MJ, Yang W, Knudsen BS, Mostaghel EA, Ye H, Garraway IP, You S, Freeman MR. ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer. Nucleic Acids Res 2024:gkae547. [PMID: 38932701 DOI: 10.1093/nar/gkae547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024] Open
Abstract
Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 gene targets include the glucocorticoid receptor (GR; NR3C1) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.
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Affiliation(s)
- Chen Qian
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Qian Yang
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mirja Rotinen
- Department of Health Sciences, Public University of Navarre, Pamplona, Navarra, Spain
| | - Rongrong Huang
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Hyoyoung Kim
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Brad Gallent
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yiwu Yan
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Radu M Cadaneanu
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Baohui Zhang
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Salma Kaochar
- Department of Medicine Section Hematology/Oncology Baylor College of Medicine, Houston, 77030 TX, USA
| | - Stephen J Freedland
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Edwin M Posadas
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Leigh Ellis
- Center for Prostate Disease Research, Mutha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences and the Walter Reed National Military Medical Center; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20814, USA
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dolores Di Vizio
- Departments of Urology, Pathology and Laboratory Medicine, and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lauren Brady
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ramachandran Murali
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Moray J Campbell
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Department of Pathology and Cancer Center, Stony Brook University, NY 11794, USA
| | - Beatrice S Knudsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84108, USA
- Department of Pathology, University of Utah, Salt Lake City, UT 84108, USA
| | - Elahe A Mostaghel
- Geriatric Research, Education and Clinical Center (GRECC), U.S. Department of Veterans Affairs Puget Sound Health Care System, Seattle, WA 98133, USA
| | - Huihui Ye
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Isla P Garraway
- Department of Surgical and Perioperative Care, VA Greater Los Angeles; Department of Urology and Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA 90095, USA
| | - Sungyong You
- Departments of Urology and Computational Biomedicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael R Freeman
- Departments of Urology and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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3
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Hu LZ, Douglass E, Turunen M, Pampou S, Grunn A, Realubit R, Antolin AA, Wang ALE, Li H, Subramaniam P, Mundi PS, Karan C, Alvarez M, Califano A. Elucidating Compound Mechanism of Action and Polypharmacology with a Large-scale Perturbational Profile Compendium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.08.561457. [PMID: 37873470 PMCID: PMC10592689 DOI: 10.1101/2023.10.08.561457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The Mechanism of Action (MoA) of a drug is generally represented as a small, non-tissue-specific repertoire of high-affinity binding targets. Yet, drug activity and polypharmacology are increasingly associated with a broad range of off-target and tissue-specific effector proteins. To address this challenge, we have leveraged a microfluidics-based Plate-Seq technology to survey drug perturbational profiles representing >700 FDA-approved and experimental oncology drugs, in cell lines selected as high-fidelity models of 23 aggressive tumor subtypes. Built on this dataset, we implemented an efficient computational framework to define a tissue-specific protein activity landscape of these drugs and reported almost 50 million differential protein activities derived from drug perturbations vs. vehicle controls. These analyses revealed thousands of highly reproducible and novel, drug-mediated modulation of tissue-specific targets, leading to generation of a proteome-wide drug functional network, characterization of MoA-related drug clusters and off-target effects, dramatical expansion of druggable human proteome, and identification and experimental validation of novel, tissue-specific inhibitors of undruggable oncoproteins, most never reported before. The drug perturbation profile resource described here represents the first, large-scale, whole-genome-wide, RNA-Seq based dataset assembled to date, with the proposed framework, which is easily extended to elucidating the MoA of novel small-molecule libraries, facilitates mechanistic exploration of drug functions, supports systematic and quantitative approaches to precision oncology, and serves as a rich data foundation for drug discovery.
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Anglada-Girotto M, Moakley DF, Zhang C, Miravet-Verde S, Califano A, Serrano L. Disentangling the splicing factor programs underlying complex molecular phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600051. [PMID: 38979366 PMCID: PMC11230296 DOI: 10.1101/2024.06.21.600051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The regulation of exon inclusion through alternative splicing tunes the cell's behavior by increasing the functional diversity of the transcriptome and the proteome. Splicing factors work in concert to generate gene isoform pools that contribute to cell phenotypes yet their activity is controlled by multiple regulatory and signaling layers. This hinders identification of functional, phenotype-specific splicing factors using traditional single-omic measurements, such as their mutational state or expression. To address this challenge, we propose repurposing the virtual inference of protein activity by enriched regulon analysis (VIPER) to measure splicing factor activity solely from their downstream exon transcriptomic inclusion signatures. This approach is effective in assessing the effect of co-occurring splicing factor perturbations, as well as their post-translational regulation. As proof of concept, we dissect recurrent splicing factor programs underlying tumorigenesis including aberrantly activated factors acting as oncogenes and inactivated ones acting as tumor suppressors, which are undetectable by more conventional methodologies. Activation and inactivation of these cancer splicing programs effectively stratifies overall survival, as well as cancer hallmarks such as proliferation and immune evasion. Altogether, repurposing network-based inference of protein activity for splicing factor networks distills common, functionally relevant splicing programs in otherwise heterogeneous molecular contexts.
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5
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Maurer HC, Garcia-Curiel A, Holmstrom SR, Castillo C, Palermo CF, Sastra SA, Andren A, Zhang L, Le Large TYS, Sagalovskiy I, Ross DR, Wong W, Shaw K, Genkinger J, Manji GA, Iuga AC, Schmid RM, Johnson K, Badgley MA, Lyssiotis CA, Shah Y, Califano A, Olive KP. Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.19.533333. [PMID: 36993718 PMCID: PMC10055246 DOI: 10.1101/2023.03.19.533333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
To identify drivers of malignancy in human pancreatic ductal adenocarcinoma (PDAC), we performed regulatory network analysis on a large collection of expression profiles from laser capture microdissected samples of PDAC and benign precursors. We discovered that BMAL2 plays a role in the initiation, progression, post resection survival, and KRAS activity in PDAC. Functional analysis of BMAL2 target genes led us to hypothesize that it plays a role in regulating the response to hypoxia, a critical but poorly understood feature of PDAC physiology. Knockout of BMAL2 in multiple human PDAC cell lines revealed effects on viability and invasion, particularly under hypoxic conditions. Loss of BMAL2 also affected glycolysis and other metabolic processes. We found that BMAL2 directly regulates hypoxia-responsive target genes. We also found that BMAL2 is necessary for the stabilization of HIF1A upon exposure to hypoxia, but destabilizes HIF2A under hypoxia. These data demonstrate that BMAL2 is a master transcriptional regulator of hypoxia responses in PDAC and may serve as a long-sought molecular switch that distinguishes HIF1A- and HIF2A-dependent modes of hypoxic metabolism.
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Affiliation(s)
- H Carlo Maurer
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Alvaro Garcia-Curiel
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Sam R Holmstrom
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Cristina Castillo
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Carmine F Palermo
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Steven A Sastra
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Anthony Andren
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Li Zhang
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Tessa Y S Le Large
- Department of Surgery, Amsterdam UMC, Location Vrije Universiteit, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Irina Sagalovskiy
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Daniel R Ross
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Winston Wong
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Kaitlin Shaw
- Division of GI/Endocrine Surgery, Department of Surgery, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Jeanine Genkinger
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
| | - Gulam A Manji
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Alina C Iuga
- Department of Pathology, Columbia University Irving Medical Center, New York, NY
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Michael A Badgley
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Yatrik Shah
- Department of Molecular & Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Darwin Therapeutics, New York, NY
- Chan Zuckerberg Biohub, New York, NY
| | - Kenneth P Olive
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Columbia University Digestive and Liver Disease Research Center, Columbia University Irving Medical Center, New York, NY
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6
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Desai P, Takahashi N, Kumar R, Nichols S, Malin J, Hunt A, Schultz C, Cao Y, Tillo D, Nousome D, Chauhan L, Sciuto L, Jordan K, Rajapakse V, Tandon M, Lissa D, Zhang Y, Kumar S, Pongor L, Singh A, Schroder B, Sharma AK, Chang T, Vilimas R, Pinkiert D, Graham C, Butcher D, Warner A, Sebastian R, Mahon M, Baker K, Cheng J, Berger A, Lake R, Abel M, Krishnamurthy M, Chrisafis G, Fitzgerald P, Nirula M, Goyal S, Atkinson D, Bateman NW, Abulez T, Nair G, Apolo A, Guha U, Karim B, El Meskini R, Ohler ZW, Jolly MK, Schaffer A, Ruppin E, Kleiner D, Miettinen M, Brown GT, Hewitt S, Conrads T, Thomas A. Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities. Cell Rep Med 2024; 5:101610. [PMID: 38897168 PMCID: PMC11228806 DOI: 10.1016/j.xcrm.2024.101610] [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: 03/02/2023] [Revised: 08/04/2023] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intratumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the cell-extrinsic drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the TME exhibit substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAFs) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting exceptionally poor prognosis. Our work provides a comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLC's adaptable nature, opening possibilities for reprogramming the TME-tumor communications that shape SCLC tumor states.
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Affiliation(s)
- Parth Desai
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Medical Oncology, Fox Chase Cancer Center, Temple University Hospital and Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Nobuyuki Takahashi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Medical Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Rajesh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samantha Nichols
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin Malin
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison Hunt
- Women's Health Integrated Research Center, Inova Health System, Falls Church, VA, USA
| | - Christopher Schultz
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yingying Cao
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Desiree Tillo
- CCR Collaborative Bioinformatics, Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Darryl Nousome
- CCR Collaborative Bioinformatics, Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lakshya Chauhan
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Linda Sciuto
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kimberly Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Vinodh Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mayank Tandon
- CCR Collaborative Bioinformatics, Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Delphine Lissa
- Laboratory of Human Carcinogenesis, Center for Cancer Research National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yang Zhang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Suresh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lorinc Pongor
- HCEMM Cancer Genomics and Epigenetics Research Group, Szeged, Hungary
| | - Abhay Singh
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Brett Schroder
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ajit Kumar Sharma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tiangen Chang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rasa Vilimas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Pinkiert
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chante Graham
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donna Butcher
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Andrew Warner
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mimi Mahon
- Pain and Palliative care services, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Karen Baker
- Pain and Palliative care services, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Jennifer Cheng
- Pain and Palliative care services, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Ann Berger
- Pain and Palliative care services, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Ross Lake
- Laboratory of Genitourinary cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melissa Abel
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Manan Krishnamurthy
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George Chrisafis
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter Fitzgerald
- CCR Collaborative Bioinformatics, Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Micheal Nirula
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shubhank Goyal
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Devon Atkinson
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Nicholas W Bateman
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Tamara Abulez
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Govind Nair
- National Institute of Neurological Disorders and Stroke, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrea Apolo
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Baktiar Karim
- Molecular Histopathology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Rajaa El Meskini
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Zoe Weaver Ohler
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Mohit Kumar Jolly
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Alejandro Schaffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Kleiner
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - G Tom Brown
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Conrads
- Women's Health Integrated Research Center, Inova Health System, Falls Church, VA, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Moakley DF, Campbell M, Anglada-Girotto M, Feng H, Califano A, Au E, Zhang C. Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.597128. [PMID: 38915499 PMCID: PMC11195221 DOI: 10.1101/2024.06.13.597128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cell type-specific alternative splicing (AS) enables differential gene isoform expression between diverse neuron types with distinct identities and functions. Current studies linking individual RNA-binding proteins (RBPs) to AS in a few neuron types underscore the need for holistic modeling. Here, we use network reverse engineering to derive a map of the neuron type-specific AS regulatory landscape from 133 mouse neocortical cell types defined by single-cell transcriptomes. This approach reliably inferred the regulons of 350 RBPs and their cell type-specific activities. Our analysis revealed driving factors delineating neuronal identities, among which we validated Elavl2 as a key RBP for MGE-specific splicing in GABAergic interneurons using an in vitro ESC differentiation system. We also identified a module of exons and candidate regulators specific for long- and short-projection neurons across multiple neuronal classes. This study provides a resource for elucidating splicing regulatory programs that drive neuronal molecular diversity, including those that do not align with gene expression-based classifications.
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Affiliation(s)
- Daniel F Moakley
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Melissa Campbell
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Department of Neurosciences, University of California, San Diego, USA
| | - Miquel Anglada-Girotto
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Present address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Huijuan Feng
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Edmund Au
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
- Columbia Translational Neuroscience Initiative Scholar, New York, NY 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
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8
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Ferreté-Bonastre AG, Martínez-Gallo M, Morante-Palacios O, Calvillo CL, Calafell-Segura J, Rodríguez-Ubreva J, Esteller M, Cortés-Hernández J, Ballestar E. Disease activity drives divergent epigenetic and transcriptomic reprogramming of monocyte subpopulations in systemic lupus erythematosus. Ann Rheum Dis 2024; 83:865-878. [PMID: 38413168 DOI: 10.1136/ard-2023-225433] [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: 12/17/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is characterised by systemic inflammation involving various immune cell types. Monocytes, pivotal in promoting and regulating inflammation in SLE, differentiate from classic monocytes into intermediate and non-classic monocytes, assuming diverse roles and changing their proportions in inflammation. In this study, we investigated the epigenetic and transcriptomic profiles of these and novel monocyte subsets in SLE in relation to activity and progression. METHODS We obtained the DNA methylomes and transcriptomes of classic, intermediate, non-classic monocytes in patients with SLE (at first and follow-up visits) and healthy donors. We integrated these data with single-cell transcriptomics of SLE and healthy donors and interrogated their relationships with activity and progression. RESULTS In addition to shared DNA methylation and transcriptomic alterations associated with a strong interferon signature, we identified monocyte subset-specific alterations, especially in DNA methylation, which reflect an impact of SLE on monocyte differentiation. SLE classic monocytes exhibited a proinflammatory profile and were primed for macrophage differentiation. SLE non-classic monocytes displayed a T cell differentiation-related phenotype, with Th17-regulating features. Changes in monocyte proportions, DNA methylation and expression occurred in relation to disease activity and involved the STAT pathway. Integration of bulk with single-cell RNA sequencing datasets revealed disease activity-dependent expansion of SLE-specific monocyte subsets, further supported the interferon signature for classic monocytes, and associated intermediate and non-classic populations with exacerbated complement activation. CONCLUSIONS Disease activity in SLE drives a subversion of the epigenome and transcriptome programme in monocyte differentiation, impacting the function of different subsets and allowing to generate predictive methods for activity and progression.
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Affiliation(s)
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | | | - Celia Lourdes Calvillo
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Josefina Cortés-Hernández
- Rheumatology Department, Hospital Vall d'Hebron and Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, China
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9
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Malagola E, Vasciaveo A, Ochiai Y, Kim W, Zheng B, Zanella L, Wang ALE, Middelhoff M, Nienhüser H, Deng L, Wu F, Waterbury QT, Belin B, LaBella J, Zamechek LB, Wong MH, Li L, Guha C, Cheng CW, Yan KS, Califano A, Wang TC. Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury. Cell 2024; 187:3056-3071.e17. [PMID: 38848678 PMCID: PMC11164536 DOI: 10.1016/j.cell.2024.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/15/2024] [Accepted: 05/01/2024] [Indexed: 06/09/2024]
Abstract
The currently accepted intestinal epithelial cell organization model proposes that Lgr5+ crypt-base columnar (CBC) cells represent the sole intestinal stem cell (ISC) compartment. However, previous studies have indicated that Lgr5+ cells are dispensable for intestinal regeneration, leading to two major hypotheses: one favoring the presence of a quiescent reserve ISC and the other calling for differentiated cell plasticity. To investigate these possibilities, we studied crypt epithelial cells in an unbiased fashion via high-resolution single-cell profiling. These studies, combined with in vivo lineage tracing, show that Lgr5 is not a specific ISC marker and that stemness potential exists beyond the crypt base and resides in the isthmus region, where undifferentiated cells participate in intestinal homeostasis and regeneration following irradiation (IR) injury. Our results provide an alternative model of intestinal epithelial cell organization, suggesting that stemness potential is not restricted to CBC cells, and neither de-differentiation nor reserve ISC are drivers of intestinal regeneration.
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Affiliation(s)
- Ermanno Malagola
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Yosuke Ochiai
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Woosook Kim
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Biyun Zheng
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Gastroenterology, Fujian Medical University Union Hospital, Fujian 350000, China
| | - Luca Zanella
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Alexander L E Wang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Moritz Middelhoff
- Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Henrik Nienhüser
- Department of General, Visceral and Transplant Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Lu Deng
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66107, USA
| | - Feijing Wu
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Quin T Waterbury
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Bryana Belin
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Jonathan LaBella
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Leah B Zamechek
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Melissa H Wong
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, L215, Portland, OR, USA
| | - Linheng Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66107, USA
| | - Chandan Guha
- Department of Radiation Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Chia-Wei Cheng
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Kelley S Yan
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA; Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Columbia University Digestive and Liver Disease Research Center, New York, NY 10032, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA; Chan Zuckerberg Biohub NY, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, Department of Medicine and Irving Cancer Research Center, Columbia University Medical Center, New York, NY 10032, USA; Columbia University Digestive and Liver Disease Research Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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10
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Yang Z, Peng Y, Wang Y, Yang P, Huang Z, Quan T, Xu X, Sun P, Sun Y, Lv J, Wei D, Zhou GQ. KLF5 regulates actin remodeling to enhance the metastasis of nasopharyngeal carcinoma. Oncogene 2024; 43:1779-1795. [PMID: 38649438 DOI: 10.1038/s41388-024-03033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
Transcription factors (TFs) engage in various cellular essential processes including differentiation, growth and migration. However, the master TF involved in distant metastasis of nasopharyngeal carcinoma (NPC) remains largely unclear. Here we show that KLF5 regulates actin remodeling to enhance NPC metastasis. We analyzed the msVIPER algorithm-generated transcriptional regulatory networks and identified KLF5 as a master TF of metastatic NPC linked to poor clinical outcomes. KLF5 regulates actin remodeling and lamellipodia formation to promote the metastasis of NPC cells in vitro and in vivo. Mechanistically, KLF5 preferentially occupies distal enhancer regions of ACTN4 to activate its transcription, whereby decoding the informative DNA sequences. ACTN4, extensively localized within actin cytoskeleton, facilitates dense and branched actin networks and lamellipodia formation at the cell leading edge, empowering cells to migrate faster. Collectively, our findings reveal that KLF5 controls robust transcription program of ACTN4 to modulate actin remodeling and augment cell motility which enhances NPC metastasis, and provide new potential biomarkers and therapeutic interventions for NPC.
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Affiliation(s)
- Zhenyu Yang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Yanfu Peng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Yaqin Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Panyang Yang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Zhuohui Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Tingqiu Quan
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Xudong Xu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Peng Sun
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Ying Sun
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Jiawei Lv
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China.
| | - Denghui Wei
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China.
| | - Guan-Qun Zhou
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China.
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11
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Tan J, Virtue S, Norris DM, Conway OJ, Yang M, Bidault G, Gribben C, Lugtu F, Kamzolas I, Krycer JR, Mills RJ, Liang L, Pereira C, Dale M, Shun-Shion AS, Baird HJ, Horscroft JA, Sowton AP, Ma M, Carobbio S, Petsalaki E, Murray AJ, Gershlick DC, Nathan JA, Hudson JE, Vallier L, Fisher-Wellman KH, Frezza C, Vidal-Puig A, Fazakerley DJ. Limited oxygen in standard cell culture alters metabolism and function of differentiated cells. EMBO J 2024; 43:2127-2165. [PMID: 38580776 PMCID: PMC11148168 DOI: 10.1038/s44318-024-00084-7] [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: 01/12/2024] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/07/2024] Open
Abstract
The in vitro oxygen microenvironment profoundly affects the capacity of cell cultures to model physiological and pathophysiological states. Cell culture is often considered to be hyperoxic, but pericellular oxygen levels, which are affected by oxygen diffusivity and consumption, are rarely reported. Here, we provide evidence that several cell types in culture actually experience local hypoxia, with important implications for cell metabolism and function. We focused initially on adipocytes, as adipose tissue hypoxia is frequently observed in obesity and precedes diminished adipocyte function. Under standard conditions, cultured adipocytes are highly glycolytic and exhibit a transcriptional profile indicative of physiological hypoxia. Increasing pericellular oxygen diverted glucose flux toward mitochondria, lowered HIF1α activity, and resulted in widespread transcriptional rewiring. Functionally, adipocytes increased adipokine secretion and sensitivity to insulin and lipolytic stimuli, recapitulating a healthier adipocyte model. The functional benefits of increasing pericellular oxygen were also observed in macrophages, hPSC-derived hepatocytes and cardiac organoids. Our findings demonstrate that oxygen is limiting in many terminally-differentiated cell types, and that considering pericellular oxygen improves the quality, reproducibility and translatability of culture models.
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Affiliation(s)
- Joycelyn Tan
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sam Virtue
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Olivia J Conway
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Guillaume Bidault
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Christopher Gribben
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Fatima Lugtu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Ioannis Kamzolas
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - James R Krycer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Lu Liang
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Martin Dale
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Harry Jm Baird
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - James A Horscroft
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Alice P Sowton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Marcella Ma
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stefania Carobbio
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Andrew J Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Kelsey H Fisher-Wellman
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC, 27834, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Antonio Vidal-Puig
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain.
| | - Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
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12
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Chen Q, Gao F, Wu J, Zhang K, Du T, Chen Y, Cai R, Zhao D, Deng R, Tang J. Comprehensive pan-cancer analysis of mitochondrial outer membrane permeabilisation activity reveals positive immunomodulation and assists in identifying potential therapeutic targets for immunotherapy resistance. Clin Transl Med 2024; 14:e1735. [PMID: 38899748 PMCID: PMC11187817 DOI: 10.1002/ctm2.1735] [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: 01/25/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Mitochondrial outer membrane permeabilisation (MOMP) plays a pivotal role in cellular death and immune activation. A deeper understanding of the impact of tumour MOMP on immunity will aid in guiding more effective immunotherapeutic strategies. METHODS A comprehensive pan-cancer dataset comprising 30 cancer-type transcriptomic cohorts, 20 immunotherapy transcriptomic cohorts and three immunotherapy scRNA-seq datasets was collected and analysed to determine the influence of tumour MOMP activity on clinical prognosis, immune infiltration and immunotherapy effectiveness. Leveraging 65 scRNA-Seq datasets, the MOMP signature (MOMP.Sig) was developed to accurately reflect tumour MOMP activity. The clinical predictive value of MOMP.Sig was explored through machine learning models. Integration of the MOMP.Sig model and a pan-cancer immunotherapy CRISPR screen further investigated potential targets to overcome immunotherapy resistance, which subsequently underwent clinical validation. RESULTS Our research revealed that elevated MOMP activity reduces mortality risk in cancer patients, drives the formation of an anti-tumour immune environment and enhances the response to immunotherapy. This finding emphasises the potential clinical application value of MOMP activity in immunotherapy. MOMP.Sig, offering a more precise indicator of tumour cell MOMP activity, demonstrated outstanding predictive efficacy in machine-learning models. Moreover, with the assistance of the MOMP.Sig model, FOXO1 was identified as a core modulator that promotes immune resistance. Finally, these findings were successfully validated in clinical immunotherapy cohorts of skin cutaneous melanoma and triple-negative breast cancer patients. CONCLUSIONS This study enhances our understanding of MOMP activity in immune modulation, providing valuable insights for more effective immunotherapeutic strategies across diverse tumours.
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Affiliation(s)
- Qingshan Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Fenglin Gao
- Department of Respiratory and Critical Care MedicineThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Junwan Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Biotherapy Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Kaiming Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Tian Du
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Yuhong Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Ruizhao Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Rong Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Jun Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Breast OncologySun Yat‐sen University Cancer CenterGuangzhouChina
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13
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Geng H, Huang C, Xu L, Zhou Y, Dong Z, Zhong Y, Li Q, Yang C, Huang S, Liao W, Lin Y, Liu Z, Li Q, Zhang Z, Zhu C. Targeting cellular senescence as a therapeutic vulnerability in gastric cancer. Life Sci 2024; 346:122631. [PMID: 38621585 DOI: 10.1016/j.lfs.2024.122631] [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: 12/29/2023] [Revised: 03/17/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
AIMS Cellular senescence (CS) represents an intracellular defense mechanism responding to stress signals and can be leveraged as a "vulnerability" in cancer treatment. This study aims to construct a CS atlas for gastric cancer (GC) and uncover potential therapeutics for GC patients. MATERIALS AND METHODS 38 senescence-associated regulators with prognostic significance in GC were obtained from the CellAge database to construct Gastric cancer-specific Senescence Score (GSS). Using eXtreme Sum algorism, GSS-based drug repositioning was conducted to identify drugs that could antagonize GSS in CMap database. In vitro experiments were conducted to test the effect of combination of palbociclib and exisulind in eliminating GC cells. KEY FINDINGS Patients with high GSS exhibited CS-related features, such as CS markers upregulation, adverse clinical outcomes and hypomethylation status. scRNA-seq data showed malignant cells with high GSS exhibited enhanced senescence state and more immunosuppressive signals such as PVR-CD96 compared with malignant cells with low GSS. In addition, the GSS-High cancer associated fibroblasts might secrete cytokines and chemokines such as IL-6, CXCL1, CXCL12, and CCL2 to from an immunosuppressive microenvironment, and GSS could serve as an indicator for immunotherapy resistance. Exisulind exhibited the greatest potential to reverse GSS. In vitro experiments demonstrated that exisulind could induce apoptosis and suppress the proliferation of palbociclib-induced senescent GC cells. SIGNIFICANCE Overall, GSS offers a framework for better understanding of correlation between senescence and GC, which might provide new insights into the development of novel therapeutics in GC.
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Affiliation(s)
- Haigang Geng
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Xu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| | - Yangyang Zhou
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Zhongyi Dong
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiqing Zhong
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Li
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chen Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, China; Immune Regulation in Cancer Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Shaozhuo Huang
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Weixin Liao
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Yuxuan Lin
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhicheng Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| | - Qing Li
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Zizhen Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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14
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Zou W, Fang Z, Feng Y, Gong S, Li Z, Li M, Sun Y, Ruan X, Fang X, Qu H, Li H. Transcriptomic and genomic characteristics of intrahepatic metastases of primary liver cancer. BMC Cancer 2024; 24:672. [PMID: 38824541 PMCID: PMC11144329 DOI: 10.1186/s12885-024-12428-x] [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: 10/16/2023] [Accepted: 05/24/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Patients with primary multifocal hepatocellular carcinoma (HCC) have a poor prognosis and often experience a high rate of treatment failure. Multifocal HCC is mainly caused by intrahepatic metastasis (IM), and though portal vein tumor thrombosis (PVTT) is considered a hallmark of IM, the molecular mechanism by which primary HCC cells invade the portal veins remains unclear. Therefore, it is necessary to recognize the early signs of metastasis of HCC to arrange better treatment for patients. RESULTS To determine the differential molecular features between primary HCC with and without phenotype of metastasis, we used the CIBERSORTx software to deconvolute cell types from bulk RNA-Seq based on a single-cell transcriptomic dataset. According to the relative abundance of tumorigenic and metastatic hepatoma cells, VEGFA+ macrophages, effector memory T cells, and natural killer cells, HCC samples were divided into five groups: Pro-T, Mix, Pro-Meta, NKC, and MemT, and the transcriptomic and genomic features of the first three groups were analyzed. We found that the Pro-T group appeared to retain native hepatic metabolic activity, whereas the Pro-Meta group underwent dedifferentiation. Genes highly expressed in the group Pro-Meta often signify a worse outcome. CONCLUSIONS The HCC cohort can be well-typed and prognosis predicted according to tumor microenvironment components. Primary hepatocellular carcinoma may have obtained corresponding molecular features before metastasis occurred.
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Affiliation(s)
- Weilong Zou
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhanjie Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Feng
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Shangjin Gong
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziqiang Li
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Meng Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Sun
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiuyan Ruan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Haiyang Li
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China.
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15
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Taylor MA, Kandyba E, Halliwill K, Delrosario R, Khoroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam SR, Mirzoeva OK, Akhurst RJ, Balmain A. Stem-cell states converge in multistage cutaneous squamous cell carcinoma development. Science 2024; 384:eadi7453. [PMID: 38815020 DOI: 10.1126/science.adi7453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 04/05/2024] [Indexed: 06/01/2024]
Abstract
Stem cells play a critical role in cancer development by contributing to cell heterogeneity, lineage plasticity, and drug resistance. We created gene expression networks from hundreds of mouse tissue samples (both normal and tumor) and integrated these with lineage tracing and single-cell RNA-seq, to identify convergence of cell states in premalignant tumor cells expressing markers of lineage plasticity and drug resistance. Two of these cell states representing multilineage plasticity or proliferation were inversely correlated, suggesting a mutually exclusive relationship. Treatment of carcinomas in vivo with chemotherapy repressed the proliferative state and activated multilineage plasticity whereas inhibition of differentiation repressed plasticity and potentiated responses to cell cycle inhibitors. Manipulation of this cell state transition point may provide a source of potential combinatorial targets for cancer therapy.
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Affiliation(s)
- Mark A Taylor
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Clinical Research Centre, Medical University of Bialystok, Bialystok 15-089, Poland
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kyle Halliwill
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- AbbVie, South San Francisco, CA 94080, USA
| | - Reyno Delrosario
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matvei Khoroshkin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Hani Goodarzi
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94518, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94518, USA
- Arc Institute, Palo Alto, CA 94304, USA
| | - David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94518, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA 94518, USA
| | - Yun Rose Li
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Cancer Genetics & Epigenetics, City of Hope National Medical Center, Duarte, CA 91010, USA
- Division of Quantitative Medicine & Systems Biology, Translational Genomics Research Institute, Phoenix, CA 85004, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Saumya R Bollam
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 94518, USA
| | - Olga K Mirzoeva
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rosemary J Akhurst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94518, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94518, USA
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16
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Matsui Y, Togayachi A, Sakamoto K, Angata K, Kadomatsu K, Nishihara S. Integrated Systems Analysis Deciphers Transcriptome and Glycoproteome Links in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.25.573290. [PMID: 38234803 PMCID: PMC10793412 DOI: 10.1101/2023.12.25.573290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Glycosylation is increasingly recognized as a potential therapeutic target in Alzheimer's disease. In recent years, evidence of Alzheimer's disease-specific glycoproteins has been established. However, the mechanisms underlying their dysregulation, including tissue- and cell-type specificity, are not fully understood. We aimed to explore the upstream regulators of aberrant glycosylation by integrating multiple data sources using a glycogenomics approach. We identified dysregulation of the glycosyltransferase PLOD3 in oligodendrocytes as an upstream regulator of cerebral vessels and found that it is involved in COL4A5 synthesis, which is strongly correlated with amyloid fiber formation. Furthermore, COL4A5 has been suggested to interact with astrocytes via extracellular matrix receptors as a ligand. This study suggests directions for new therapeutic strategies for Alzheimer's disease targeting glycosyltransferases.
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Affiliation(s)
- Yusuke Matsui
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Biomedical and Health Informatics Unit, Department of Integrated Health Science, Nagoya University Graduate School of Medicine, Daiko-minami, Higashi-ku, Nagoya, 461-8673, Japan
| | - Akira Togayachi
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Kazuma Sakamoto
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kiyohiko Angata
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Kenji Kadomatsu
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Shoko Nishihara
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
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17
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Chen C, Padi M. Flexible modeling of regulatory networks improves transcription factor activity estimation. NPJ Syst Biol Appl 2024; 10:58. [PMID: 38806476 PMCID: PMC11133322 DOI: 10.1038/s41540-024-00386-w] [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: 01/19/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024] Open
Abstract
Transcriptional regulation plays a crucial role in determining cell fate and disease, yet inferring the key regulators from gene expression data remains a significant challenge. Existing methods for estimating transcription factor (TF) activity often rely on static TF-gene interaction databases and cannot adapt to changes in regulatory mechanisms across different cell types and disease conditions. Here, we present a new algorithm - Transcriptional Inference using Gene Expression and Regulatory data (TIGER) - that overcomes these limitations by flexibly modeling activation and inhibition events, up-weighting essential edges, shrinking irrelevant edges towards zero through a sparse Bayesian prior, and simultaneously estimating both TF activity levels and changes in the underlying regulatory network. When applied to yeast and cancer TF knock-out datasets, TIGER outperforms comparable methods in terms of prediction accuracy. Moreover, our application of TIGER to tissue- and cell-type-specific RNA-seq data demonstrates its ability to uncover differences in regulatory mechanisms. Collectively, our findings highlight the utility of modeling context-specific regulation when inferring transcription factor activities.
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Affiliation(s)
- Chen Chen
- Department of Epidemiology and Biostatistics, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Megha Padi
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.
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18
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Thatikonda V, Supper V, Wachter J, Kaya O, Kombara A, Bilgilier C, Ravichandran MC, Lipp JJ, Sharma R, Badertscher L, Boghossian AS, Rees MG, Ronan MM, Roth JA, Grosche S, Neumüller RA, Mair B, Mauri F, Popa A. Genetic dependencies associated with transcription factor activities in human cancer cell lines. Cell Rep 2024; 43:114175. [PMID: 38691456 DOI: 10.1016/j.celrep.2024.114175] [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: 03/14/2023] [Revised: 02/02/2024] [Accepted: 04/16/2024] [Indexed: 05/03/2024] Open
Abstract
Transcription factors (TFs) are important mediators of aberrant transcriptional programs in cancer cells. In this study, we focus on TF activity (TFa) as a biomarker for cell-line-selective anti-proliferative effects, in that high TFa predicts sensitivity to loss of function of a given gene (i.e., genetic dependencies [GDs]). Our linear-regression-based framework identifies 3,047 pan-cancer and 3,952 cancer-type-specific candidate TFa-GD associations from cell line data, which are then cross-examined for impact on survival in patient cohorts. One of the most prominent biomarkers is TEAD1 activity, whose associations with its predicted GDs are validated through experimental evidence as proof of concept. Overall, these TFa-GD associations represent an attractive resource for identifying innovative, biomarker-driven hypotheses for drug discovery programs in oncology.
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Affiliation(s)
- Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria.
| | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Johannes Wachter
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Onur Kaya
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Anju Kombara
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Ceren Bilgilier
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | | | - Jesse J Lipp
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Rahul Sharma
- Myllia Biotechnology GmbH, Am Kanal 27, Vienna 1110, Austria
| | | | | | - Matthew G Rees
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Melissa M Ronan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Grosche
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Federico Mauri
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, Vienna 1120, Austria.
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19
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Fan C, Chen F, Chen Y, Huang L, Wang M, Liu Y, Wang Y, Guo H, Zheng N, Liu Y, Wang H, Ma L. irGSEA: the integration of single-cell rank-based gene set enrichment analysis. Brief Bioinform 2024; 25:bbae243. [PMID: 38801700 PMCID: PMC11129768 DOI: 10.1093/bib/bbae243] [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: 12/08/2023] [Revised: 03/06/2024] [Indexed: 05/29/2024] Open
Abstract
irGSEA is an R package designed to assess the outcomes of various gene set scoring methods when applied to single-cell RNA sequencing data. This package incorporates six distinct scoring methods that rely on the expression ranks of genes, emphasizing relative expression levels over absolute values. The implemented methods include AUCell, UCell, singscore, ssGSEA, JASMINE and Viper. Previous studies have demonstrated the robustness of these methods to variations in dataset size and composition, generating enrichment scores based solely on the relative gene expression of individual cells. By employing the robust rank aggregation algorithm, irGSEA amalgamates results from all six methods to ascertain the statistical significance of target gene sets across diverse scoring methods. The package prioritizes user-friendliness, allowing direct input of expression matrices or seamless interaction with Seurat objects. Furthermore, it facilitates a comprehensive visualization of results. The irGSEA package and its accompanying documentation are accessible on GitHub (https://github.com/chuiqin/irGSEA).
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Affiliation(s)
- Chuiqin Fan
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen 518038, China
| | - Fuyi Chen
- Department of Obstetrics and Gynecology; Department of Pediatrics; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affi1iated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Yuanguo Chen
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen 518038, China
| | - Liangping Huang
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen 518038, China
| | - Manna Wang
- Department of Obstetrics and Gynecology; Department of Pediatrics; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affi1iated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Yulin Liu
- Department of Pediatrics, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Yu Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen 518038, China
| | - Huijie Guo
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen 518038, China
| | - Nanpeng Zheng
- Department of Pediatrics, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Yanbing Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen 518038, China
| | - Hongwu Wang
- Department of Pediatrics, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Lian Ma
- Department of Obstetrics and Gynecology; Department of Pediatrics; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affi1iated Hospital of Guangzhou Medical University, Guangzhou 510150, China
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen 518038, China
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20
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Wei G, Zhang X, Liu S, Hou W, Dai Z. Comprehensive data mining reveals RTK/RAS signaling pathway as a promoter of prostate cancer lineage plasticity through transcription factors and CNV. Sci Rep 2024; 14:11688. [PMID: 38778150 PMCID: PMC11111877 DOI: 10.1038/s41598-024-62256-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: 01/04/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Prostate cancer lineage plasticity is a key driver in the transition to neuroendocrine prostate cancer (NEPC), and the RTK/RAS signaling pathway is a well-established cancer pathway. Nevertheless, the comprehensive link between the RTK/RAS signaling pathway and lineage plasticity has received limited investigation. In particular, the intricate regulatory network governing the interplay between RTK/RAS and lineage plasticity remains largely unexplored. The multi-omics data were clustered with the coefficient of argument and neighbor joining algorithm. Subsequently, the clustered results were analyzed utilizing the GSEA, gene sets related to stemness, multi-lineage state datasets, and canonical cancer pathway gene sets. Finally, a comprehensive exploration of the data based on the ssGSEA, WGCNA, GSEA, VIPER, prostate cancer scRNA-seq data, and the GPSAdb database was conducted. Among the six modules in the clustering results, there are 300 overlapping genes, including 3 previously unreported prostate cancer genes that were validated to be upregulated in prostate cancer through RT-qPCR. Function Module 6 shows a positive correlation with prostate cancer cell stemness, multi-lineage states, and the RTK/RAS signaling pathway. Additionally, the 19 leading-edge genes of the RTK/RAS signaling pathway promote prostate cancer lineage plasticity through a complex network of transcriptional regulation and copy number variations. In the transcriptional regulation network, TP63 and FOXO1 act as suppressors of prostate cancer lineage plasticity, whereas RORC exerts a promoting effect. This study provides a comprehensive perspective on the role of the RTK/RAS pathway in prostate cancer lineage plasticity and offers new clues for the treatment of NEPC.
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Affiliation(s)
- Guanyun Wei
- Co-Innovation Center of Neuroregeneration, School of Life Sciences, Nantong Laboratory of Development and Diseases, Nantong University, Nantong, China
| | - Xu Zhang
- Clinical Medical Research Center, Jiangnan University Medical Center, Wuxi No.2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Siyuan Liu
- School of Life Sciences, Nantong University, Nantong, China
| | - Wanxin Hou
- Research Center for Intelligent Information Technology, Nantong University, Nantong, China
| | - Zao Dai
- Research Center for Intelligent Information Technology, Nantong University, Nantong, China.
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21
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Mori Y, Okimoto Y, Sakai H, Kanda Y, Ohata H, Shiokawa D, Suzuki M, Yoshida H, Ueda H, Sekizuka T, Tamura R, Yamawaki K, Ishiguro T, Mateos RN, Shiraishi Y, Yatabe Y, Hamada A, Yoshihara K, Enomoto T, Okamoto K. Targeting PDGF signaling of cancer-associated fibroblasts blocks feedback activation of HIF-1α and tumor progression of clear cell ovarian cancer. Cell Rep Med 2024; 5:101532. [PMID: 38670097 PMCID: PMC11149410 DOI: 10.1016/j.xcrm.2024.101532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 01/04/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Ovarian clear cell carcinoma (OCCC) is a gynecological cancer with a dismal prognosis; however, the mechanism underlying OCCC chemoresistance is not well understood. To explore the intracellular networks associated with the chemoresistance, we analyze surgical specimens by performing integrative analyses that combine single-cell analyses and spatial transcriptomics. We find that a chemoresistant OCCC subpopulation with elevated HIF activity localizes mainly in areas populated by cancer-associated fibroblasts (CAFs) with a myofibroblastic phenotype, which is corroborated by quantitative immunostaining. CAF-enhanced chemoresistance and HIF-1α induction are recapitulated in co-culture assays, which show that cancer-derived platelet-derived growth factor (PDGF) contributes to the chemoresistance and HIF-1α induction via PDGF receptor signaling in CAFs. Ripretinib is identified as an effective receptor tyrosine kinase inhibitor against CAF survival. In the co-culture system and xenograft tumors, ripretinib prevents CAF survival and suppresses OCCC proliferation in the presence of carboplatin, indicating that combination of conventional chemotherapy and CAF-targeted agents is effective against OCCC.
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MESH Headings
- Female
- Humans
- Cancer-Associated Fibroblasts/metabolism
- Cancer-Associated Fibroblasts/pathology
- Cancer-Associated Fibroblasts/drug effects
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/drug therapy
- Ovarian Neoplasms/genetics
- Platelet-Derived Growth Factor/metabolism
- Signal Transduction/drug effects
- Animals
- Mice
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Disease Progression
- Coculture Techniques
- Cell Proliferation/drug effects
- Mice, Nude
- Adenocarcinoma, Clear Cell/metabolism
- Adenocarcinoma, Clear Cell/pathology
- Adenocarcinoma, Clear Cell/drug therapy
- Adenocarcinoma, Clear Cell/genetics
- Feedback, Physiological/drug effects
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Yutaro Mori
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan; Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Yoshie Okimoto
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan
| | - Hiroaki Sakai
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan
| | - Yusuke Kanda
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan
| | - Hirokazu Ohata
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan
| | - Daisuke Shiokawa
- Ehime University Hospital Translational Research Center, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Mikiko Suzuki
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Haruka Ueda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Tomoyuki Sekizuka
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Raul Nicolas Mateos
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8520, Japan
| | - Koji Okamoto
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo 173-0003, Japan.
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22
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Worley J, Noh H, You D, Turunen MM, Ding H, Paull E, Griffin AT, Grunn A, Zhang M, Guillan K, Bush EC, Brosius SJ, Hibshoosh H, Mundi PS, Sims P, Dalerba P, Dela Cruz FS, Kung AL, Califano A. Identification and Pharmacological Targeting of Treatment-Resistant, Stem-like Breast Cancer Cells for Combination Therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.562798. [PMID: 38798673 PMCID: PMC11118419 DOI: 10.1101/2023.11.08.562798] [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
Tumors frequently harbor isogenic yet epigenetically distinct subpopulations of multi-potent cells with high tumor-initiating potential-often called Cancer Stem-Like Cells (CSLCs). These can display preferential resistance to standard-of-care chemotherapy. Single-cell analyses can help elucidate Master Regulator (MR) proteins responsible for governing the transcriptional state of these cells, thus revealing complementary dependencies that may be leveraged via combination therapy. Interrogation of single-cell RNA sequencing profiles from seven metastatic breast cancer patients, using perturbational profiles of clinically relevant drugs, identified drugs predicted to invert the activity of MR proteins governing the transcriptional state of chemoresistant CSLCs, which were then validated by CROP-seq assays. The top drug, the anthelmintic albendazole, depleted this subpopulation in vivo without noticeable cytotoxicity. Moreover, sequential cycles of albendazole and paclitaxel-a commonly used chemotherapeutic -displayed significant synergy in a patient-derived xenograft (PDX) from a TNBC patient, suggesting that network-based approaches can help develop mechanism-based combinatorial therapies targeting complementary subpopulations.
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Affiliation(s)
- Jeremy Worley
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
| | - Heeju Noh
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mikko M Turunen
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Hongxu Ding
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pharmacy Practice & Science, College of Pharmacy, University of Arizona, Tucson, Arizona, USA 85721
| | - Evan Paull
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Aaron T Griffin
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Adina Grunn
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Mingxuan Zhang
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Kristina Guillan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erin C Bush
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Samantha J Brosius
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hanina Hibshoosh
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, USA 10032
| | - Prabhjot S Mundi
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
| | - Peter Sims
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Piero Dalerba
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, USA 10032
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, USA 10032
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
| | - Filemon S Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Califano
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biochemistry & Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA 10032
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY USA 10032
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23
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Hu YM, Zhao F, Graff JN, Chen C, Zhao X, Thomas GV, Wu H, Kardosh A, Mills GB, Alumkal JJ, Moran AE, Xia Z. Androgen receptor activity inversely correlates with immune cell infiltration and immunotherapy response across multiple cancer lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593181. [PMID: 38798471 PMCID: PMC11118439 DOI: 10.1101/2024.05.08.593181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
There is now increasing recognition of the important role of androgen receptor (AR) in modulating immune function. To gain a comprehensive understanding of the effects of AR activity on cancer immunity, we employed a computational approach to profile AR activity in 33 human tumor types using RNA-Seq datasets from The Cancer Genome Atlas. Our pan-cancer analysis revealed that the genes most negatively correlated with AR activity across cancers are involved in active immune system processes. Importantly, we observed a significant negative correlation between AR activity and IFNγ pathway activity at the pan-cancer level. Indeed, using a matched biopsy dataset from subjects with prostate cancer before and after AR-targeted treatment, we verified that inhibiting AR enriches immune cell abundances and is associated with higher IFNγ pathway activity. Furthermore, by analyzing immunotherapy datasets in multiple cancers, our results demonstrate that low AR activity was significantly associated with a favorable response to immunotherapy. Together, our data provide a comprehensive assessment of the relationship between AR signaling and tumor immunity.
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Affiliation(s)
- Ya-Mei Hu
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Faming Zhao
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Julie N. Graff
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - Canping Chen
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Xiyue Zhao
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - George V. Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Hui Wu
- Division of Biomaterial and Biomedical Sciences, Department of Oral Rehabilitation and Biosciences, Oregon Health & Science University, Portland, OR, USA
| | - Adel Kardosh
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Gordon B. Mills
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Joshi J. Alumkal
- Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Amy E. Moran
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Zheng Xia
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Center for Biomedical Data Science, Oregon Health & Science University, Portland, OR, USA
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24
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Nakagawa S, Carnevali D, Tan X, Alvarez MJ, Parfitt DE, Di Vicino U, Arumugam K, Shin W, Aranda S, Normanno D, Sebastian-Perez R, Cannatá C, Cortes P, Neguembor MV, Shen MM, Califano A, Cosma MP. The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development. Stem Cell Reports 2024; 19:689-709. [PMID: 38701778 PMCID: PMC11103935 DOI: 10.1016/j.stemcr.2024.04.004] [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: 06/23/2022] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Embryo size, specification, and homeostasis are regulated by a complex gene regulatory and signaling network. Here we used gene expression signatures of Wnt-activated mouse embryonic stem cell (mESC) clones to reverse engineer an mESC regulatory network. We identify NKX1-2 as a novel master regulator of preimplantation embryo development. We find that Nkx1-2 inhibition reduces nascent RNA synthesis, downregulates genes controlling ribosome biogenesis, RNA translation, and transport, and induces severe alteration of nucleolus structure, resulting in the exclusion of RNA polymerase I from nucleoli. In turn, NKX1-2 loss of function leads to chromosome missegregation in the 2- to 4-cell embryo stages, severe decrease in blastomere numbers, alterations of tight junctions (TJs), and impairment of microlumen coarsening. Overall, these changes impair the blastocoel expansion-collapse cycle and embryo cavitation, leading to altered lineage specification and developmental arrest.
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Affiliation(s)
- Shoma Nakagawa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Davide Carnevali
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Xiangtian Tan
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University, New York, NY, USA; DarwinHealth Inc, New York, NY, USA
| | - David-Emlyn Parfitt
- Departments of Medicine, Genetics and Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Umberto Di Vicino
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Karthik Arumugam
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - William Shin
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Sergi Aranda
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Davide Normanno
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Institute of Human Genetics, CNRS, Montpellier, France
| | - Ruben Sebastian-Perez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Chiara Cannatá
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Paola Cortes
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Maria Victoria Neguembor
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael M Shen
- Department of Systems Biology, Columbia University, New York, NY, USA; Departments of Medicine, Genetics and Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA; Chan Zuckerberg Biohub New York, New York, NY, USA.
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg.Lluis Companys 23, 08010 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu District, Guangzhou 510080, China.
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25
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Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nat Commun 2024; 15:3909. [PMID: 38724493 PMCID: PMC11082183 DOI: 10.1038/s41467-024-47957-3] [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: 03/18/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. Leveraging progress in proteomic technologies and network-based methodologies, we introduce Virtual Enrichment-based Signaling Protein-activity Analysis (VESPA)-an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations-and use it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogating tumor-specific enzyme/substrate interactions accurately infers kinase and phosphatase activity, based on their substrate phosphorylation state, effectively accounting for signal crosstalk and sparse phosphoproteome coverage. The analysis elucidates time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring, experimentally confirmed by CRISPR knock-out assays, suggesting broad applicability to cancer and other diseases.
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Affiliation(s)
- George Rosenberger
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Mikko Turunen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jing He
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Prem S Subramaniam
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sergey Pampou
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron T Griffin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Karan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Patrick Kerwin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Diana Murray
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Barry Honig
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
- Chan Zuckerberg Biohub New York, New York, NY, USA.
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26
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Zhang W, Wu C, Huang H, Bleu P, Zambare W, Alvarez J, Wang L, Paty PB, Romesser PB, Smith JJ, Chen XS. Enhancing Chemotherapy Response Prediction via Matched Colorectal Tumor-Organoid Gene Expression Analysis and Network-Based Biomarker Selection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.24.24301749. [PMID: 38343861 PMCID: PMC10854336 DOI: 10.1101/2024.01.24.24301749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Colorectal cancer (CRC) poses significant challenges in chemotherapy response prediction due to its molecular heterogeneity. This study introduces an innovative methodology that leverages gene expression data generated from matched colorectal tumor and organoid samples to enhance prediction accuracy. By applying Consensus Weighted Gene Co-expression Network Analysis (WGCNA) across multiple datasets, we identify critical gene modules and hub genes that correlate with patient responses, particularly to 5-fluorouracil (5-FU). This integrative approach advances precision medicine by refining chemotherapy regimen selection based on individual tumor profiles. Our predictive model demonstrates superior accuracy over traditional methods on independent datasets, illustrating significant potential in addressing the complexities of high-dimensional genomic data for cancer biomarker research.
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27
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Xiao T, Lee J, Gauntner TD, Velegraki M, Lathia JD, Li Z. Hallmarks of sex bias in immuno-oncology: mechanisms and therapeutic implications. Nat Rev Cancer 2024; 24:338-355. [PMID: 38589557 DOI: 10.1038/s41568-024-00680-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 04/10/2024]
Abstract
Sex differences are present across multiple non-reproductive organ cancers, with male individuals generally experiencing higher incidence of cancer with poorer outcomes. Although some mechanisms underlying these differences are emerging, the immunological basis is not well understood. Observations from clinical trials also suggest a sex bias in conventional immunotherapies with male individuals experiencing a more favourable response and female individuals experiencing more severe adverse events to immune checkpoint blockade. In this Perspective article, we summarize the major biological hallmarks underlying sex bias in immuno-oncology. We focus on signalling from sex hormones and chromosome-encoded gene products, along with sex hormone-independent and chromosome-independent epigenetic mechanisms in tumour and immune cells such as myeloid cells and T cells. Finally, we highlight opportunities for future studies on sex differences that integrate sex hormones and chromosomes and other emerging cancer hallmarks such as ageing and the microbiome to provide a more comprehensive view of how sex differences underlie the response in cancer that can be leveraged for more effective immuno-oncology approaches.
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Affiliation(s)
- Tong Xiao
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Juyeun Lee
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Timothy D Gauntner
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Maria Velegraki
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Justin D Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Cleveland, OH, USA.
- Rose Ella Burkhardt Brain Tumour Center, Cleveland Clinic, Cleveland, OH, USA.
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA.
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28
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Sykes M. Tolerance in intestinal transplantation. Hum Immunol 2024; 85:110793. [PMID: 38580539 PMCID: PMC11144570 DOI: 10.1016/j.humimm.2024.110793] [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: 01/31/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
Intestinal transplantation (ITx) is highly immunogenic, resulting in the need for high levels of immunosuppression, with frequent complications along with high rejection rates. Tolerance induction would provide a solution to these limitations. Detailed studies of alloreactive T cell clones as well as multiparameter flow cytometry in the graft and peripheral tissues have provided evidence for several tolerance mechanisms that occur spontaneously following ITx, which might provide targets for further interventions. These include the frequent occurrence of macrochimerism and engraftment in the recipient bone marrow of donor hematopoietic stem and progenitor cells carried in the allograft. These phenomena are seen most frequently in recipients of multivisceral transplants and are associated with reduced rejection rates. They reflect powerful graft-vs-host responses that enter the peripheral lymphoid system and bone marrow after expanding within and emigrating from the allograft. Several mechanisms of tolerance that may result from this lymphohematopoietic graft-vs-host response are discussed. Transcriptional profiling in quiescent allografts reveals tolerization of pre-existing host-vs-graft-reactive T cells that enter the allograft mucosa and become tissue-resident memory cells. Dissection of the pathways driving and maintaining this tolerant tissue-resident state among donor-reactive T cells will allow controlled tolerance induction through specific therapeutic approaches.
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Affiliation(s)
- Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Department of Microbiology and Immunology and Department of Surgery, Columbia University, New York, NY, USA.
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29
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Meimetis N, Lauffenburger DA, Nilsson A. Inference of drug off-target effects on cellular signaling using interactome-based deep learning. iScience 2024; 27:109509. [PMID: 38591003 PMCID: PMC11000001 DOI: 10.1016/j.isci.2024.109509] [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: 11/10/2023] [Revised: 02/04/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Many diseases emerge from dysregulated cellular signaling, and drugs are often designed to target specific signaling proteins. Off-target effects are, however, common and may ultimately result in failed clinical trials. Here we develop a computer model of the cell's transcriptional response to drugs for improved understanding of their mechanisms of action. The model is based on ensembles of artificial neural networks and simultaneously infers drug-target interactions and their downstream effects on intracellular signaling. With this, it predicts transcription factors' activities, while recovering known drug-target interactions and inferring many new ones, which we validate with an independent dataset. As a case study, we analyze the effects of the drug Lestaurtinib on downstream signaling. Alongside its intended target, FLT3, the model predicts an inhibition of CDK2 that enhances the downregulation of the cell cycle-critical transcription factor FOXM1. Our approach can therefore enhance our understanding of drug signaling for therapeutic design.
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Affiliation(s)
- Nikolaos Meimetis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Avlant Nilsson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Cell and Molecular Biology, SciLifeLab, Karolinska Institutet, Stockholm, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE 41296, Sweden
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30
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Stokes ME, Vasciaveo A, Small JC, Zask A, Reznik E, Smith N, Wang Q, Daniels J, Forouhar F, Rajbhandari P, Califano A, Stockwell BR. Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers. Cell Chem Biol 2024; 31:805-819.e9. [PMID: 38061356 PMCID: PMC11031350 DOI: 10.1016/j.chembiol.2023.11.007] [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: 11/02/2022] [Revised: 07/18/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Transcription factors have proven difficult to target with small molecules because they lack pockets necessary for potent binding. Disruption of protein expression can suppress targets and enable therapeutic intervention. To this end, we developed a drug discovery workflow that incorporates cell-line-selective screening and high-throughput expression profiling followed by regulatory network analysis to identify compounds that suppress regulatory drivers of disease. Applying this approach to neuroblastoma (NBL), we screened bioactive molecules in cell lines representing its MYC-dependent (MYCNA) and mesenchymal (MES) subtypes to identify selective compounds, followed by PLATESeq profiling of treated cells. This revealed compounds that disrupt a sub-network of MYCNA-specific regulatory proteins, resulting in MYCN degradation in vivo. The top hit was isopomiferin, a prenylated isoflavonoid that inhibited casein kinase 2 (CK2) in cells. Isopomiferin and its structural analogs inhibited MYC and MYCN in NBL and lung cancer cells, highlighting the general MYC-inhibiting potential of this unique scaffold.
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Affiliation(s)
- Michael E Stokes
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Alessandro Vasciaveo
- Department of Systems Biology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Jonnell Candice Small
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Eduard Reznik
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Nailah Smith
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Qian Wang
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Jacob Daniels
- Department of Pharmacology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Farhad Forouhar
- Proteomics and Macromolecular Crystallography Shared Resource (PMCSR), Columbia University Medical Center, New York City, NY 10032, USA
| | - Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Medical Center, New York City, NY 10032, USA.
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA; Department of Chemistry, Columbia University, New York City, NY 10027, USA; Department of Pathology and Cell Biology and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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31
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Katebi A, Chen X, Ramirez D, Li S, Lu M. Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML. NPJ Syst Biol Appl 2024; 10:38. [PMID: 38594351 PMCID: PMC11003984 DOI: 10.1038/s41540-024-00366-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of poorly differentiated myeloid cells, with a heterogenous mutational landscape. Mutations in IDH1 and IDH2 are found in 20% of the AML cases. Although much effort has been made to identify genes associated with leukemogenesis, the regulatory mechanism of AML state transition is still not fully understood. To alleviate this issue, here we develop a new computational approach that integrates genomic data from diverse sources, including gene expression and ATAC-seq datasets, curated gene regulatory interaction databases, and mathematical modeling to establish models of context-specific core gene regulatory networks (GRNs) for a mechanistic understanding of tumorigenesis of AML with IDH mutations. The approach adopts a new optimization procedure to identify the top network according to its accuracy in capturing gene expression states and its flexibility to allow sufficient control of state transitions. From GRN modeling, we identify key regulators associated with the function of IDH mutations, such as DNA methyltransferase DNMT1, and network destabilizers, such as E2F1. The constructed core regulatory network and outcomes of in-silico network perturbations are supported by survival data from AML patients. We expect that the combined bioinformatics and systems-biology modeling approach will be generally applicable to elucidate the gene regulation of disease progression.
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Affiliation(s)
- Ataur Katebi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Xiaowen Chen
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Daniel Ramirez
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Sheng Li
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA.
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
| | - Mingyang Lu
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA.
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32
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de Biase MS, Massip F, Wei TT, Giorgi FM, Stark R, Stone A, Gladwell A, O'Reilly M, Schütte D, de Santiago I, Meyer KB, Markowetz F, Ponder BAJ, Rintoul RC, Schwarz RF. Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk. Genome Med 2024; 16:54. [PMID: 38589970 PMCID: PMC11000304 DOI: 10.1186/s13073-024-01317-4] [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: 03/31/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to modifiable lifestyle risk in the form of tobacco smoke has long been established. More than 50% of all smoking-related lung cancers occur in former smokers, 40% of which occur more than 15 years after smoking cessation. Despite extensive research, the molecular processes for persistent lung cancer risk remain unclear. We thus set out to examine whether risk stratification in the clinic and in the general population can be improved upon by the addition of genetic data and to explore the mechanisms of the persisting risk in former smokers. METHODS We analysed transcriptomic data from accessible airway tissues of 487 subjects, including healthy volunteers and clinic patients of different smoking statuses. We developed a computational model to assess smoking-associated gene expression changes and their reversibility after smoking is stopped, comparing healthy subjects to clinic patients with and without lung cancer. RESULTS We find persistent smoking-associated immune alterations to be a hallmark of the clinic patients. Integrating previous GWAS data using a transcriptional network approach, we demonstrate that the same immune- and interferon-related pathways are strongly enriched for genes linked to known genetic risk factors, demonstrating a causal relationship between immune alteration and lung cancer risk. Finally, we used accessible airway transcriptomic data to derive a non-invasive lung cancer risk classifier. CONCLUSIONS Our results provide initial evidence for germline-mediated personalized smoke injury response and risk in the general population, with potential implications for managing long-term lung cancer incidence and mortality.
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Affiliation(s)
- Maria Stella de Biase
- Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Strasse 28, 10115, Berlin, Germany.
| | - Florian Massip
- Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Strasse 28, 10115, Berlin, Germany.
- MINES Paris, PSL University, CBIO-Centre for Computational Biology, 60 bd Saint Michel, 75006, Paris, France.
- Institut Curie, Cedex, Paris, France.
- INSERM, U900, Cedex, Paris, France.
| | - Tzu-Ting Wei
- Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Strasse 28, 10115, Berlin, Germany
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Federico M Giorgi
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0AY, UK
- Present Address: Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Rory Stark
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0AY, UK
| | - Amanda Stone
- Papworth Trials Unit Collaboration, Department of Oncology, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0AY, UK
| | - Amy Gladwell
- Papworth Trials Unit Collaboration, Department of Oncology, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0AY, UK
| | - Martin O'Reilly
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0AY, UK
- Present Address: MRC Toxicology Unit, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Daniel Schütte
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Am Weyertal 115C, Gebäude 74, 50931, Cologne, Germany
| | - Ines de Santiago
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0AY, UK
- Present Address: e-therapeutics plc, 17 Blenheim Office Park, Long Hanborough, OX29 8LN, UK
| | - Kerstin B Meyer
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0AY, UK
- Present Address: The Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0AY, UK
| | - Bruce A J Ponder
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0AY, UK.
| | - Robert C Rintoul
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0AY, UK.
- Papworth Trials Unit Collaboration, Department of Oncology, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0AY, UK.
- Department of Oncology, Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK.
| | - Roland F Schwarz
- Berlin Institute of Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Strasse 28, 10115, Berlin, Germany.
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Am Weyertal 115C, Gebäude 74, 50931, Cologne, Germany.
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Jamison JK, May MS, Raufi AG, Luk L, Wong W, Mundi PS, Manji GA. A Somatic BRCA2-Mutated Pancreatic Adenocarcinoma With Sustained Exceptional Response to Modified FOLFIRINOX. Oncologist 2024; 29:350-355. [PMID: 38394390 PMCID: PMC10994267 DOI: 10.1093/oncolo/oyad315] [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: 08/10/2023] [Accepted: 11/04/2023] [Indexed: 02/25/2024] Open
Abstract
Homologous recombination repair (HRR) pathway deficiency opens multiple therapeutic avenues within pancreatic cancer. Patients with HRR deficiency-associated gene mutations such as BRCA1, BRCA2, and PALB2 are more susceptible to platinum-based chemotherapies and in those with somatic BRCA mutations, PARP inhibitor therapy prolongs progression-free survival. The case discussed herein illustrates the therapeutic opportunities offered through the identification of HRR deficiency in pancreatic cancer, as well as the challenges associated with treatment and prevention of central nervous system metastases in long-term survivors of pancreatic cancer.
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Affiliation(s)
| | - Michael S May
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Alexander G Raufi
- Division of Hematology/Oncology, Department of Medicine, Lifespan Health System and Brown University, Providence, RI, USA
| | - Lyndon Luk
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Winston Wong
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prabhjot S Mundi
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gulam A Manji
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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34
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Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P, Bergamini G, Bantscheff M, Fälth-Savitski M, Saez-Rodriguez J. Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition. Mol Syst Biol 2024; 20:458-474. [PMID: 38454145 PMCID: PMC10987601 DOI: 10.1038/s44320-024-00025-w] [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: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
Complex disease phenotypes often span multiple molecular processes. Functional characterization of these processes can shed light on disease mechanisms and drug effects. Thermal Proteome Profiling (TPP) is a mass-spectrometry (MS) based technique assessing changes in thermal protein stability that can serve as proxies of functional protein changes. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a multi-omics integration framework, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover consequences of Poly (ADP-ribose) polymerase (PARP) inhibition in ovarian cancer cells on cell cycle and DNA damage response as well as interferon and hippo signaling. We found that TPP offers a complementary perspective to other omics data modalities, and that its integration allowed us to obtain a more complete molecular overview of PARP inhibition. We anticipate that this strategy can be used to integrate functional proteomics with other omics to study molecular processes.
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Affiliation(s)
- Mira L Burtscher
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Martin Garrido-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | | | | | - Katharina Zirngibl
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
| | | | | | | | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany.
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35
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Balboni N, Babini G, Poeta E, Protti M, Mercolini L, Magnifico MC, Barile SN, Massenzio F, Pignataro A, Giorgi FM, Lasorsa FM, Monti B. Transcriptional and metabolic effects of aspartate-glutamate carrier isoform 1 (AGC1) downregulation in mouse oligodendrocyte precursor cells (OPCs). Cell Mol Biol Lett 2024; 29:44. [PMID: 38553684 PMCID: PMC10979587 DOI: 10.1186/s11658-024-00563-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Aspartate-glutamate carrier isoform 1 (AGC1) is a carrier responsible for the export of mitochondrial aspartate in exchange for cytosolic glutamate and is part of the malate-aspartate shuttle, essential for the balance of reducing equivalents in the cells. In the brain, mutations in SLC25A12 gene, encoding for AGC1, cause an ultra-rare genetic disease, reported as a neurodevelopmental encephalopathy, whose symptoms include global hypomyelination, arrested psychomotor development, hypotonia and seizures. Among the biological components most affected by AGC1 deficiency are oligodendrocytes, glial cells responsible for myelination processes, and their precursors [oligodendrocyte progenitor cells (OPCs)]. The AGC1 silencing in an in vitro model of OPCs was documented to cause defects of proliferation and differentiation, mediated by alterations of histone acetylation/deacetylation. Disrupting AGC1 activity could possibly reduce the availability of acetyl groups, leading to perturbation of many biological pathways, such as histone modifications and fatty acids formation for myelin production. Here, we explore the transcriptome of mouse OPCs partially silenced for AGC1, reporting results of canonical analyses (differential expression) and pathway enrichment analyses, which highlight a disruption in fatty acids synthesis from both a regulatory and enzymatic stand. We further investigate the cellular effects of AGC1 deficiency through the identification of most affected transcriptional networks and altered alternative splicing. Transcriptional data were integrated with differential metabolite abundance analysis, showing downregulation of several amino acids, including glutamine and aspartate. Taken together, our results provide a molecular foundation for the effects of AGC1 deficiency in OPCs, highlighting the molecular mechanisms affected and providing a list of actionable targets to mitigate the effects of this pathology.
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Affiliation(s)
- Nicola Balboni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Babini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Eleonora Poeta
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Michele Protti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Laura Mercolini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Maria Chiara Magnifico
- Department of Biosciences, Biotechnologies and Environment, University of Bari, Bari, Italy
| | - Simona Nicole Barile
- Department of Biosciences, Biotechnologies and Environment, University of Bari, Bari, Italy
| | - Francesca Massenzio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Antonella Pignataro
- Department of Biosciences, Biotechnologies and Environment, University of Bari, Bari, Italy
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | | | - Barbara Monti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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36
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Krull JE, Wenzl K, Hopper MA, Manske MK, Sarangi V, Maurer MJ, Larson MC, Mondello P, Yang Z, Novak JP, Serres M, Whitaker KR, Villasboas Bisneto JC, Habermann TM, Witzig TE, Link BK, Rimsza LM, King RL, Ansell SM, Cerhan JR, Novak AJ. Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments. Cell Rep Med 2024; 5:101443. [PMID: 38428430 PMCID: PMC10983045 DOI: 10.1016/j.xcrm.2024.101443] [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: 09/16/2022] [Revised: 08/14/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Follicular lymphoma (FL) is an indolent non-Hodgkin lymphoma of germinal center origin, which presents with significant biologic and clinical heterogeneity. Using RNA-seq on B cells sorted from 87 FL biopsies, combined with machine-learning approaches, we identify 3 transcriptional states that divide the biological ontology of FL B cells into inflamed, proliferative, and chromatin-modifying states, with relationship to prior GC B cell phenotypes. When integrated with whole-exome sequencing and immune profiling, we find that each state was associated with a combination of mutations in chromatin modifiers, copy-number alterations to TNFAIP3, and T follicular helper cells (Tfh) cell interactions, or primarily by a microenvironment rich in activated T cells. Altogether, these data define FL B cell transcriptional states across a large cohort of patients, contribute to our understanding of FL heterogeneity at the tumor cell level, and provide a foundation for guiding therapeutic intervention.
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Affiliation(s)
| | - Kerstin Wenzl
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Matthew J Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Melissa C Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - ZhiZhang Yang
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Brian K Link
- Division of Hematology, Oncology, and Blood & Marrow Transplantation, University of Iowa, Iowa City, IA, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Rebecca L King
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anne J Novak
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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37
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Fernández EC, Tomassoni L, Zhang X, Wang J, Obradovic A, Laise P, Griffin AT, Vlahos L, Minns HE, Morales DV, Simmons C, Gallitto M, Wei HJ, Martins TJ, Becker PS, Crawford JR, Tzaridis T, Wechsler-Reya RJ, Garvin J, Gartrell RD, Szalontay L, Zacharoulis S, Wu CC, Zhang Z, Califano A, Pavisic J. Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585370. [PMID: 38559080 PMCID: PMC10979998 DOI: 10.1101/2024.03.17.585370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Diffuse Midline Gliomas (DMGs) are universally fatal, primarily pediatric malignancies affecting the midline structures of the central nervous system. Despite decades of clinical trials, treatment remains limited to palliative radiation therapy. A major challenge is the coexistence of molecularly distinct malignant cell states with potentially orthogonal drug sensitivities. To address this challenge, we leveraged established network-based methodologies to elucidate Master Regulator (MR) proteins representing mechanistic, non-oncogene dependencies of seven coexisting subpopulations identified by single-cell analysis-whose enrichment in essential genes was validated by pooled CRISPR/Cas9 screens. Perturbational profiles of 372 clinically relevant drugs helped identify those able to invert the activity of subpopulation-specific MRs for follow-up in vivo validation. While individual drugs predicted to target individual subpopulations-including avapritinib, larotrectinib, and ruxolitinib-produced only modest tumor growth reduction in orthotopic models, systemic co-administration induced significant survival extension, making this approach a valuable contribution to the rational design of combination therapy.
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38
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Yashar WM, Estabrook J, Holly HD, Somers J, Nikolova O, Babur Ö, Braun TP, Demir E. Predicting transcription factor activity using prior biological information. iScience 2024; 27:109124. [PMID: 38455978 PMCID: PMC10918219 DOI: 10.1016/j.isci.2024.109124] [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: 07/27/2023] [Revised: 10/20/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.
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Affiliation(s)
- William M. Yashar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hannah D. Holly
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia Somers
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Olga Nikolova
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts, Boston, MA 02125, USA
| | - Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Pacific Northwest National Laboratories, Richland, WA 99354, USA
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39
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Fan X, Huang K, Wu Y, Jin S, Pang L, Wang Y, Jin B, Sun X. A specific inflammatory suppression fibroblast subpopulation characterized by MHCII expression in human dilated cardiomyopathy. Mol Cell Biochem 2024:10.1007/s11010-024-04939-9. [PMID: 38462549 DOI: 10.1007/s11010-024-04939-9] [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: 09/25/2023] [Accepted: 01/12/2024] [Indexed: 03/12/2024]
Abstract
Dilated cardiomyopathy (DCM) is a significant cause of heart failure that requires heart transplantation. Fibroblasts play a central role in the fibro-inflammatory microenvironment of DCM. However, their cellular heterogeneity and interaction with immune cells have not been well identified. An integrative analysis was conducted on single-cell RNA sequencing (ScRNA-Seq) data from human left ventricle tissues, which comprised 4 hearts from healthy donors and 6 hearts with DCM. The specific antigen-presenting fibroblast (apFB) was explored as a subtype of fibroblasts characterized by expressing MHCII genes, the existence of which was confirmed by immunofluorescence staining of 3 cardiac tissues from DCM patients with severe heart failure. apFB highly expressed the genes that response to IFN-γ, and it also have a high activity of the JAK-STAT pathway and the transcription factor RFX5. In addition, the analysis of intercellular communication between apFBs and CD4+T cells revealed that the anti-inflammatory ligand-receptor pairs TGFB-TGFR, CLEC2B-KLRB1, and CD46-JAG1 were upregulated in DCM. The apFB signature exhibited a positive correlation with immunosuppression and demonstrated diagnostic and prognostic value when evaluated using a bulk RNA dataset comprising 166 donors and 166 DCM samples. In conclusion, the present study identified a novel subpopulation of fibroblasts that specifically expresses MHCII-encoding genes. This specific apFBs can suppress the inflammation occurring in DCM. Our findings further elucidate the composition of the fibro-inflammatory microenvironment in DCM, and provide a novel therapeutic target.
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Affiliation(s)
- Xi Fan
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China
| | - Kai Huang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China
| | - Yuming Wu
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Sheng Jin
- Department of Physiology, Hebei Medical University, Shijiazhuang, China
| | - Liewen Pang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China
| | - Yiqing Wang
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China.
| | - Bo Jin
- Department of Cardiology, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China.
| | - Xiaotian Sun
- Department of Cardiothoracic Surgery, Huashan Hospital of Fudan University, 12 Wulumuqi Rd, Shanghai, 200040, China.
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40
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Yabaji SM, Zhernovkov V, Araveti PB, Lata S, Rukhlenko OS, Abdullatif SA, Alekseev Y, Ma Q, Dayama G, Lau NC, Bishai WR, Crossland NA, Campbell JD, Kholodenko BN, Gimelbrant AA, Kobzik L, Kramnik I. Myc Dysregulation in Activated Macrophages Initiates Iron-Mediated Lipid Peroxidation that Fuels Type I Interferon and Compromises TB Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583602. [PMID: 38496444 PMCID: PMC10942339 DOI: 10.1101/2024.03.05.583602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
A quarter of human population is infected with Mycobacterium tuberculosis, but less than 10% of those infected develop clinical, mostly pulmonary, TB. To dissect mechanisms of susceptibility in immunocompetent individuals, we developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining feature of human TB: development of necrotic lung lesions after infection with virulent Mtb. In this study, we explored the connectivity of the sst1-regulated pathways during prolonged macrophage activation with TNF. We determined that the aberrant response of the sst1-susceptible macrophages to TNF was primarily driven by conflicting Myc and antioxidant response pathways that resulted in a coordinated failure to properly sequester intracellular iron and activate ferroptosis inhibitor enzymes. Consequently, iron-mediated lipid peroxidation fueled IFNβ superinduction and sustained the Type I Interferon (IFN-I) pathway hyperactivity that locked the sst1-susceptible macrophages in a state of unresolving stress and compromised their resistance to Mtb. The accumulation of the aberrantly activated, stressed, macrophages within granuloma microenvironment led to the local failure of anti-tuberculosis immunity and tissue necrosis. Our findings suggest a novel link between metabolic dysregulation in macrophages and susceptibility to TB, offering insights into potential therapeutic targets aimed at modulating macrophage function and improving TB control.
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Affiliation(s)
- Shivraj M. Yabaji
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
| | - Vadim Zhernovkov
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
| | | | - Suruchi Lata
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
| | - Oleksii S. Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Salam Al Abdullatif
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Yuriy Alekseev
- The Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118
| | - Qicheng Ma
- Department of Biochemistry, and Cell Biology and Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine
| | - Gargi Dayama
- Department of Biochemistry, and Cell Biology and Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine
| | - Nelson C. Lau
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
- Department of Biochemistry, and Cell Biology and Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine
| | - William R. Bishai
- Center for TB Research, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Nicholas A. Crossland
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
- The Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118
| | - Joshua D. Campbell
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven CT, USA
| | | | | | - Igor Kramnik
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
- Pulmonary Center, The Department of Medicine, Boston University Chobanian & Avedisian School of Medicine
- Dept. of Microbiology, Boston University Chobanian & Avedisian School of Medicine
- Lead contact
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41
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Gerbaldo F, Sonder E, Fischer V, Frei S, Wang J, Gapp K, Robinson MD, Germain PL. On the identification of differentially-active transcription factors from ATAC-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583825. [PMID: 38496482 PMCID: PMC10942475 DOI: 10.1101/2024.03.06.583825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (chromVAR-limma with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs - in our case NFkB - at the protein level.
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Affiliation(s)
- Felix Gerbaldo
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Emanuel Sonder
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Vincent Fischer
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Selina Frei
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Jiayi Wang
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Katharina Gapp
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Pierre-Luc Germain
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
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42
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Malla SB, Byrne RM, Lafarge MW, Corry SM, Fisher NC, Tsantoulis PK, Mills ML, Ridgway RA, Lannagan TRM, Najumudeen AK, Gilroy KL, Amirkhah R, Maguire SL, Mulholland EJ, Belnoue-Davis HL, Grassi E, Viviani M, Rogan E, Redmond KL, Sakhnevych S, McCooey AJ, Bull C, Hoey E, Sinevici N, Hall H, Ahmaderaghi B, Domingo E, Blake A, Richman SD, Isella C, Miller C, Bertotti A, Trusolino L, Loughrey MB, Kerr EM, Tejpar S, Maughan TS, Lawler M, Campbell AD, Leedham SJ, Koelzer VH, Sansom OJ, Dunne PD. Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer. Nat Genet 2024; 56:458-472. [PMID: 38351382 PMCID: PMC10937375 DOI: 10.1038/s41588-024-01654-5] [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: 12/04/2022] [Accepted: 01/03/2024] [Indexed: 02/29/2024]
Abstract
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC: PDS1 tumors, which are canonical/LGR5+ stem-rich, highly proliferative and display good prognosis; PDS2 tumors, which are regenerative/ANXA1+ stem-rich, with elevated stromal and immune tumor microenvironmental lineages; and PDS3 tumors, which represent a previously overlooked slow-cycling subset of tumors within CMS2 with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease. These PDS3 phenotypic traits are evident across numerous bulk and single-cell datasets, and demark a series of subtle biological states that are currently under-represented in pre-clinical models and are not identified using existing subtyping classifiers.
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Affiliation(s)
- Sudhir B Malla
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Ryan M Byrne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Maxime W Lafarge
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Shania M Corry
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | | | | | | | | | - Raheleh Amirkhah
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sarah L Maguire
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Elena Grassi
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Marco Viviani
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Emily Rogan
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Keara L Redmond
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Svetlana Sakhnevych
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Aoife J McCooey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Courtney Bull
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emily Hoey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Nicoleta Sinevici
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Holly Hall
- Cancer Research UK Scotland Institute, Glasgow, UK
| | - Baharak Ahmaderaghi
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK
| | - Enric Domingo
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Andrew Blake
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Susan D Richman
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Claudio Isella
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Crispin Miller
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Andrea Bertotti
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Maurice B Loughrey
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Department of Cellular Pathology, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Emma M Kerr
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Sabine Tejpar
- Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Timothy S Maughan
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Mark Lawler
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | | | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Owen J Sansom
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip D Dunne
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
- Cancer Research UK Scotland Institute, Glasgow, UK.
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43
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Franceschini GM, Quaini O, Mizuno K, Orlando F, Ciani Y, Ku SY, Sigouros M, Rothmann E, Alonso A, Benelli M, Nardella C, Auh J, Freeman D, Hanratty B, Adil M, Elemento O, Tagawa ST, Feng FY, Caffo O, Buttigliero C, Basso U, Nelson PS, Corey E, Haffner MC, Attard G, Aparicio A, Demichelis F, Beltran H. Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation. Cancer Discov 2024; 14:424-445. [PMID: 38197680 PMCID: PMC10905672 DOI: 10.1158/2159-8290.cd-23-0754] [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: 07/11/2023] [Revised: 10/31/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
Abstract
Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with phenotypic subtypes that drive therapy response and outcome differences. Histologic transformation to castration-resistant neuroendocrine prostate cancer (CRPC-NE) is associated with distinct epigenetic alterations, including changes in DNA methylation. The current diagnosis of CRPC-NE is challenging and relies on metastatic biopsy. We developed a targeted DNA methylation assay to detect CRPC-NE using plasma cell-free DNA (cfDNA). The assay quantifies tumor content and provides a phenotype evidence score that captures diverse CRPC phenotypes, leveraging regions to inform transcriptional state. We tested the design in independent clinical cohorts (n = 222 plasma samples) and qualified it achieving an AUC > 0.93 for detecting pathology-confirmed CRPC-NE (n = 136). Methylation-defined cfDNA tumor content was associated with clinical outcomes in two prospective phase II clinical trials geared towards aggressive variant CRPC and CRPC-NE. These data support the application of targeted DNA methylation for CRPC-NE detection and patient stratification. SIGNIFICANCE Neuroendocrine prostate cancer is an aggressive subtype of treatment-resistant prostate cancer. Early detection is important, but the diagnosis currently relies on metastatic biopsy. We describe the development and validation of a plasma cell-free DNA targeted methylation panel that can quantify tumor fraction and identify patients with neuroendocrine prostate cancer noninvasively. This article is featured in Selected Articles from This Issue, p. 384.
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Affiliation(s)
- Gian Marco Franceschini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Orsetta Quaini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Kei Mizuno
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Francesco Orlando
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sheng-Yu Ku
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael Sigouros
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Emily Rothmann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alicia Alonso
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | | | - Caterina Nardella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Joonghoon Auh
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brian Hanratty
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mohamed Adil
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Olivier Elemento
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Scott T. Tagawa
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Felix Y. Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Orazio Caffo
- Department of Medical Oncology, Santa Chiara Hospital, Trento, Italy
| | - Consuelo Buttigliero
- Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Turin, Italy
| | - Umberto Basso
- Department of Oncology, Istituto Oncologico Veneto IOV - IRCCS, Padua, Italy
| | | | - Eva Corey
- University of Washington, Seattle, Washington
| | - Michael C. Haffner
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- University of Washington, Seattle, Washington
| | - Gerhardt Attard
- Cancer Institute and University College London Hospitals, University College London, London, United Kingdom
| | - Ana Aparicio
- Department of GU Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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44
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Pettinella F, Mariotti B, Lattanzi C, Bruderek K, Donini M, Costa S, Marini O, Iannoto G, Gasperini S, Caveggion E, Castellucci M, Calzetti F, Bianchetto-Aguilera F, Gardiman E, Giani M, Dusi S, Cantini M, Vassanelli A, Pavone D, Milella M, Pilotto S, Biondani P, Höing B, Schleupner MC, Hussain T, Hadaschik B, Kaspar C, Visco C, Tecchio C, Koenderman L, Bazzoni F, Tamassia N, Brandau S, Cassatella MA, Scapini P. Surface CD52, CD84, and PTGER2 mark mature PMN-MDSCs from cancer patients and G-CSF-treated donors. Cell Rep Med 2024; 5:101380. [PMID: 38242120 PMCID: PMC10897522 DOI: 10.1016/j.xcrm.2023.101380] [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: 03/07/2023] [Revised: 08/11/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024]
Abstract
Precise molecular characterization of circulating polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) is hampered by their mixed composition of mature and immature cells and lack of specific markers. Here, we focus on mature CD66b+CD10+CD16+CD11b+ PMN-MDSCs (mPMN-MDSCs) from either cancer patients or healthy donors receiving G-CSF for stem cell mobilization (GDs). By RNA sequencing (RNA-seq) experiments, we report the identification of a distinct gene signature shared by the different mPMN-MDSC populations under investigation, also validated in mPMN-MDSCs from GDs and tumor-associated neutrophils (TANs) by single-cell RNA-seq (scRNA-seq) experiments. Analysis of such a gene signature uncovers a specific transcriptional program associated with mPMN-MDSC differentiation and allows us to identify that, in patients with either solid or hematologic tumors and in GDs, CD52, CD84, and prostaglandin E receptor 2 (PTGER2) represent potential mPMN-MDSC-associated markers. Altogether, our findings indicate that mature PMN-MDSCs distinctively undergo specific reprogramming during differentiation and lay the groundwork for selective immunomonitoring, and eventually targeting, of mature PMN-MDSCs.
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Affiliation(s)
- Francesca Pettinella
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Barbara Mariotti
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Chiara Lattanzi
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Kirsten Bruderek
- Research Division, Department of Otorhinolaryngology, University Hospital Essen, 45122 Essen, Germany
| | - Marta Donini
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Sara Costa
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Olivia Marini
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Giulia Iannoto
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Sara Gasperini
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Elena Caveggion
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | | | - Federica Calzetti
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | | | - Elisa Gardiman
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Matteo Giani
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Stefano Dusi
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Maurizio Cantini
- Transfusion Medicine Department, University and Hospital Trust (AOUI), Verona, Italy
| | - Aurora Vassanelli
- Transfusion Medicine Department, University and Hospital Trust (AOUI), Verona, Italy
| | - Denise Pavone
- Transfusion Medicine Department, University and Hospital Trust (AOUI), Verona, Italy
| | - Michele Milella
- Section of Innovation Biomedicine - Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona, Verona, Italy
| | - Sara Pilotto
- Section of Innovation Biomedicine - Oncology Area, Department of Engineering for Innovation Medicine (DIMI), University of Verona, Verona, Italy
| | - Pamela Biondani
- Section of Oncology, University and Hospital Trust (AOUI) of Verona, Verona, Italy
| | - Benedikt Höing
- Department of Otorhinolaryngology, University Hospital Essen, Essen, Germany
| | | | - Timon Hussain
- Department of Otorhinolaryngology, University Hospital Essen, Essen, Germany
| | - Boris Hadaschik
- Department of Urology, University Hospital Essen, Essen, Germany
| | - Cordelia Kaspar
- Department of Urology, University Hospital Essen, Essen, Germany
| | - Carlo Visco
- Section of Hematology and Bone Marrow Transplant Unit, Department of Engineering for Innovation Medicine (DIMI), University of Verona, Verona, Italy
| | - Cristina Tecchio
- Section of Hematology and Bone Marrow Transplant Unit, Department of Engineering for Innovation Medicine (DIMI), University of Verona, Verona, Italy
| | - Leo Koenderman
- Department of Respiratory Medicine and Center for Translational Immunology, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Flavia Bazzoni
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Nicola Tamassia
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Sven Brandau
- Research Division, Department of Otorhinolaryngology, University Hospital Essen, 45122 Essen, Germany; German Cancer Consortium, Partner Site Essen-Düsseldorf, Essen, Germany
| | - Marco A Cassatella
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy.
| | - Patrizia Scapini
- Section of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy.
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45
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Jin W, Dai Y, Chen L, Zhu H, Dong F, Zhu H, Meng G, Li J, Chen S, Chen Z, Fang H, Wang K. Cellular hierarchy insights reveal leukemic stem-like cells and early death risk in acute promyelocytic leukemia. Nat Commun 2024; 15:1423. [PMID: 38365836 PMCID: PMC10873341 DOI: 10.1038/s41467-024-45737-7] [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: 04/20/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
Acute promyelocytic leukemia (APL) represents a paradigm for targeted differentiation therapy, with a minority of patients experiencing treatment failure and even early death. We here report a comprehensive single-cell analysis of 16 APL patients, uncovering cellular compositions and their impact on all-trans retinoic acid (ATRA) response in vivo and early death. We unveil a cellular differentiation hierarchy within APL blasts, rooted in leukemic stem-like cells. The oncogenic PML/RARα fusion protein exerts branch-specific regulation in the APL trajectory, including stem-like cells. APL cohort analysis establishes an association of leukemic stemness with elevated white blood cell counts and FLT3-ITD mutations. Furthermore, we construct an APL-specific stemness score, which proves effective in assessing early death risk. Finally, we show that ATRA induces differentiation of primitive blasts and patients with early death exhibit distinct stemness-associated transcriptional programs. Our work provides a thorough survey of APL cellular hierarchies, offering insights into cellular dynamics during targeted therapy.
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Affiliation(s)
- Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Honghu Zhu
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Fangyi Dong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hongming Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guoyu Meng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Deschildre J, Vandemoortele B, Loers JU, De Preter K, Vermeirssen V. Evaluation of single-sample network inference methods for precision oncology. NPJ Syst Biol Appl 2024; 10:18. [PMID: 38360881 PMCID: PMC10869342 DOI: 10.1038/s41540-024-00340-w] [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: 07/11/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
A major challenge in precision oncology is to detect targetable cancer vulnerabilities in individual patients. Modeling high-throughput omics data in biological networks allows identifying key molecules and processes of tumorigenesis. Traditionally, network inference methods rely on many samples to contain sufficient information for learning, resulting in aggregate networks. However, to implement patient-tailored approaches in precision oncology, we need to interpret omics data at the level of individual patients. Several single-sample network inference methods have been developed that infer biological networks for an individual sample from bulk RNA-seq data. However, only a limited comparison of these methods has been made and many methods rely on 'normal tissue' samples as reference, which are not always available. Here, we conducted an evaluation of the single-sample network inference methods SSN, LIONESS, SWEET, iENA, CSN and SSPGI using transcriptomic profiles of lung and brain cancer cell lines from the CCLE database. The methods constructed functional gene networks with distinct network characteristics. Hub gene analyses revealed different degrees of subtype-specificity across methods. Single-sample networks were able to distinguish between tumor subtypes, as exemplified by node strength clustering, enrichment of known subtype-specific driver genes among hubs and differential node strength. We also showed that single-sample networks correlated better to other omics data from the same cell line as compared to aggregate networks. We conclude that single-sample network inference methods can reflect sample-specific biology when 'normal tissue' samples are absent and we point out peculiarities of each method.
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Affiliation(s)
- Joke Deschildre
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Boris Vandemoortele
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jens Uwe Loers
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Lab of Translational Onco-genomics and Bio-informatics, Center for Medical Biotechnology (VIB-UGent), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Vanessa Vermeirssen
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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Leuzzi G, Vasciaveo A, Taglialatela A, Chen X, Firestone TM, Hickman AR, Mao W, Thakar T, Vaitsiankova A, Huang JW, Cuella-Martin R, Hayward SB, Kesner JS, Ghasemzadeh A, Nambiar TS, Ho P, Rialdi A, Hebrard M, Li Y, Gao J, Gopinath S, Adeleke OA, Venters BJ, Drake CG, Baer R, Izar B, Guccione E, Keogh MC, Guerois R, Sun L, Lu C, Califano A, Ciccia A. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Cell 2024; 187:861-881.e32. [PMID: 38301646 PMCID: PMC10980358 DOI: 10.1016/j.cell.2024.01.008] [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: 08/18/2022] [Revised: 07/23/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA translocase SMARCAL1 as a factor that favors tumor immune evasion by a dual mechanism involving both the suppression of innate immune signaling and the induction of PD-L1-mediated immune checkpoint responses. Mechanistically, SMARCAL1 limits endogenous DNA damage, thereby suppressing cGAS-STING-dependent signaling during cancer cell growth. Simultaneously, it cooperates with the AP-1 family member JUN to maintain chromatin accessibility at a PD-L1 transcriptional regulatory element, thereby promoting PD-L1 expression in cancer cells. SMARCAL1 loss hinders the ability of tumor cells to induce PD-L1 in response to genomic instability, enhances anti-tumor immune responses and sensitizes tumors to immune checkpoint blockade in a mouse melanoma model. Collectively, these studies uncover SMARCAL1 as a promising target for cancer immunotherapy.
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Affiliation(s)
- Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alessandro Vasciaveo
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | | | - Wendy Mao
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tanay Thakar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alina Vaitsiankova
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jordan S Kesner
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ali Ghasemzadeh
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander Rialdi
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxime Hebrard
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jinmei Gao
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | | | - Charles G Drake
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Raphael Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lu Sun
- EpiCypher Inc., Durham, NC 27709, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D’Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol 2024; 14:1282859. [PMID: 38414974 PMCID: PMC10897000 DOI: 10.3389/fimmu.2023.1282859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/22/2023] [Indexed: 02/29/2024] Open
Abstract
Introduction The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
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Affiliation(s)
- Anna Niarakis
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Inna Kuperstein
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - Marc E. Gillespie
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- St. John’s University, Queens, NY, United States
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Marcio Luis Acencio
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ahmed Hemedan
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Michael Aichem
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
| | - Tobias Czauderna
- Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Felicia Burtscher
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Takahiro G. Yamada
- Department of Biosciences and Informatics, Keio University, Kanagawa, Japan
| | - Yusuke Hiki
- Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa, Japan
| | - Noriko F. Hiroi
- Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa, Japan
- Keio University School of Medicine, Tokyo, Japan
| | - Finterly Hu
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Nhung Pham
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Alberto Valdeolivas
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Francesco Messina
- Department of Epidemiology, Preclinical Research and Advanced Diagnostic, National Institute for Infectious Diseases’ Lazzaro Spallanzani’ - IRCCS, Rome, Italy
| | - Marina Esteban-Medina
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
| | - Maria Peña-Chilet
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
| | - Kinza Rian
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
| | - Sylvain Soliman
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Sara Sadat Aghamiri
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Aurélien Naldi
- Lifeware Group, Inria, Saclay-île de France, Palaiseau, France
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Vidisha Singh
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde - Genhotel, Univ Evry, Evry, France
| | | | - Viviam Bermudez
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eirini Tsirvouli
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arnau Montagud
- Barcelona Supercomputing Center (BSC.), Barcelona, Spain
| | - Vincent Noël
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | | | | | - Benjamin M. Gyori
- Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
| | - John A. Bachman
- Harvard Medical School, Laboratory of Systems Pharmacology, Boston, MA, United States
| | - Augustin Luna
- Computational Biology Branch, National Library of Medicine, Bethesda, MD, United States
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Janet Piñero
- Medbioinformatics Solutions SL, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Laura I. Furlong
- Medbioinformatics Solutions SL, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irina Balaur
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Adrien Rougny
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan
- Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan
| | - Yohan Jarosz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rupert W. Overall
- Institute for Biology, Humboldt University of Berlin, Berlin, Germany
| | - Robert Phair
- Integrative Bioinformatics, Inc., Mountain View, CA, United States
| | - Livia Perfetto
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Lisa Matthews
- Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
| | | | | | - Luis Cristobal Monraz Gomez
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Jean Marie Ravel
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Bijay Jassal
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Frankfurt Institute for Advanced Studies, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Guanming Wu
- Oregon Health Sciences University, Portland, OR, United States
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laurence Calzone
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Peter D’Eustachio
- Department of Biochemistry & Molecular Pharmacology, NYU. Langone Medical Center, New York, NY, United States
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Victoria, VIC, Australia
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Joaquin Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Seville, Spain
- FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC.), Barcelona, Spain
- I.C.R.E.A., Pg. Lluís Companys 23, Barcelona, Spain
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
- Leibniz Institute for Food Systems Biology, at the Technical University Munich, Munich, Germany
| | | | - Emmanuel Barillot
- Institut Curie, P.S.L. Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | | | - Rudi Balling
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Savage TM, Fortson KT, de Los Santos-Alexis K, Oliveras-Alsina A, Rouanne M, Rae SS, Gamarra JR, Shayya H, Kornberg A, Cavero R, Li F, Han A, Haeusler RA, Adam J, Schwabe RF, Arpaia N. Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis. Immunity 2024; 57:303-318.e6. [PMID: 38309273 PMCID: PMC10922825 DOI: 10.1016/j.immuni.2024.01.009] [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: 09/23/2022] [Revised: 11/20/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
Production of amphiregulin (Areg) by regulatory T (Treg) cells promotes repair after acute tissue injury. Here, we examined the function of Treg cells in non-alcoholic steatohepatitis (NASH), a setting of chronic liver injury. Areg-producing Treg cells were enriched in the livers of mice and humans with NASH. Deletion of Areg in Treg cells, but not in myeloid cells, reduced NASH-induced liver fibrosis. Chronic liver damage induced transcriptional changes associated with Treg cell activation. Mechanistically, Treg cell-derived Areg activated pro-fibrotic transcriptional programs in hepatic stellate cells via epidermal growth factor receptor (EGFR) signaling. Deletion of Areg in Treg cells protected mice from NASH-dependent glucose intolerance, which also was dependent on EGFR signaling on hepatic stellate cells. Areg from Treg cells promoted hepatocyte gluconeogenesis through hepatocyte detection of hepatic stellate cell-derived interleukin-6. Our findings reveal a maladaptive role for Treg cell-mediated tissue repair functions in chronic liver disease and link liver damage to NASH-dependent glucose intolerance.
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Affiliation(s)
- Thomas M Savage
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Katherine T Fortson
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | | | | | - Mathieu Rouanne
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Sarah S Rae
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | | | - Hani Shayya
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Adam Kornberg
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA; Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Renzo Cavero
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Fangda Li
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA
| | - Arnold Han
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA; Columbia Center for Translational Immunology, Columbia University, New York, NY, USA; Department of Medicine, Columbia University, New York, NY, USA
| | - Rebecca A Haeusler
- Naomi Berrie Diabetes Center, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Julien Adam
- Pathology Department, Hopital Paris Saint-Joseph, Paris, France; INSERM U1186, Gustave Roussy, Villejuif, France
| | | | - Nicholas Arpaia
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
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50
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Lu C, Donners MMPC, de Baaij JBJ, Jin H, Otten JJT, Manca M, van Zonneveld AJ, Jukema JW, Kraaijeveld A, Kuiper J, Pasterkamp G, Mees B, Sluimer JC, Cavill R, Karel JMH, Goossens P, Biessen EAL. Identification of a gene network driving the attenuated response to lipopolysaccharide of monocytes from hypertensive coronary artery disease patients. Front Immunol 2024; 15:1286382. [PMID: 38410507 PMCID: PMC10894924 DOI: 10.3389/fimmu.2024.1286382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction The impact of cardiovascular disease (CVD) risk factors, encompassing various biological determinants and unhealthy lifestyles, on the functional dynamics of circulating monocytes-a pivotal cell type in CVD pathophysiology remains elusive. In this study, we aimed to elucidate the influence of CVD risk factors on monocyte transcriptional responses to an infectious stimulus. Methods We conducted a comparative analysis of monocyte gene expression profiles from the CTMM - CIRCULATING CELLS Cohort of coronary artery disease (CAD) patients, at baseline and after lipopolysaccharide (LPS) stimulation. Gene co-expression analysis was used to identify gene modules and their correlations with CVD risk factors, while pivotal transcription factors controlling the hub genes in these modules were identified by regulatory network analyses. The identified gene module was subjected to a drug repurposing screen, utilizing the LINCS L1000 database. Results Monocyte responsiveness to LPS showed a highly significant, negative correlation with blood pressure levels (ρ< -0.4; P<10-80). We identified a ZNF12/ZBTB43-driven gene module closely linked to diastolic blood pressure, suggesting that monocyte responses to infectious stimuli, such as LPS, are attenuated in CAD patients with elevated diastolic blood pressure. This attenuation appears associated with a dampening of the LPS-induced suppression of oxidative phosphorylation. Finally, we identified the serine-threonine inhibitor MW-STK33-97 as a drug candidate capable of reversing this aberrant LPS response. Conclusions Monocyte responses to infectious stimuli may be hampered in CAD patients with high diastolic blood pressure and this attenuated inflammatory response may be reversed by the serine-threonine inhibitor MW-STK33-97. Whether the identified gene module is a mere indicator of, or causal factor in diastolic blood pressure and the associated dampened LPS responses remains to be determined.
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Affiliation(s)
- Chang Lu
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| | - Marjo M P C Donners
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands
| | - Julius B J de Baaij
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands
| | - Han Jin
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jeroen J T Otten
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
- Netherlands Heart Institute, Utrecht, Netherlands
| | - Adriaan Kraaijeveld
- Department of Cardiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Johan Kuiper
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Gerard Pasterkamp
- Circulatory Health Research Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Barend Mees
- Department of Vascular Surgery, Maastricht University Medical Center, Maastricht, Netherlands
| | - Judith C Sluimer
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands
- Centre for Cardiovascular Science (CVS), University of Edinburgh, Edinburgh, United Kingdom
| | - Rachel Cavill
- Department of Advanced Computing Sciences, Maastricht University, Maastricht, Netherlands
| | - Joël M H Karel
- Department of Advanced Computing Sciences, Maastricht University, Maastricht, Netherlands
| | - Pieter Goossens
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands
| | - Erik A L Biessen
- Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center, Maastricht, Netherlands
- Institute for Molecular Cardiovascular Research, Klinikum RWTH Aachen, Aachen, Germany
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