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Wei H, Luo X, Lan R, Xiong Y, Yang S, Wang S, Yang L, Lv Y. Integrated analysis of patients with bladder cancer from prospective transcription factor activity: Implications for personalized treatment approaches. Methods 2024; 230:32-43. [PMID: 39079653 DOI: 10.1016/j.ymeth.2024.07.006] [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: 06/25/2024] [Revised: 07/07/2024] [Accepted: 07/23/2024] [Indexed: 08/05/2024] Open
Abstract
Transcription factors are a specialized group of proteins that play important roles in regulating gene expression in human. These proteins control the transcription and translation of genes by binding to specific sites on DNA, thereby regulating key biological processes such as cell differentiation, proliferation, immune response, and neural development. Moreover, transcription factors are also involved in apoptosis and the pathogenesis of various diseases. By investigating transcription factors, researchers can uncover the mechanisms of gene regulation in organisms and develop more effective methods for preventing and treating human diseases. In the present study, the Virtual Inference of Protein-activity by Enriched Regulon algorithm was utilized to calculate the protein activity of transcription factors, and the metabolic-related protein activity were used for classifying bladder cancer patients into different subtype. To identify chemotherapy drugs with clinical benefits, the differences in prognosis and drug sensitivity between two distinct subtypes of bladder cancer patients were investigated. Simultaneously, the master regulators that display varying levels of transcription factor activity between two different bladder cancer subtypes were explored. Additionally, the potential transcriptional regulatory mechanisms and targets of these factors were investigated, thereby generating novel insights into bladder cancer research at the transcriptional regulation level.
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Affiliation(s)
- Haodong Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xu Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Rifang Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yuqiang Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Siru Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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2
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Martinez-Sarmiento JA, Cosma MP, Lakadamyali M. Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. Cell Rep 2024; 43:114170. [PMID: 38700983 PMCID: PMC11195307 DOI: 10.1016/j.celrep.2024.114170] [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: 08/09/2023] [Revised: 03/08/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the single-cell level. Here, we employ the heterokaryon-mediated reprogramming system as a single-cell model to dissect key temporal events during early stages of pluripotency conversion using super-resolution imaging. We reveal that, following heterokaryon formation, the somatic nucleus undergoes global chromatin decompaction and removal of repressive histone modifications H3K9me3 and H3K27me3 without acquisition of active modifications H3K4me3 and H3K9ac. The pluripotency gene OCT4 (POU5F1) shows nascent and mature RNA transcription within the first 24 h after cell fusion without requiring an initial open chromatin configuration at its locus. NANOG, conversely, has significant nascent RNA transcription only at 48 h after cell fusion but, strikingly, exhibits genomic reopening early on. These findings suggest that the temporal relationship between chromatin compaction and gene activation during cellular reprogramming is gene context dependent.
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Affiliation(s)
- Jose A Martinez-Sarmiento
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080 Guangzhou, China.
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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3
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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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4
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Breindl M, Spitzer D, Gerasimaitė R, Kairys V, Schubert T, Henfling R, Schwartz U, Lukinavičius G, Manelytė L. Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex. Nucleic Acids Res 2024; 52:337-354. [PMID: 38000389 PMCID: PMC10783490 DOI: 10.1093/nar/gkad1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Baz2B is a regulatory subunit of the ATP-dependent chromatin remodeling complexes BRF1 and BRF5, which control access to DNA during DNA-templated processes. Baz2B has been implicated in several diseases and also in unhealthy ageing, however limited information is available on the domains and cellular roles of Baz2B. To gain more insight into the Baz2B function, we biochemically characterized the TAM (Tip5/ARBP/MBD) domain with the auxiliary AT-hook motifs and the bromodomain (BRD). We observed alterations in histone code recognition in bromodomains carrying cancer-associated point mutations, suggesting their potential involvement in disease. Furthermore, the depletion of Baz2B in the Hap1 cell line resulted in altered cell morphology, reduced colony formation and perturbed transcriptional profiles. Despite that, super-resolution microscopy images revealed no changes in the overall chromatin structure in the absence of Baz2B. These findings provide insights into the biological function of Baz2B.
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Affiliation(s)
- Matthias Breindl
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Dominika Spitzer
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Visvaldas Kairys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | | | - Ramona Henfling
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Uwe Schwartz
- NGS Analysis Center, University of Regensburg, Regensburg DE-93053, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Laura Manelytė
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
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5
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Gallrein C, Williams AB, Meyer DH, Messling JE, Garcia A, Schumacher B. baz-2 enhances systemic proteostasis in vivo by regulating acetylcholine metabolism. Cell Rep 2023; 42:113577. [PMID: 38100354 DOI: 10.1016/j.celrep.2023.113577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
Neurodegenerative disorders, such as Alzheimer's disease (AD) or Huntington's disease (HD), are linked to protein aggregate neurotoxicity. According to the "cholinergic hypothesis," loss of acetylcholine (ACh) signaling contributes to the AD pathology, and therapeutic restoration of ACh signaling is a common treatment strategy. How disease causation and the effect of ACh are linked to protein aggregation and neurotoxicity remains incompletely understood, thus limiting the development of more effective therapies. Here, we show that BAZ-2, the Caenorhabditis elegans ortholog of human BAZ2B, limits ACh signaling. baz-2 mutations reverse aggregation and toxicity of amyloid-beta as well as polyglutamine peptides, thereby restoring health and lifespan in nematode models of AD and HD, respectively. The neuroprotective effect of Δbaz-2 is mediated by choline acetyltransferase, phenocopied by ACh-esterase depletion, and dependent on ACh receptors. baz-2 reduction or ectopic ACh treatment augments proteostasis via induction of the endoplasmic reticulum unfolded protein response and the ubiquitin proteasome system.
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Affiliation(s)
- Christian Gallrein
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ashley B Williams
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - David H Meyer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Jan-Erik Messling
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Antonio Garcia
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.
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6
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Cazzanelli G, Vedove AD, Parolin E, D'Agostino VG, Unzue A, Nevado C, Caflisch A, Lolli G. Reevaluation of bromodomain ligands targeting BAZ2A. Protein Sci 2023; 32:e4752. [PMID: 37574751 PMCID: PMC10464297 DOI: 10.1002/pro.4752] [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: 04/22/2023] [Revised: 06/25/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]
Abstract
BAZ2A promotes migration and invasion in prostate cancer. Two chemical probes, the specific BAZ2-ICR, and the BAZ2/BRD9 cross-reactive GSK2801, interfere with the recognition of acetylated lysines in histones by the bromodomains of BAZ2A and of its BAZ2B paralog. The two chemical probes were tested in prostate cancer cell lines with opposite androgen susceptibility. BAZ2-ICR and GSK2801 showed different cellular efficacies in accordance with their unequal selectivity profiles. Concurrent inhibition of BAZ2 and BRD9 did not reproduce the effects observed with GSK2801, indicating possible off-targets for this chemical probe. On the other hand, the single BAZ2 inhibition by BAZ2-ICR did not phenocopy genetic ablation, demonstrating that bromodomain interference is not sufficient to strongly affect BAZ2A functionality and suggesting a PROTAC-based chemical ablation as an alternative optimization strategy and a possible therapeutic approach. In this context, we also present the crystallographic structures of BAZ2A in complex with the above chemical probes. Binding poses of TP-238 and GSK4027, chemical probes for the bromodomain subfamily I, and two ligands of the CBP/EP300 bromodomains identify additional headgroups for the development of BAZ2A ligands.
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Affiliation(s)
- Giulia Cazzanelli
- Department of Cellular, Computational and Integrative Biology—CIBIOUniversity of TrentoTrentoItaly
| | - Andrea Dalle Vedove
- Department of Cellular, Computational and Integrative Biology—CIBIOUniversity of TrentoTrentoItaly
| | - Eleonora Parolin
- Department of Cellular, Computational and Integrative Biology—CIBIOUniversity of TrentoTrentoItaly
| | - Vito Giuseppe D'Agostino
- Department of Cellular, Computational and Integrative Biology—CIBIOUniversity of TrentoTrentoItaly
| | - Andrea Unzue
- Department of ChemistryUniversity of ZürichZürichSwitzerland
| | - Cristina Nevado
- Department of ChemistryUniversity of ZürichZürichSwitzerland
| | - Amedeo Caflisch
- Department of BiochemistryUniversity of ZürichZürichSwitzerland
| | - Graziano Lolli
- Department of Cellular, Computational and Integrative Biology—CIBIOUniversity of TrentoTrentoItaly
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7
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Su D, Xiong Y, Wei H, Wang S, Ke J, Liang P, Zhang H, Yu Y, Zuo Y, Yang L. Integrated analysis of ovarian cancer patients from prospective transcription factor activity reveals subtypes of prognostic significance. Heliyon 2023; 9:e16147. [PMID: 37215759 PMCID: PMC10199194 DOI: 10.1016/j.heliyon.2023.e16147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023] Open
Abstract
Transcription factors are protein molecules that act as regulators of gene expression. Aberrant protein activity of transcription factors can have a significant impact on tumor progression and metastasis in tumor patients. In this study, 868 immune-related transcription factors were identified from the transcription factor activity profile of 1823 ovarian cancer patients. The prognosis-related transcription factors were identified through univariate Cox analysis and random survival tree analysis, and two distinct clustering subtypes were subsequently derived based on these transcription factors. We assessed the clinical significance and genomics landscape of the two clustering subtypes and found statistically significant differences in prognosis, response to immunotherapy, and chemotherapy among ovarian cancer patients with different subtypes. Multi-scale Embedded Gene Co-expression Network Analysis was used to identify differential gene modules between the two clustering subtypes, which allowed us to conduct further analysis of biological pathways that exhibited significant differences between them. Finally, a ceRNA network was constructed to analyze lncRNA-miRNA-mRNA regulatory pairs with differential expression levels between two clustering subtypes. We expected that our study may provide some useful references for stratifying and treating patients with ovarian cancer.
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Affiliation(s)
- Dongqing Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yuqiang Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Haodong Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jiawei Ke
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Pengfei Liang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Haoxin Zhang
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yao Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd., Hohhot, 010010, China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
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8
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Basu J, Madhulika S, Murmu KC, Mohanty S, Samal P, Das A, Mahapatra S, Saha S, Sinha I, Prasad P. Molecular and epigenetic alterations in normal and malignant myelopoiesis in human leukemia 60 (HL60) promyelocytic cell line model. Front Cell Dev Biol 2023; 11:1060537. [PMID: 36819104 PMCID: PMC9932920 DOI: 10.3389/fcell.2023.1060537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
In vitro cell line model systems are essential in supporting the research community due to their low cost, uniform culturing conditions, homogeneous biological resources, and easy experimental design to study the cause and effect of a gene or a molecule. Human leukemia 60 (HL60) is an in-vitro hematopoietic model system that has been used for decades to study normal myeloid differentiation and leukemia biology. Here, we show that IMDM supplemented with 20% FBS is an optimal culturing condition and induces effective myeloid differentiation compared with RPMI supplemented with 10% FBS when HL60 is induced with 1α,25-dihydroxyvitamin D3 (Vit D3) and all-trans retinoic acid (ATRA). The chromatin organization is compacted, and the repressive epigenetic mark H3K27me3 is enhanced upon HL60-mediated terminal differentiation. Differential gene expression analysis obtained from RNA sequencing in HL60 cells during myeloid differentiation showed the induction of pathways involved in epigenetic regulation, myeloid differentiation, and immune regulation. Using high-throughput transcriptomic data (GSE74246), we show the similarities (genes that did not satisfy |log2FC|>1 and FDR<0.05) and differences (FDR <0.05 and |log2FC|>1) between granulocyte-monocyte progenitor vs HL60 cells, Vit D3 induced monocytes (vMono) in HL60 cells vs primary monocytes (pMono), and HL60 cells vs leukemic blasts at the transcriptomic level. We found striking similarities in biological pathways between these comparisons, suggesting that the HL60 model system can be effectively used for studying myeloid differentiation and leukemic aberrations. The differences obtained could be attributed to the fact that the cellular programs of the leukemic cell line and primary cells are different. We validated several gene expression patterns for different comparisons with CD34+ cells derived from cord blood for myeloid differentiation and AML patients. In addition to the current knowledge, our study further reveals the significance of using HL60 cells as in vitro model system under optimal conditions to understand its potential as normal myeloid differentiation model as well as leukemic model at the molecular level.
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Affiliation(s)
- Jhinuk Basu
- Chromatin and Epigenetics Unit, Institute of Life Sciences, Bhubaneswar, India,RCB, Regional Centre for Biotechnology, Faridabad, India
| | - Swati Madhulika
- Chromatin and Epigenetics Unit, Institute of Life Sciences, Bhubaneswar, India,RCB, Regional Centre for Biotechnology, Faridabad, India
| | - Krushna Chandra Murmu
- Chromatin and Epigenetics Unit, Institute of Life Sciences, Bhubaneswar, India,RCB, Regional Centre for Biotechnology, Faridabad, India
| | - Smrutishree Mohanty
- Chromatin and Epigenetics Unit, Institute of Life Sciences, Bhubaneswar, India,RCB, Regional Centre for Biotechnology, Faridabad, India
| | - Priyanka Samal
- IMS and SUM Hospital, Siksha ‘O' Anusandhan University, Bhubaneswar, India
| | - Asima Das
- Department of Obstetrics and Gynecology, KIMS, Bhubaneswar, India
| | - Soumendu Mahapatra
- Chromatin and Epigenetics Unit, Institute of Life Sciences, Bhubaneswar, India,Kalinga Institute of Industrial Technology (KIIT), School of Biotechnology, Bhubaneswar, India
| | - Subha Saha
- Chromatin and Epigenetics Unit, Institute of Life Sciences, Bhubaneswar, India
| | - Indranil Sinha
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Punit Prasad
- Chromatin and Epigenetics Unit, Institute of Life Sciences, Bhubaneswar, India,*Correspondence: Punit Prasad,
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9
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [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: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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10
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Bingen JM, Clark LV, Band MR, Munzir I, Carrithers MD. Differential DNA methylation associated with multiple sclerosis and disease modifying treatments in an underrepresented minority population. Front Genet 2023; 13:1058817. [PMID: 36685876 PMCID: PMC9845287 DOI: 10.3389/fgene.2022.1058817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
Black and Hispanic American patients frequently develop earlier onset of multiple sclerosis (MS) and a more severe disease course that can be resistant to disease modifying treatments. The objectives were to identify differential methylation of genomic DNA (gDNA) associated with disease susceptibility and treatment responses in a cohort of MS patients from underrepresented minority populations. Patients with MS and controls with non-inflammatory neurologic conditions were consented and enrolled under an IRB-approved protocol. Approximately 64% of donors identified as Black or African American and 30% as White, Hispanic-Latino. Infinium MethylationEPIC bead arrays were utilized to measure epigenome-wide gDNA methylation of whole blood. Data were analyzed in the presence and absence of adjustments for unknown covariates in the dataset, some of which corresponded to disease modifying treatments. Global patterns of differential methylation associated with MS were strongest for those probes that showed relative demethylation of loci with lower M values. Pathway analysis revealed unexpected associations with shigellosis and amoebiasis. Enrichment analysis revealed an over-representation of probes in enhancer regions and an under-representation in promoters. In the presence of adjustments for covariates that included disease modifying treatments, analysis revealed 10 differentially methylated regions (DMR's) with an FDR <1E-77. Five of these genes (ARID5B, BAZ2B, RABGAP1, SFRP2, WBP1L) are associated with cancer risk and cellular differentiation and have not been previously identified in MS studies. Hierarchical cluster and multi-dimensional scaling analysis of differential DNA methylation at 147 loci within those DMR's was sufficient to differentiate MS donors from controls. In the absence of corrections for disease modifying treatments, differential methylation in patients treated with dimethyl fumarate was associated with immune regulatory pathways that regulate cytokine and chemokine signaling, axon guidance, and adherens junctions. These results demonstrate possible associations of gastrointestinal pathogens and regulation of cellular differentiation with MS susceptibility in our patient cohort. This work further suggests that analyses can be performed in the presence and absence of corrections for immune therapies. Because of their high representation in our patient cohort, these results may be of specific relevance in the regulation of disease susceptibility and treatment responses in Black and Hispanic Americans.
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Affiliation(s)
- Jeremy M. Bingen
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States
- Physiology and Biophysics, University of Illinois College of Medicine, Chicago, IL, United States
| | - Lindsay V. Clark
- High Performance Biological Computing, and Roy J Carver Biotechnology Center, University of Illinois, Champaign, IL, United States
| | - Mark R. Band
- High Performance Biological Computing, and Roy J Carver Biotechnology Center, University of Illinois, Champaign, IL, United States
| | - Ilyas Munzir
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Michael D. Carrithers
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States
- Physiology and Biophysics, University of Illinois College of Medicine, Chicago, IL, United States
- Neurology, Jesse Brown Veterans Administration Hospital, Chicago, IL, United States
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11
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Laise P, Bosker G, Califano A, Alvarez MJ. A Patient-to-Model-to-Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture. Curr Protoc 2022; 2:e544. [PMID: 36083100 DOI: 10.1002/cpz1.544] [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] [Indexed: 06/15/2023]
Abstract
The current Achilles heel of cancer drug discovery is the inability to forge precise and predictive connections among mechanistic drivers of the cancer cell state, therapeutically significant molecular targets, effective drugs, and responsive patient subgroups. Although advances in molecular biology have helped identify molecular markers and stratify patients into molecular subtypes, these associational strategies typically fail to provide a mechanistic rationale to identify cancer vulnerabilities. Recently, integrative systems biology methodologies have been used to reverse engineer cellular networks and identify master regulators (MRs), proteins whose activity is both necessary and sufficient to implement phenotypic states under physiological and pathological conditions, which are organized into highly interconnected regulatory modules called tumor checkpoints. Because of their functional relevance, MRs represent ideal pharmacological targets and biomarkers. Here, we present a six-step patient-to-model-to-patient protocol that employs computational and experimental methodologies to reconstruct and interrogate the regulatory logic of human cancer cells for identifying and therapeutically targeting the tumor checkpoint with novel as well as existing pharmacological agents. This protocol systematically identifies, from specific patient tumor samples, the MRs that comprise the tumor checkpoint. Then, it identifies in vitro and in vivo models that, by recapitulating the patient's tumor checkpoint, constitute the appropriate cell lines and xenografts to further elucidate the tissue context-specific drug mechanism of action (MOA) and permit precise, biomarker-based preclinical validations of drug efficacy. The combination of determination of a drug's context-specific MOA and precise identification of patients' tumor checkpoints provides a personalized, mechanism-based biomarker to enrich prospective clinical trials with patients likely to respond. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Pasquale Laise
- DarwinHealth, New York, New York
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York
| | | | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, New York
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Mariano J Alvarez
- DarwinHealth, New York, New York
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York
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12
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Xiong Y, Wang S, Wei H, Li H, Lv Y, Chi M, Su D, Lu Q, Yu Y, Zuo Y, Yang L. Deep learning-based transcription factor activity for stratification of breast cancer patients. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194838. [PMID: 35690313 DOI: 10.1016/j.bbagrm.2022.194838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/19/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Transcription factors directly bind to DNA and regulate the expression of the gene, causing epigenetic modification of the DNA. They often mediate epigenetic parameters of transcriptional and posttranscriptional mechanisms, and their expression activities can be used to characterize genomic aberrations in cancer cell. In this study, the activity profile of transcription factors inferred by VIPER algorithm. The autoencoder model was applied for compressing the transcription factor activity profile for obtaining more useful transformed features for stratifying patients into two different breast cancer subtypes. The deep learning-based subtypes exhibited superior prognostic value and yielded better risk-stratification than the transcription factor activity-based method. Importantly, according to transformed features, a deep neural network was constructed to predict the subtypes, and achieved the accuracy of 94.98% and area under the ROC curve of 0.9663, respectively. The proposed subtypes were found to be significantly associated with immune infiltration, tumor immunogenicity and so on. Furthermore, the ceRNA network was constructed for the breast cancer subtypes. Besides, 11 master regulators were found to be associated with patients in cluster 1. Given the robustness performance of our deep learning model over multiple breast cancer cohorts, we expected this model may be useful in the area of prognosis prediction and lead some possibility for personalized medicine in breast cancer patients.
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Affiliation(s)
- Yuqiang Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Haodong Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hanshuang Li
- The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Meng Chi
- Department of Anesthesiology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Dongqing Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qianzi Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yao Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongchun Zuo
- The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China; Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mingolia Wesure Date Technology Co., Ltd., Hohhot 010010, China.
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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13
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Xu H, Winnink J, Pang H, Wen S, Chen L. Breakthrough potential of emerging research topics based on citation diffusion features. J Inf Sci 2022. [DOI: 10.1177/01655515211061219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This article uses the characteristics of citation curves in emerging research topics (ERTs) and combines them with the ERTs’ knowledge bases to draw conclusions by comparing their development patterns. The goal of this study is to enrich the toolset for predicting breakthroughs in scientific research. A set of multidimensional and practical bibliometric indicators is used to identify ERTs, to further identify the knowledge bases of ERTs and construct citation curves for both ERTs and their knowledge bases. The development trends of the citation curves of ERTs and their knowledge bases in different time periods are compared and analysed from two dimensions: knowledge transition and continuous growth. We use the field of stem cell research to test our method. Based on the outcome of the analysis, we can assess the breakthrough potential of ERTs. The stratification, transition and recent changes of the citation curve can be used as a basis for analysing and assessing the ERTs’ breakthrough potential. The combination of different citation diffusion patterns of ERTs and their knowledge bases can improve the effectiveness of identifying ERTs that can become breakthrough innovations.
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Affiliation(s)
- Haiyun Xu
- Business School, Shandong University of Technology, China
| | - Jos Winnink
- Centre for Science and Technology Studies (CWTS), Leiden University, The Netherlands
| | | | - Shuhao Wen
- School of Public Administration, Sichuan University, China
| | - Liang Chen
- Institute of Scientific and Technical Information of China (ISTIC), China
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14
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Abstract
BAZ2B is a regulatory subunit of the ISWI (Imitation Switch) remodeling complex and engages in nucleosome remodeling. Loss-of-function and haploinsufficiency of BAZ2B are associated with different diseases. BAZ2B is a large multidomain protein. In addition to the epigenetic reader domains plant homeodomain (PHD) and bromodomain (BRD), BAZ2B also has a Tip5/ARBP/MBD (TAM) domain. Sequence alignment revealed that the TAM domains of BAZ2A and BAZ2B share 53% sequence identity. How the BAZ2A TAM domain bound with DNA has been characterized recently, however, the DNA binding ability and methylation preference, as well as the structural basis of the BAZ2B TAM domain are not studied yet. In this study, we measured the DNA binding affinity of the TAM domain of BAZ2B, and also determined its apo crystal structure. We found that the TAM domains of BAZ2A and BAZ2B adopt almost the same fold, and like BAZ2A, the BAZ2B TAM domain also binds to dsDNA without methyl-cytosine preference, implying that the BAZ2B TAM domain might recognize DNA in a similar binding mode to that of the BAZ2A TAM domain. These results provide clues for the biological function study of BAZ2B in the future.
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15
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Ghosal S, Banerjee S. Investigating the potential molecular players and therapeutic drug molecules in carfilzomib resistant multiple myeloma by comprehensive bioinformatics analysis. Leuk Lymphoma 2022; 63:2545-2556. [DOI: 10.1080/10428194.2022.2087064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Somnath Ghosal
- School of Biological Sciences, Ramakrishna Mission Vivekananda Educational and Research Institute (RKMVERI), Kolkata, India
| | - Subrata Banerjee
- School of Biological Sciences, Ramakrishna Mission Vivekananda Educational and Research Institute (RKMVERI), Kolkata, India
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16
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Obradovic A, Graves D, Korrer M, Wang Y, Roy S, Naveed A, Xu Y, Luginbuhl A, Curry J, Gibson M, Idrees K, Hurley P, Jiang P, Liu XS, Uppaluri R, Drake CG, Califano A, Kim YJ. Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer. Clin Cancer Res 2022; 28:2094-2109. [PMID: 35262677 PMCID: PMC9161438 DOI: 10.1158/1078-0432.ccr-21-3570] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/15/2021] [Accepted: 03/07/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Cancer-associated fibroblasts (CAF) have been implicated as potential mediators of checkpoint immunotherapy response. However, the extensive heterogeneity of these cells has precluded rigorous understanding of their immunoregulatory role in the tumor microenvironment. EXPERIMENTAL DESIGN We performed high-dimensional single-cell RNA sequencing (scRNA-seq) on four patient tumors pretreatment and posttreatment from a neoadjuvant trial of patients with advanced-stage head and neck squamous cell carcinoma that were treated with the αPD-1 therapy, nivolumab. The head and neck CAF (HNCAF) protein activity profiles, derived from this cohort of paired scRNA-seq, were used to perform protein activity enrichment analysis on the 28-patient parental cohort of clinically annotated bulk transcriptomic profiles. Ex vivo coculture assays were used to test functional relevance of HNCAF subtypes. RESULTS Fourteen distinct cell types were identified with the fibroblast population showing significant changes in abundance following nivolumab treatment. Among the fibroblast subtypes, HNCAF-0/3 emerged as predictive of nivolumab response, while HNCAF-1 was associated with immunosuppression. Functionally, HNCAF-0/3 were found to reduce TGFβ-dependent PD-1+TIM-3+ exhaustion of CD8 T cells, increase CD103+NKG2A+ resident memory phenotypes, and enhance the overall cytolytic profile of T cells. CONCLUSIONS Our findings demonstrate the functional importance of distinct HNCAF subsets in modulating the immunoregulatory milieu of human HNSCC. In addition, we have identified clinically actionable HNCAF subtypes that can be used as a biomarker of response and resistance in future clinical trials.
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Affiliation(s)
- Aleksandar Obradovic
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY, USA
- Department of Systems Biology, HICC, New York, NY, USA
| | - Diana Graves
- Department of Pathology, Microbiology & Immunology, Vanderbilt University, Nashville, TN, USA
| | - Michael Korrer
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Wang
- Department of Biostatistics, Vanderbilt University Medical Center. Nashville, TN, USA
| | - Sohini Roy
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Abdullah Naveed
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center. Nashville, TN, USA
| | - Adam Luginbuhl
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, Philadelphia, PA, USA
| | - Joseph Curry
- Department of Otolaryngology-Head and Neck Surgery, Thomas Jefferson University, Philadelphia, PA, USA
| | - Michael Gibson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kamran Idrees
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paula Hurley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peng Jiang
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - X. Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ravindra Uppaluri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Charles G. Drake
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, HICC, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, New York, NY, USA
| | - Young J. Kim
- Department of Pathology, Microbiology & Immunology, Vanderbilt University, Nashville, TN, USA
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Regeneron Pharmaceutical, Tarrytown, NY, USA
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17
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Li Y, Gong H, Wang P, Zhu Y, Peng H, Cui Y, Li H, Liu J, Wang Z. The emerging role of ISWI chromatin remodeling complexes in cancer. J Exp Clin Cancer Res 2021; 40:346. [PMID: 34736517 PMCID: PMC8567610 DOI: 10.1186/s13046-021-02151-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Disordered chromatin remodeling regulation has emerged as an essential driving factor for cancers. Imitation switch (ISWI) family are evolutionarily conserved ATP-dependent chromatin remodeling complexes, which are essential for cellular survival and function through multiple genetic and epigenetic mechanisms. Omics sequencing and a growing number of basic and clinical studies found that ISWI family members displayed widespread gene expression and genetic status abnormalities in human cancer. Their aberrant expression is closely linked to patient outcome and drug response. Functional or componential alteration in ISWI-containing complexes is critical for tumor initiation and development. Furthermore, ISWI-non-coding RNA regulatory networks and some non-coding RNAs derived from exons of ISWI member genes play important roles in tumor progression. Therefore, unveiling the transcriptional regulation mechanism underlying ISWI family sparked a booming interest in finding ISWI-based therapies in cancer. This review aims at describing the current state-of-the-art in the role of ISWI subunits and complexes in tumorigenesis, tumor progression, immunity and drug response, and presenting deep insight into the physiological and pathological implications of the ISWI transcription machinery in cancers.
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Affiliation(s)
- Yanan Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Han Gong
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Pan Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yajuan Cui
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Heng Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
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18
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Obradovic A, Chowdhury N, Haake SM, Ager C, Wang V, Vlahos L, Guo XV, Aggen DH, Rathmell WK, Jonasch E, Johnson JE, Roth M, Beckermann KE, Rini BI, McKiernan J, Califano A, Drake CG. Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages. Cell 2021; 184:2988-3005.e16. [PMID: 34019793 PMCID: PMC8479759 DOI: 10.1016/j.cell.2021.04.038] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
Clear cell renal carcinoma (ccRCC) is a heterogeneous disease with a variable post-surgical course. To assemble a comprehensive ccRCC tumor microenvironment (TME) atlas, we performed single-cell RNA sequencing (scRNA-seq) of hematopoietic and non-hematopoietic subpopulations from tumor and tumor-adjacent tissue of treatment-naive ccRCC resections. We leveraged the VIPER algorithm to quantitate single-cell protein activity and validated this approach by comparison to flow cytometry. The analysis identified key TME subpopulations, as well as their master regulators and candidate cell-cell interactions, revealing clinically relevant populations, undetectable by gene-expression analysis. Specifically, we uncovered a tumor-specific macrophage subpopulation characterized by upregulation of TREM2/APOE/C1Q, validated by spatially resolved, quantitative multispectral immunofluorescence. In a large clinical validation cohort, these markers were significantly enriched in tumors from patients who recurred following surgery. The study thus identifies TREM2/APOE/C1Q-positive macrophage infiltration as a potential prognostic biomarker for ccRCC recurrence, as well as a candidate therapeutic target.
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MESH Headings
- Adult
- Apolipoproteins E/genetics
- Apolipoproteins E/metabolism
- Biomarkers, Tumor/genetics
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cohort Studies
- Female
- Gene Expression/genetics
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Kidney/metabolism
- Kidney Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/pathology
- Macrophages/metabolism
- Male
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Middle Aged
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Prognosis
- Receptors, Complement/genetics
- Receptors, Complement/metabolism
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Sequence Analysis, RNA/methods
- Single-Cell Analysis/methods
- Tumor Microenvironment
- Tumor-Associated Macrophages/metabolism
- Tumor-Associated Macrophages/physiology
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Affiliation(s)
- Aleksandar Obradovic
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA; Department of Systems Biology, HICC, New York, NY 10032, USA
| | - Nivedita Chowdhury
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Casey Ager
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA
| | - Vinson Wang
- Department of Urology, Herbert Irving Comprehensive Cancer Center (HICC), New York, NY 10032, USA
| | - Lukas Vlahos
- Department of Systems Biology, HICC, New York, NY 10032, USA
| | - Xinzheng V Guo
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA
| | - David H Aggen
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA
| | | | - Eric Jonasch
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Marc Roth
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Brian I Rini
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - James McKiernan
- Department of Urology, Herbert Irving Comprehensive Cancer Center (HICC), New York, NY 10032, USA; HICC, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, HICC, New York, NY 10032, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; HICC, Columbia University, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY; Department of Biomedical Informatics, Columbia University, New York, NY, USA; Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA; J.P. Sulzberger Columbia Genome Center, New York, NY, USA.
| | - Charles G Drake
- Columbia Center for Translational Immunology (CCTI), Columbia University Irving Medical Center (CUMC), New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center (HICC), New York, NY 10032, USA; HICC, Columbia University, New York, NY, USA.
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