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White BS, de Reyniès A, Newman AM, Waterfall JJ, Lamb A, Petitprez F, Lin Y, Yu R, Guerrero-Gimenez ME, Domanskyi S, Monaco G, Chung V, Banerjee J, Derrick D, Valdeolivas A, Li H, Xiao X, Wang S, Zheng F, Yang W, Catania CA, Lang BJ, Bertus TJ, Piermarocchi C, Caruso FP, Ceccarelli M, Yu T, Guo X, Bletz J, Coller J, Maecker H, Duault C, Shokoohi V, Patel S, Liliental JE, Simon S, Saez-Rodriguez J, Heiser LM, Guinney J, Gentles AJ. Community assessment of methods to deconvolve cellular composition from bulk gene expression. Nat Commun 2024; 15:7362. [PMID: 39191725 DOI: 10.1038/s41467-024-50618-0] [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: 08/28/2023] [Accepted: 07/11/2024] [Indexed: 08/29/2024] Open
Abstract
We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states.
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Affiliation(s)
- Brian S White
- Sage Bionetworks, Seattle, WA, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Aurélien de Reyniès
- Centre de Recherche des Cordeliers, INSERM U1138, Université Paris Cité, Paris, France
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Joshua J Waterfall
- INSERM U830 and Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | | | - Florent Petitprez
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
- MRC Centre for Reproductive Health, the Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Yating Lin
- Xiamen University, Xiamen, Fujian, China
| | | | - Martin E Guerrero-Gimenez
- Institute of Biochemistry and Biotechnology, School of Medicine, National University of Cuyo, Mendoza, Argentina
| | | | - Gianni Monaco
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
| | | | | | - Daniel Derrick
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alberto Valdeolivas
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Haojun Li
- Xiamen University, Xiamen, Fujian, China
| | - Xu Xiao
- Xiamen University, Xiamen, Fujian, China
| | - Shun Wang
- Department of Pathology, Cancer Hospital, Chinese Aacdemy of Medical Science, Beijing, China
| | | | | | - Carlos A Catania
- Laboratory of Intelligent Systems (LABSIN), Engineering School, National University of Cuyo, Mendoza, Argentina
| | - Benjamin J Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | - Francesca P Caruso
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
| | - Michele Ceccarelli
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
- Sylvester Comprehensive Cancer Center, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | | | | | - John Coller
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Caroline Duault
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Vida Shokoohi
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - Shailja Patel
- Translational Applications Service Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanna E Liliental
- Translational Applications Service Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Laura M Heiser
- Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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Berdnikovs S, Newcomb DC, McKernan KE, Kuehnle SN, Haruna NF, Gebretsadik T, McKennan C, Ma S, Cephus JY, Rosas-Salazar C, Anderson LJ, Gern JE, Hartert T. Single cell profiling to determine influence of wheeze and early-life viral infection on developmental programming of airway epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602506. [PMID: 39026695 PMCID: PMC11257436 DOI: 10.1101/2024.07.08.602506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Although childhood asthma is in part an airway epithelial disorder, the development of the airway epithelium in asthma is not understood. We sought to characterize airway epithelial developmental phenotypes in those with and without recurrent wheeze and the impact of infant infection with respiratory syncytial virus (RSV). Nasal airway epithelial cells (NAECs) were collected at age 2-3 years from an a priori designed nested birth cohort of children from four mutually exclusive groups of wheezers/non-wheezers and RSV-infected/uninfected in the first year of life. NAECs were cultured in air-liquid interface differentiation conditions followed by a combined analysis of single cell RNA sequencing (scRNA-seq) and in vitro infection with respiratory syncytial virus (RSV). NAECs from children with a wheeze phenotype were characterized by abnormal differentiation and basal cell activation of developmental pathways, plasticity in precursor differentiation and a delayed onset of maturation. NAECs from children with wheeze also had increased diversity of currently known RSV receptors and blunted anti-viral immune responses to in vitro infection. The most dramatic changes in differentiation of cultured epithelium were observed in NAECs derived from children that had both wheeze and RSV in the first year of life. Together this suggests that airway epithelium in children with wheeze is developmentally reprogrammed and characterized by increased barrier permeability, decreased antiviral response, and increased RSV receptors, which may predispose to and amplify the effects of RSV infection in infancy and susceptibility to other asthma risk factors that interact with the airway mucosa. SUMMARY Nasal airway epithelial cells from children with wheeze are characterized by altered development and increased susceptibility to RSV infection.
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Sato Y, Kobayashi M, Ohira M, Funayama R, Maekawa M, Karasawa H, Kashiwagi R, Aoyama Y, Mano N, Ohnuma S, Unno M, Nakayama K. Downregulation of ABCC3 activates MAPK signaling through accumulation of deoxycholic acid in colorectal cancer cells. Cancer Sci 2024; 115:1778-1790. [PMID: 38566304 PMCID: PMC11145118 DOI: 10.1111/cas.16132] [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: 10/24/2023] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 04/04/2024] Open
Abstract
ABCC3 (also known as MRP3) is an ATP binding cassette transporter for bile acids, whose expression is downregulated in colorectal cancer through the Wnt/β-catenin signaling pathway. However, it remained unclear how downregulation of ABCC3 expression contributes to colorectal carcinogenesis. We explored the role of ABCC3 in the progression of colorectal cancer-in particular, focusing on the regulation of bile acid export. Gene expression analysis of colorectal adenoma isolated from familial adenomatous polyposis patients revealed that genes related to bile acid secretion including ABCC3 were downregulated as early as at the stage of adenoma formation. Knockdown or overexpression of ABCC3 increased or decreased intracellular concentration of deoxycholic acid, a secondary bile acid, respectively, in colorectal cancer cells. Forced expression of ABCC3 suppressed deoxycholic acid-induced activation of MAPK signaling. Finally, we found that nonsteroidal anti-inflammatory drugs increased ABCC3 expression in colorectal cancer cells, suggesting that ABCC3 could be one of the targets for therapeutic intervention of familial adenomatous polyposis. Our data thus suggest that downregulation of ABCC3 expression contributes to colorectal carcinogenesis through the regulation of intracellular accumulation of bile acids and activity of MAPK signaling.
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Affiliation(s)
- Yukihiro Sato
- Department of Cell Proliferation, ART, Graduate School of MedicineTohoku UniversitySendaiJapan
- Department of Surgery, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Minoru Kobayashi
- Department of Surgery, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Masahiro Ohira
- Department of Cell Proliferation, ART, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Ryo Funayama
- Department of Cell Proliferation, ART, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Masamitsu Maekawa
- Department of Pharmaceutical SciencesTohoku University HospitalSendaiJapan
| | - Hideaki Karasawa
- Department of Surgery, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Ryosuke Kashiwagi
- Department of Surgery, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Yayoi Aoyama
- Department of Investigative Pathology, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Nariyasu Mano
- Department of Pharmaceutical SciencesTohoku University HospitalSendaiJapan
| | - Shinobu Ohnuma
- Department of Surgery, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Michiaki Unno
- Department of Surgery, Graduate School of MedicineTohoku UniversitySendaiJapan
| | - Keiko Nakayama
- Department of Cell Proliferation, ART, Graduate School of MedicineTohoku UniversitySendaiJapan
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Datta A, Lee JH, Truong T, Flandrin O, Yang Y, Evans DJ, Fleiszig SMJ. Persistence of Contact Lens-Induced Corneal Parainflammation Following Lens Removal. Invest Ophthalmol Vis Sci 2024; 65:8. [PMID: 38466283 DOI: 10.1167/iovs.65.3.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
Purpose Contact lens wear induces corneal parainflammation involving increased immune cell numbers after 24 hours' (CD11c+, Lyz2+, γδ-T cells) and six days' (Ly6G+ cells) wear. We investigated the time course of onset and resolution of these responses. Methods LysMcre or C57BL/6J mice were fitted with a contact lens (four to 48 hours). Contralateral eyes did not wear lenses. After lens removal, Lyz2+, MHC-II+ or Ly6G+ cells were examined by quantitative imaging. RT-qPCR determined cytokine gene expression. Results Lens wear for 24 hours increased corneal Lyz2+ cells versus contralateral eyes approximately two-fold. Corneas remained free of visible pathology. The Lyz2+ response was not observed after four or 12 hours' wear, nor after 12 hours' wear plus 12 hours' no wear. Lens removal after 24 hours' wear further increased Lyz2+ cells (∼48% after one day), which persisted for four days, returning to baseline by seven days. Lyz2+ cells in contralateral eyes remained at baseline. MHC-II+ cells showed a similar response but without increasing after lens removal. Lens wear for 48 hours showed reduced Lyz2+ cells versus 24 hours' wear with one day discontinuation, correlating with reduced IL-1β and IL-18 gene expression. Lens wear for 24 hours did not induce Ly6G+ responses six days after removal. Conclusions Lens-induced corneal parainflammation involving Lyz2+ cells requires 24 hours' wear but persists after lens discontinuation, requiring seven days for reversal. Lens wear for 48 hours may suppress initial Lyz2+ cell and cytokine responses. The significance of parainflammation during and after lens wear remains to be determined.
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Affiliation(s)
- Ananya Datta
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, California, United States
| | - Ji Hyun Lee
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, California, United States
| | - Tiffany Truong
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, California, United States
| | - Orneika Flandrin
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, California, United States
| | - Yujia Yang
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, California, United States
| | - David J Evans
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, California, United States
- College of Pharmacy, Touro University California, Vallejo, California, United States
| | - Suzanne M J Fleiszig
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, California, United States
- Graduate groups in Vision Science, Microbiology, and Infectious Diseases & Immunity, University of California, Berkeley, California, United States
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Shi S, Tang X, Liu H. Disulfidptosis-Related lncRNA for the Establishment of Novel Prognostic Signature and Therapeutic Response Prediction to Endometrial Cancer. Reprod Sci 2024; 31:811-822. [PMID: 37880552 DOI: 10.1007/s43032-023-01382-x] [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: 07/23/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Disulfidptosis, a newly discovered cellular death mechanism initiated by disulfide stress, features elevated expression of SLC7A11 and restricted glucose availability, rendering it a possible therapeutic target for cancer. Endometrial cancer of the uterine corpus (ECUC) ranks among prevalent gynecological malignancies. Long non-coding RNAs (lncRNAs) have been implicated in ECUC's metabolic pathways, invasive capabilities, and metastatic processes. Yet, the prognostic implications of Disulfidptosis-Linked lncRNAs (DLLs) in ECUC remain ambiguous. Transcriptome and clinical datasets related to ECUC were sourced from The Cancer Genome Atlas (TCGA), while genes linked with disulfidptosis were identified from existing literature. A panel of ten DLLs was discerned through least absolute shrinkage and selection operator (LASSO) coupled with Cox regression methods to formulate and validate risk prognostic models. We engineered a nomogram for ECUC patient prognosis forecasting and further examined the model via gene set enrichment analysis (GSEA), principal component analysis (PCA), gene set analysis (GSA), immune profiling, and sensitivity to antineoplastic agents. Prognostic models employing a set of ten DLLs (including AC005034.2, AC020765.2, AL158071.4, AL161663.2, AP000787.1, CR392039.3, EMSLR, SEC24B-AS1, Z69733.1, Z94721.3) were established. Based on median risk values, patient samples were stratified into high- and low-risk cohorts, revealing notable differences in survival across both training and validation datasets. The risk scores, when amalgamated with clinical variables, acted as standalone predictors of prognosis. GSEA findings indicated that the high-risk category predominantly aligned with pathways like extracellular matrix interactions and cell adhesion molecules, suggesting a likely association with metastatic potential. Concurrently, we scrutinized disparities in immune function and tumor mutational burden across risk categories and identified anticancer drugs with likely efficacy. In summary, a set of ten DLLs proved useful in forecasting patient outcomes and holds potential for informing targeted therapeutic approaches in ECUC.
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Affiliation(s)
- Shanping Shi
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Xiaojian Tang
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Hua Liu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
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Zou T, Zhou M, Gupta A, Zhuang P, Fishbein AR, Wei HY, Capcha-Rodriguez D, Zhang Z, Cherniack AD, Meyerson M. XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells. Cell Rep 2024; 43:113600. [PMID: 38261514 PMCID: PMC10989277 DOI: 10.1016/j.celrep.2023.113600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/12/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene expression. XRN1 deletion causes PKR pathway activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-β stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR and how this interaction creates a vulnerability in cancer cells with an activated interferon cell state.
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Affiliation(s)
- Tao Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Meng Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Akansha Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Patrick Zhuang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alyssa R Fishbein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hope Y Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Diego Capcha-Rodriguez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zhouwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Edrei Y, Levy R, Kaye D, Marom A, Radlwimmer B, Hellman A. Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation. Genome Biol 2023; 24:264. [PMID: 38012713 PMCID: PMC10683314 DOI: 10.1186/s13059-023-03094-6] [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: 05/23/2022] [Accepted: 10/23/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible involvement of gene transcriptional-variation, we produce a DNA methylation-oriented, driver-gene-wide dataset of regulatory elements in human glioblastomas and study their effect on inter-patient gene expression variation. RESULTS In 175 of 177 analyzed gene regulatory domains, transcriptional enhancers and silencers are intermixed. Under experimental conditions, DNA methylation induces enhancers to alter their enhancing effects or convert into silencers, while silencers are affected inversely. High-resolution mapping of the association between DNA methylation and gene expression in intact genomes reveals methylation-related regulatory units (average size = 915.1 base-pairs). Upon increased methylation of these units, their target-genes either increased or decreased in expression. Gene-enhancing and silencing units constitute cis-regulatory networks of genes. Mathematical modeling of the networks highlights indicative methylation sites, which signified the effect of key regulatory units, and add up to make the overall transcriptional effect of the network. Methylation variation in these sites effectively describe inter-patient expression variation and, compared with DNA sequence-alterations, appears as a major contributor of gene-expression variation among glioblastoma patients. CONCLUSIONS We describe complex cis-regulatory networks, which determine gene expression by summing the effects of positive and negative transcriptional inputs. In these networks, DNA methylation induces both enhancing and silencing effects, depending on the context. The revealed mechanism sheds light on the regulatory role of DNA methylation, explains inter-individual gene-expression variation, and opens the way for monitoring the driving forces behind deferential courses of cancer and other diseases.
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Affiliation(s)
- Yifat Edrei
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Revital Levy
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Daniel Kaye
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Anat Marom
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Asaf Hellman
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel.
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Shen K, Chen B, Yang L, Gao W. KYNU as a Biomarker of Tumor-Associated Macrophages and Correlates with Immunosuppressive Microenvironment and Poor Prognosis in Gastric Cancer. Int J Genomics 2023; 2023:4662480. [PMID: 37954130 PMCID: PMC10635752 DOI: 10.1155/2023/4662480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/14/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Abstract
Background Kynureninase (KYNU) is a potential prognostic marker for various tumor types. However, no reports on the biological effects and prognostic value of KYNU in gastric cancer (GC) exist. Methods GC-associated single-cell RNA sequencing and bulk RNA sequencing (bulk-seq) data were obtained from the Gene Expression Omnibus and The Cancer Genome Atlas databases, respectively. The differential expression of KYNU between GC and normal gastric tissues was first analyzed based on the bulk-seq data, followed by an exploration of the relationship between KYNU and various clinicopathological features. The Kaplan-Meier survival and Cox regression analyses were performed to determine the prognostic value of KYNU. The relationship between KYNU expression and immune cell infiltration and immune checkpoints was also explored. The biological function of KYNU was further examined at the single-cell level, and in vitro experiments were performed to examine the effect of KYNU on GC cell proliferation and invasion. Results KYNU expression was significantly elevated in GC samples. Clinical features and survival analysis indicated that high KYNU expression was associated with poor clinical phenotypes and prognosis, whereas Cox analysis showed that KYNU was an independent risk factor for patients with GC. Notably, high expression of KYNU induced a poor immune microenvironment and contributed to the upregulation of immune checkpoints. KYNU-overexpressing macrophages drove GC progression through unique ligand-receptor pairs and transcription factors and were associated with adverse clinical phenotypes in GC. KYNU was overexpressed in GC cells in vitro, and KYNU knockout significantly inhibited GC cell proliferation and invasion. Conclusion High KYNU expression promotes an adverse immune microenvironment and low survival rates in GC. KYNU and KYNU-related macrophages may serve as novel molecular targets in the treatment of GC.
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Affiliation(s)
- Kaiyu Shen
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Binyu Chen
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Liu Yang
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Wencang Gao
- Department of Oncology, The Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou 310005, China
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Zhang N, Ji C, Bao X, Peng X, Tang M, Yuan C. Uncovering potential new biomarkers and immune infiltration characteristics in primary Sjögren's syndrome by integrated bioinformatics analysis. Medicine (Baltimore) 2023; 102:e35534. [PMID: 37832090 PMCID: PMC10578719 DOI: 10.1097/md.0000000000035534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Primary Sjögren's syndrome (pSS) is known as autoimmune disease characterized by damage to endocrine glands, such as the salivary and lacrimal glands. This study aimed to identify potential biomarkers for pSS using integrated bioinformatics analysis and explore the relationship between differentially expressed genes (DEGs) and immune infiltration. Three pSS datasets (GSE7451, GSE23117, and GSE40611) from the gene expression omnibus database were integrated. All the datasets were processed in R (version 4.0.3). A total of 16 immune cells and 13 immune functions were obtained. The top immune cell and immune function were "activated" dendritic cells and major histocompatibility complex class I. Correlation analysis showed the top correlation among 16 immune cells were B cells and tumor infiltrating lymphocytes, check-point and T cell co-stimulation, respectively. In comparisons of immune score, "activated" dendritic cells (.657 vs 594, P < .001), B cells (.492 vs 434, P = .004), macrophages (.631 vs 601, P = .010), inflammation-promoting (.545 vs 478, P < .001), Type I interferon Reponse (.728 vs 625, P < .001) and so on were higher in pSS than control group. In correlation analysis, the up-regulation of interferon induced protein with tetratricopeptide repeats 1 gene was strongly correlated with Type I interferon response with a correlation coefficient of .87. The receiver operating characteristic curve of 5 genes showed that the area under curve was.891. In the verification model, the area under curve was.881. In addition, disease ontology analysis supported the association between DEGs and pSS. In summary, pSS has a variety of DEGs in immune infiltration, which is worthy of the attention from clinicians.
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Affiliation(s)
- Naidan Zhang
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang, China
| | - Chaixia Ji
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang, China
| | - Xiao Bao
- Department of Rheumatology, Peoples Hospital of Deyang City, Deyang, China
| | - Xinyin Peng
- Chengdu University of Chinese Medicine, Chengdu, China
| | - Maoju Tang
- North Sichuan Medical College, Nanchong, China
| | - Chengliang Yuan
- Department of Clinical Laboratory, Peoples Hospital of Deyang City, Deyang, China
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Kuang Y, Yang K, Meng L, Mao Y, Xu F, Liu H. Identification and validation of ferroptosis-related biomarkers and the related pathogenesis in precancerous lesions of gastric cancer. Sci Rep 2023; 13:16074. [PMID: 37752199 PMCID: PMC10522668 DOI: 10.1038/s41598-023-43198-4] [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: 05/31/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
Using advanced bioinformatics techniques, we conducted an analysis of ferroptosis-related genes (FRGs) in precancerous lesions of gastric cancer (PLGC). We also investigated their connection to immune cell infiltration and diagnostic value, ultimately identifying new molecular targets that could be used for PLGC patient treatment. The Gene Expression Omnibus (GEO) and FerrDb V2 databases were used to identify FRGs. These genes were analysed via ClueGO pathways and Gene Ontology (GO) enrichment analysis, as well as single-cell dataset GSE134520 analysis. A machine learning model was applied to identify hub genes associated with ferroptosis in PLGC patients. Receiver Operating Characteristics (ROC) curve analysis was conducted to verify the diagnostic efficacy of these genes, and a PLGC diagnosis model nomogram was established based on hub genes. R software was utilized to conduct functional, pathway, gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) on the identified diagnostic genes. Hub gene expression levels and survival times in gastric cancer were analysed using online databases to determine the prognostic value of these genes. MCPcounter and single-sample gene set enrichment analysis (ssGSEA) algorithms were used to investigate the correlation between hub genes and immune cells. Finally, noncoding RNA regulatory mechanisms and transcription factor regulatory networks for hub genes were mapped using multiple databases. Eventually, we identified 23 ferroptosis-related genes in PLGC. Enrichment analyses showed that ferroptosis-related genes were closely associated with iron uptake and transport and ferroptosis in the development of PLGC. After differential analysis using machine learning algorithms, we identified four hub genes in PLGC patients, including MYB, CYB5R1, LIFR and DPP4. Consequently, we established a ferroptosis diagnosis model nomogram. GSVA and GSEA mutual verification analysis helped uncover potential regulatory mechanisms of hub genes. MCPcounter and ssGSEA analysed immune infiltration in the disease and indicated that B cells and parainflammation played an important role in disease progression. Finally, we constructed noncoding RNA regulatory networks and transcription factor regulatory networks. Our study identified ferroptosis-related diagnostic genes and therapeutic targets for PLGC, providing novel insights and a theoretical foundation for research into the molecular mechanisms, clinical diagnosis, and treatment of this disease.
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Affiliation(s)
- Yuhui Kuang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301608, China
| | - Kuo Yang
- Department of Digestive Diseases, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, 300120, China
| | - Lingkai Meng
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301608, China
| | - Yijia Mao
- Department of Digestive Diseases, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, 300120, China
| | - Fangbiao Xu
- Graduate School, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Huayi Liu
- Department of Digestive Diseases, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, 300120, China.
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11
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Qin Z, Liu H, Sheng Q, Dan J, Wu X, Li H, Wang L, Zhang S, Yuan C, Yuan H, Wang H, Zhou R, Luo Y, Xie X. Mutant p53 leads to low-grade IFN-I-induced inflammation and impairs cGAS-STING signalling in mice. Eur J Immunol 2023; 53:e2250211. [PMID: 37377275 DOI: 10.1002/eji.202250211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/09/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023]
Abstract
Type I interferons (IFN-Is) are a class of proinflammatory cytokines produced in response to viruses and environmental stimulations, resulting in chronic inflammation and even carcinogenesis. However, the connection between IFN-I and p53 mutation is poorly understood. Here, we investigated IFN-I status in the context of mutant p53 (p53N236S , p53S). We observed significant cytosolic double-stranded DNA (dsDNA) derived from nuclear heterochromatin in p53S cells, along with an increased expression of IFN-stimulated genes. Further study revealed that p53S promoted cyclic GMP-AMP synthase (cGAS) and IFN-regulatory factor 9 (IRF9) expression, thus activating the IFN-I pathway. However, p53S/S mice were more susceptible to herpes simplex virus 1 infection, and the cGAS-stimulator of IFN genes (STING) pathway showed a decline trend in p53S cells in response to poly(dA:dT) accompanied with decreased IFN-β and IFN-stimulated genes, whereas the IRF9 increased in response to IFN-β stimulation. Our results illustrated the p53S mutation leads to low-grade IFN-I-induced inflammation via consistent low activation of the cGAS-STING-IFN-I axis, and STAT1-IRF9 pathway, therefore, impairs the protective cGAS-STING signalling and IFN-I response encountered with exogenous DNA attack. These results suggested the dual molecular mechanisms of p53S mutation in inflammation regulation. Our results could be helping in further understanding of mutant p53 function in chronic inflammation and provide information for developing new therapeutic strategies for chronic inflammatory diseases or cancer.
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Affiliation(s)
- Ziyi Qin
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Huan Liu
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Qihuan Sheng
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Juhua Dan
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xiaoming Wu
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hao Li
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Lulin Wang
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shuojie Zhang
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chao Yuan
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hongjun Yuan
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hui Wang
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ruoyu Zhou
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ying Luo
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Development on Common Chronic Diseases, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoli Xie
- Molecular Genetics Laboratory of Aging and Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
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12
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Tang S, Xu L, Wu Z, Wen Q, Li H, Li N. A novel immunogenomic classification for prognosis in non-small cell lung cancer. J Cancer Res Clin Oncol 2023; 149:10951-10964. [PMID: 37329462 DOI: 10.1007/s00432-023-04887-9] [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: 04/10/2023] [Accepted: 05/19/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVE To facilitate immunotherapy and prognostic assessment of non-small cell lung cancer (NSCLC), we established a novel immunogenomic classification to provide valid identification criteria. METHODS The immune enrichment scores were calculated by single sample gene set enrichment analysis (ssGSEA) and clustered into Immunity_L and Immunity_H, and the reliability of this classification was demonstrated. Immune microenvironment score and immune cell infiltration analysis of NSCLC were also performed. Randomly divided into training group and test group, a prognosis-related immune profile was developed using least absolute shrinkage and selection operator (LASSO) and stepwise COX proportional hazards model to construct a prognostic mode. RESULTS The risk score for this immune profile was identified as an independent prognostic factor and can be used as a powerful prognostic tool to refine tumor immunotherapy. Our study identified two NSCLC classifications based on immunomic profiling, Immunity_H and Immunity_L. CONCLUSION In conclusion, Immunogenomic classification can distinguish the immune status of different types of NSCLC patients and contribute to the immunotherapy of NSCLC patients.
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Affiliation(s)
- Shu Tang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No. 1, East Construction Road, Zhengzhou, 450052, China.
| | - Liqing Xu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No. 1, East Construction Road, Zhengzhou, 450052, China
| | - Zhanshen Wu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No. 1, East Construction Road, Zhengzhou, 450052, China
| | - Qiang Wen
- Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, 450052, China
| | - Hui Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No. 1, East Construction Road, Zhengzhou, 450052, China
| | - Na Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, No. 1, East Construction Road, Zhengzhou, 450052, China
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13
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Zou T, Zhou M, Gupta A, Zhuang P, Fishbein AR, Wei HY, Zhang Z, Cherniack AD, Meyerson M. XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551488. [PMID: 37577567 PMCID: PMC10418227 DOI: 10.1101/2023.08.01.551488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene (ISG) expression. XRN1 deletion causes PKR activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-β stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR and nominate XRN1 as a potential therapeutic target in cancer cells with an activated interferon cell state.
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Affiliation(s)
- Tao Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Meng Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Akansha Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Patrick Zhuang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Alyssa R. Fishbein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Hope Y. Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Zhouwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Andrew D. Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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14
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Wang J, Ye J, Zhao X, Li X, Ma X. Prognostic value and model construction of preoperative inflammatory markers in patients with metastatic renal cell carcinoma. World J Surg Oncol 2023; 21:211. [PMID: 37480143 PMCID: PMC10360324 DOI: 10.1186/s12957-023-03110-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Inflammation is considered to be one of the driving factors of cancer, and chronic inflammation plays a crucial role in tumor growth and metastasis. The aim of this study was to examine the predictive value of preoperative inflammatory biomarkers for overall survival (OS) in patients with metastatic renal cell carcinoma (mRCC), including preoperative neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), and aspartate aminotransferase-to-lymphocyte ratio (ALR), a novel inflammatory biomarker. METHOD This study included 198 patients with mRCC from a single center from 2006 to 2022. The optimal cut-off levels for the three biomarkers were derived using the receiver operating characteristic curve (ROC). Cox univariate and multivariate analyses were used to assess independent prognostic inflammatory biomarkers. Finally, independent prognostic inflammatory biomarkers were incorporated into the prognostic model to establish a nomogram to predict the postoperative survival of patients with mRCC. RESULT The area under the ROC curve for NLR, LMR, and ALR, respectively, is 0.71 (CI: 0.635-0.784), 0.68 (CI: 0.604-0.755), and 0.75 (CI: 0.680-0.819). The optimal LMR, NLR, and ALR cut-off levels as evaluated by the ROC curve were 3.836, 3.106, and 68.056, respectively. Patients with NLR and ALR higher than the cut-off level and LMR lower than the cut-off level had a significant relationship with OS. Multivariate analysis revealed that tumor necrosis, lower LMR, and higher ALR were independent risk factors for OS. In addition, a nomogram that includes independent prognostic inflammatory biomarkers can accurately predict the OS in patients with mRCC. CONCLUSION ALR and LMR are independent risk factors for the prognosis of individuals with mRCC. By monitoring ALR and LMR postoperatively, the prognosis of patients with mRCC can be better evaluated.
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Affiliation(s)
- Jichen Wang
- Senior Department of Urology, the Third Medical Center of PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Jiali Ye
- Senior Department of Urology, the Third Medical Center of PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Xupeng Zhao
- Senior Department of Urology, the Third Medical Center of PLA General Hospital, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Xiubin Li
- Senior Department of Urology, the Third Medical Center of PLA General Hospital, Beijing, China.
| | - Xin Ma
- Senior Department of Urology, the Third Medical Center of PLA General Hospital, Beijing, China.
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15
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Lu Y, Yang H, Cao Y, Wang Y, Wu M, He B, Xu J, Su Z, Luo W, Liu Y, Hu W. A survival model for prognostic prediction based on ferroptosis-associated genes and the association with immune infiltration in lung squamous cell carcinoma. PLoS One 2023; 18:e0282888. [PMID: 36928232 PMCID: PMC10019706 DOI: 10.1371/journal.pone.0282888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 02/25/2023] [Indexed: 03/18/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is the primary pathological type of lung cancer with a less favorable prognosis. This study attempts to construct a ferroptosis-associated signature associated with overall survival (OS) that can predict the prognosis of LUSC and explore its relationship with immune infiltration. A 5 ferroptosis-associated gene model was constructed by LASSO-penalized regression analysis to predict the prognosis of patients with LUSC in the TCGA database and validated in the GEO and TCGA databases. Patients were stratified into high-risk and low-risk groups by the median value of the risk scores, and the former prognosis was significantly worse (P<0.001). Additionally, we found a certain association between the two risk groups and immune infiltration through CIBERSORT. Meanwhile, the differentially expressed genes (DEGs) between normal and tumor tissue were used to perform functional analysis, which showed a significant association with leukocyte transendothelial migration pathways in the TCGA cohort. In addition, immune cell infiltration analysis confirmed that M2 macrophages were significantly highly expressed in the high-risk group. Overall, the model successfully established by ferroptosis-associated genes suggests that ferroptosis may be related to immune infiltration in LUSC.
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Affiliation(s)
- Yanyi Lu
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Hua Yang
- Department of pathology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Yunliang Cao
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Yunan Wang
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Mengjia Wu
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Bo He
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Junzhu Xu
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Zixuan Su
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Wen Luo
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Yuyang Liu
- Department of pathology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
| | - Wei Hu
- Department of Thoracic Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi City, Guizhou Province, China
- * E-mail:
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16
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Xie T, Liu B, Liu D, Zhou Y, Yang Q, Wang D, Tang M, Liu W. Cuproptosis-related lncRNA signatures predict prognosis and immune relevance of kidney renal papillary cell carcinoma. Front Pharmacol 2022; 13:1103986. [PMID: 36618928 PMCID: PMC9810632 DOI: 10.3389/fphar.2022.1103986] [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: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Kidney renal papillary cell carcinoma (KIRP) has a high mortality rate and a poor prognosis. Cu concentrations differed significantly between renal cancer tissues and adjacent normal tissues. Cuproptosis is a newly identified cell death. Long non-coding RNAs (lncRNAs) play a crucial role in the progression of KIRP. In this study, we focused on constructing and validating cuproptosis-related lncRNA signatures to predict the prognosis of KIRP patients and their immune correlation. We created prognosis models using Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) algorithm. We found that patients in the high-risk group had poorer overall survival (OS) and progression-free survival (PFS) and higher mortality. Risk score and stage are prognosis factors independent of other clinical features. Kaplan-Meier analysis, receiver operating characteristic (ROC) curves, and C-index curves showed that cuproptosis-related lncRNA signatures could more accurately predict the prognosis of patients. Functional enrichment analysis suggests that the function of differentially expressed genes (DEGs) is associated with KIRP development and immunity. In immune-related function analysis, we found a significant difference in parainflammation responses between high-risk and low-risk groups. The mutation frequencies of TTN, MET, KMT2C, PKHD1, SETD2, and KMT2D genes in the high-risk group were higher than those in the low-risk group, but the mutation frequencies of MUC16, KIAA109, CUBN, USH2A, DNAH8 and HERC2 genes were significantly lower than those in the low-risk group. Survival analysis of tumor mutation burden (TMB) and combined TMB-risk showed better OS in patients with high TMB. Immune infiltration and immune checkpoint analysis assessed the immune association of six high mutation frequency genes (TTN, MET, KMT2C, PKHD1, SETD2, and KMT2D) with KIRP. Finally, we performed a drug sensitivity analysis and screened 15 potential drugs that differed between high-risk and low-risk patients. In this study, we constructed and validated cuproptosis-related lncRNA signatures that can more accurately predict the prognosis of KIRP patients and provide new potential therapeutic targets and prognosis markers for KIRP patients.
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Affiliation(s)
- Tongjin Xie
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Bin Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Dongbo Liu
- Department of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Yusong Zhou
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qingping Yang
- Department of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Dai Wang
- Xiangya School of Pharmacy, Central South University, Changsha, China
| | - Mengjie Tang
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Wei Liu
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Wei Liu,
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17
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Wan Y, He Y, Yang Q, Cheng Y, Li Y, Zhang X, Zhang W, Dai H, Yu Y, Li T, Xiong Z, Wan H. Construction of a prognostic assessment model for colon cancer patients based on immune-related genes and exploration of related immune characteristics. Front Cell Dev Biol 2022; 10:993580. [PMID: 36589748 PMCID: PMC9800979 DOI: 10.3389/fcell.2022.993580] [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: 07/13/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
Objectives: To establish a novel risk score model that could predict the survival and immune response of patients with colon cancer. Methods: We used The Cancer Genome Atlas (TCGA) database to get mRNA expression profile data, corresponding clinical information and somatic mutation data of patients with colon cancer. Limma R software package and univariate Cox regression were performed to screen out immune-related prognostic genes. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) were used for gene function enrichment analysis. The risk scoring model was established by Lasso regression and multivariate Cox regression. CIBERSORT was conducted to estimate 22 types of tumor-infiltrating immune cells and immune cell functions in tumors. Correlation analysis was used to demonstrate the relationship between the risk score and immune escape potential. Results: 679 immune-related genes were selected from 7846 differentially expressed genes (DEGs). GO and KEGG analysis found that immune-related DEGs were mainly enriched in immune response, complement activation, cytokine-cytokine receptor interaction and so on. Finally, we established a 3 immune-related genes risk scoring model, which was the accurate independent predictor of overall survival (OS) in colon cancer. Correlation analysis indicated that there were significant differences in T cell exclusion potential in low-risk and high-risk groups. Conclusion: The immune-related gene risk scoring model could contribute to predicting the clinical outcome of patients with colon cancer.
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Affiliation(s)
- Yanhua Wan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China,Department of General Surgery, The First People’s Hospital of Jiujiang, Jiujiang, China
| | - Yingcheng He
- Queen Mary College of Nanchang University, Nanchang, China
| | - Qijun Yang
- Queen Mary College of Nanchang University, Nanchang, China
| | - Yunqi Cheng
- Queen Mary College of Nanchang University, Nanchang, China
| | - Yuqiu Li
- Queen Mary College of Nanchang University, Nanchang, China
| | - Xue Zhang
- Queen Mary College of Nanchang University, Nanchang, China
| | - Wenyige Zhang
- Queen Mary College of Nanchang University, Nanchang, China
| | - Hua Dai
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yanqing Yu
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Taiyuan Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Taiyuan Li, ; Zhenfang Xiong, ; Hongping Wan,
| | - Zhenfang Xiong
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Taiyuan Li, ; Zhenfang Xiong, ; Hongping Wan,
| | - Hongping Wan
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Taiyuan Li, ; Zhenfang Xiong, ; Hongping Wan,
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18
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Zhou X, Zhang H, Duan Y, Zhu J, Dai H. m6A-related long noncoding RNAs predict prognosis and indicate therapeutic response in endometrial carcinoma. J Clin Lab Anal 2022; 37:e24813. [PMID: 36525280 PMCID: PMC9833960 DOI: 10.1002/jcla.24813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) has been identified as the most common, abundant, and conserved internal transcriptional modification. Long noncoding RNAs (lncRNAs) are noncoding RNAs consisting of more than 200 nucleotides, and the expression of various lncRNAs may affect cancer prognosis. The impact of m6A-associated lncRNAs on uterine corpus endometrial carcinoma (UCEC) prognosis is unknown. METHODS In this study, UCEC prognosis-related m6A lncRNAs were screened, bioinformatics analysis was performed, and experimental validation was conducted. Endometrial carcinoma (EC) and normal tissue samples were obtained from The Cancer Genome Atlas. The prognosis-related m6A lncRNAs screened by the least absolute shrinkage and selection operator method were used for multivariate Cox proportional risk regression modeling. Principal component analysis and Gene Ontology, immune function difference, and drug sensitivity analyses of the prognostic models were performed. Prognostic analysis was conducted for m6A-associated lncRNAs. The immune infiltration relationship of m6A-associated lncRNAs in EC was identified using the ssGSEA immune infiltration algorithm. A competing endogenouse RNA network was constructed using the LncACTdb database. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) assays were used to validate the differences in m6A-related lncRNA expression in normal and EC cells. RESULTS CDKN2B-AS1 and MIR924HG were found to be risk factors for EC. RAB11B-AS1 was a protective factor in EC patients. MIR924HG expression was upregulated in KLE and RL95-2 endometrial cancer cell lines. Prognostic models involved RAB11B-AS1, LINC01812, HM13-IT1, TPM1-AS, SLC16A1-AS1, LINC01936, and CDKN2B-AS1. The high-risk group was more sensitive to five compounds (ABT.263, ABT.888, AP.24534, ATRA, and AZD.0530) than the low-risk group. CONCLUSION These findings contribute to understanding of the function of m6A-related lncRNAs in UCEC and provide promising therapeutic strategies for UCEC.
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Affiliation(s)
- Xinying Zhou
- Department of Obstetrics and GynecologyShanghai Pudong Hospital, Fudan University Pudong Medical CenterShanghaiChina
| | - Hu Zhang
- Department of Obstetrics and GynecologyShanghai Pudong Hospital, Fudan University Pudong Medical CenterShanghaiChina
| | - Yingchun Duan
- Department of Obstetrics and GynecologyShanghai Pudong Hospital, Fudan University Pudong Medical CenterShanghaiChina
| | - Jianlong Zhu
- Department of Obstetrics and GynecologyShanghai Pudong Hospital, Fudan University Pudong Medical CenterShanghaiChina
| | - Haiyan Dai
- Department of Obstetrics and GynecologyShanghai Pudong Hospital, Fudan University Pudong Medical CenterShanghaiChina
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Liu T, Yuan Z, Wang H, Wang J, Xue L. Peroxisome-related genes in hepatocellular carcinoma correlated with tumor metabolism and overall survival. Clin Res Hepatol Gastroenterol 2022; 46:101835. [PMID: 34798303 DOI: 10.1016/j.clinre.2021.101835] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/30/2021] [Accepted: 11/10/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIM A prominent hallmark of tumors is aberrant lipid metabolism, and various peroxisome-related genes (PRGs) are associated with aberrant tumoral metabolic signaling. However, the influence of PRGs on the prognosis of hepatocellular carcinoma (HCC) patients remains debatable. Thus, the current study was designed to evaluate the effect of PRGs on HCC and construct a prognostic model for predicting survival. METHODS We initially acquired HCC-related gene expression profiles from the Cancer Genome Atlas and International Cancer Genome Consortium databases. We then utilized Cox analysis and Lasso regression to identify suitable PRGs for the risk model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to clarify the functional roles of PRGs. Single-sample gene set enrichment analysis (ssGSEA) was conducted to confirm the relationship between PRGs and immunity. RESULTS Four PRGs were correlated with HCC patient survival: 2 risk genes (MPV17, and ABCD1) and 2 protective genes (ACSL1 and ACSL6). We derived risk scores based on PRGs to construct a predictive model that could accurately predict overall survival (OS) among HCC patients. Furthermore, GO and KEGG analyses revealed that these PRGs were potentially involved in lipid metabolism and ferroptosis in HCC. Moreover, ssGSEA results demonstrated that high PRG scores were associated with immune suppressor activation, which caused the suppression of immune effectors (CD8+ T-cells, B cells, and NK cells) and the attenuation of the immune-mediated antitumor effect. CONCLUSION PRGs act as key regulators in tumorigenesis and tumor progression by affecting lipid synthesis and utilization, which we used to predict the outcome of HCC patients. Moreover, PRGs have been shown to promote tumoral immune resistance by serving as a vital bridge between metabolism and immunity. Thus, a personalized treatment approach targeting PRGs would clinically benefit patients by blocking the interaction between tumor metabolism and immunity.
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Affiliation(s)
- Tong Liu
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Haidian District, 49 Huayuan North Road, Beijing 100191, China
| | - Zhuhui Yuan
- Department of Radiation Oncology, Peking University Third Hospital, Haidian District, 49 Huayuan North Road, Beijing, China
| | - Hao Wang
- Department of Radiation Oncology, Peking University Third Hospital, Haidian District, 49 Huayuan North Road, Beijing, China
| | - Junjie Wang
- Department of Radiation Oncology, Peking University Third Hospital, Haidian District, 49 Huayuan North Road, Beijing, China.
| | - Lixiang Xue
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Haidian District, 49 Huayuan North Road, Beijing 100191, China; Biobank, Peking University Third Hospital, Haidian District, 49 Huayuan North Road, Beijing 100191, China.
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20
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Khan M, Lin J, Wang B, Chen C, Huang Z, Tian Y, Yuan Y, Bu J. A novel necroptosis-related gene index for predicting prognosis and a cold tumor immune microenvironment in stomach adenocarcinoma. Front Immunol 2022; 13:968165. [PMID: 36389725 PMCID: PMC9646549 DOI: 10.3389/fimmu.2022.968165] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/05/2022] [Indexed: 11/30/2022] Open
Abstract
Background Gastric cancer (GC) represents a major global clinical problem with very limited therapeutic options and poor prognosis. Necroptosis, a recently discovered inflammatory form of cell death, has been implicated in carcinogenesis and inducing necroptosis has also been considered as a therapeutic strategy. Objective We aim to evaluate the role of this pathway in gastric cancer development, prognosis and immune aspects of its tumor microenvironment. Methods and results In this study, we evaluated the gene expression of 55 necroptosis-related genes (NRGs) that were identified via carrying out a comprehensive review of the medical literature. Necroptosis pathway was deregulated in gastric cancer samples (n=375) as compared to adjacent normal tissues (n=32) obtained from the “The Cancer Genome Atlas (TCGA)”. Based on the expression of these NRGs, two molecular subtypes were obtained through consensus clustering that also showed significant prognostic difference. Differentially expressed genes between these two clusters were retrieved and subjected to prognostic evaluation via univariate cox regression analysis and LASSO cox regression analysis. A 13-gene risk signature, termed as necroptosis-related genes prognostic index (NRGPI), was constructed that comprehensively differentiated the gastric cancer patients into high- and low-risk subgroups. The prognostic significance of NRGPI was validated in the GEO cohort (GSE84437: n=408). The NRGPI-high subgroup was characterized by upregulation of 10 genes (CYTL1, PLCL1, CGB5, CNTN1, GRP, APOD, CST6, GPX3, FCN1, SERPINE1) and downregulation of 3 genes (EFNA3, E2F2, SOX14). Further dissection of these two risk groups by differential gene expression analysis indicated involvement of signaling pathways associated with cancer cell progression and immune suppression such as WNT and TGF-β signaling pathway. Para-inflammation and type-II interferon pathways were activated in NRGPI-high patients with an increased infiltration of Tregs and M2 macrophage indicating an exhausted immune phenotype of the tumor microenvironment. These molecular characteristics were mainly driven by the eight NRGPI oncogenes (CYTL1, PLCL1, CNTN1, GRP, APOD, GPX3, FCN1, SERPINE1) as validated in the gastric cancer cell lines and clinical samples. NRGPI-high patients showed sensitivity to a number of targeted agents, in particular, the tyrosine kinase inhibitors. Conclusions Necroptosis appears to play a critical role in the development of gastric cancer, prognosis and shaping of its tumor immune microenvironment. NRGPI can be used as a promising prognostic biomarker to identify gastric cancer patients with a cold tumor immune microenvironment and poor prognosis who may response to selected molecular targeted therapy.
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Affiliation(s)
- Muhammad Khan
- Department of Oncology, Guangdong Second Provincial General Hospital, Guangzhou, China
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jie Lin
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Baiyao Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Chengcong Chen
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Zhong Huang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yunhong Tian
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yawei Yuan
- Department of Oncology, Guangdong Second Provincial General Hospital, Guangzhou, China
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Junguo Bu, ; Yawei Yuan,
| | - Junguo Bu
- Department of Oncology, Guangdong Second Provincial General Hospital, Guangzhou, China
- *Correspondence: Junguo Bu, ; Yawei Yuan,
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Zhang Q, Ma L, Zhou H, Zhou Y, Liu S, Li Q. A prognostic signature of cuproptosis and TCA-related genes for hepatocellular carcinoma. Front Oncol 2022; 12:1040736. [PMID: 36324575 PMCID: PMC9619237 DOI: 10.3389/fonc.2022.1040736] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/03/2022] [Indexed: 11/26/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common malignant tumor of the liver. Cuproptosis is a newly defined form of cell death. Copper ion induces cell death by binding to the tricarboxylic acid cycle (TCA). The effect of cuproptosis-related and TCA-related genes on the clinical prognosis of HCC is still unclear. In this study, we explores the genetic changes of cuproptosis-related genes that affect the TCA process and their potential therapeutic value in HCC patients. Methods The cuproptosis and TCA-related genes were obtained from cuproptosis-related articles and the molecular signatures database. The prognosis signatures of eight related genes were constructed using the last absolute shrinkage and selection operator (LASSO), and Receiver Operating Characteristic (ROC) curves were used to evaluate the signature. In addition, we analyzed downstream functional enrichment and immune infiltration to explore cuproptosis-inducing drugs and immunotherapeutic responses. All these analyses were validated using multiple datasets of the International Cancer Genome Consortium (ICGC). Results TCA and copper malnutrition-related genes (CDKN2A, IDH1, OGDHL, IDH3G, IDH3B, GLS, DLAT, LIPT1) were finally included. According to the risk score, they were divided into high-risk and low-risk groups. Survival analysis showed that the overall survival (OS) of the high-risk group was significantly lower than that of the low-risk group. We established a risk prognostic feature to predict the OS of patients with HCC. Based on this feature and the clinical stage, we constructed a nomogram. Functional enrichment analysis revealed pathways related to organelle division and the cell cycle. Different risk scores had different immune abundances in immune cells (including macrophages and regulatory T-cells) and immune pathways (including antigen-presenting cells co-stimulation). Moreover, the drug sensitivity of eleschomol and PD-L1 in the high-risk group was better than that in the low-risk group. The status of TP53 somatic mutation was also closely related to the risk score. Conclusion In this study, we established a new prediction signature of eight genes related to cuproptosis and the TCA process, which can effectively predict the prognosis of HCC patients.
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22
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Cheng X, Deng W, Zhang Z, Zeng Z, Liu Y, Zhou X, Zhang C, Wang G. Novel amino acid metabolism‐related gene signature to predict prognosis in clear cell renal cell carcinoma. Front Genet 2022; 13:982162. [PMID: 36118874 PMCID: PMC9478740 DOI: 10.3389/fgene.2022.982162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Amino acid metabolism (AAM) deregulation, an emerging metabolic hallmark of malignancy, plays an essential role in tumour proliferation, invasion, and metastasis. However, the expression of AAM-related genes and their correlation with prognosis in clear cell renal cell carcinoma (ccRCC) remain elusive. This study aims to develop a novel consensus signature based on the AAM-related genes. Methods: The RNA-seq expression data and clinical information for ccRCC were downloaded from the TCGA (KIRC as training dataset) and ArrayExpress (E-MTAB-1980 as validation dataset) databases. The AAM‐related differentially expressed genes were screened via the “limma” package in TCGA cohorts for further analysis. The machine learning algorithms (Lasso and stepwise Cox (direction = both)) were then utilised to establish a novel consensus signature in TCGA cohorts, which was validated by the E-MTAB-1980 cohorts. The optimal cutoff value determined by the “survminer” package was used to categorise patients into two risk categories. The Kaplan-Meier curve, the receiver operating characteristic (ROC) curve, and multivariate Cox regression were utilised to evaluate the prognostic value. The nomogram based on the gene signature was constructed, and its performance was analysed using ROC and calibration curves. Gene Set Enrichment Analysis (GSEA) and immune cell infiltration analysis were conducted on its potential mechanisms. The relationship between the gene signature and key immune checkpoint, N6-methyladenosine (m6A)-related genes, and sensitivity to chemotherapy was assessed. Results: A novel consensus AMM‐related gene signature consisting of IYD, NNMT, ACADSB, GLDC, and PSAT1 is developed to predict prognosis in TCGA cohorts. Kaplan-Meier survival shows that overall survival in the high-risk group was more dismal than in the low-risk group in the TCGA cohort, validated by the E-MTAB-1980 cohort. Multivariate regression analysis also demonstrates that the gene signature is an independent predictor of ccRCC. Immune infiltration analysis highlighted that the high-risk group indicates an immunosuppressive microenvironment. It is also closely related to the level of key immune checkpoints, m6A modification, and sensitivity to chemotherapy drugs. Conclusion: In this study, a novel consensus AAM-related gene signature is developed and validated as an independent predictor to robustly predict the overall survival from ccRCC, which would further improve the clinical outcomes.
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Affiliation(s)
- Xiaofeng Cheng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Wen Deng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Zhicheng Zhang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Zhenhao Zeng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Yifu Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Xiaochen Zhou
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Gongxian Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
- *Correspondence: Gongxian Wang,
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Ferroptosis-Related lncRNA for the Establishment of Novel Prognostic Signature and Therapeutic Response Prediction to Endometrial Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2056913. [PMID: 35937391 PMCID: PMC9352484 DOI: 10.1155/2022/2056913] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/16/2022] [Accepted: 07/08/2022] [Indexed: 01/07/2023]
Abstract
Background Ferroptosis is a recently described form of intentional cellular damage that is iron-dependent and separate from apoptosis, cellular necrosis, and autophagy. It has been demonstrated to be adequately regulated by long noncoding RNAs (lncRNAs) in various cancers. However, the predictive profile of ferroptosis-related lncRNAs (FRLs) in endometrial carcinoma (EC) is unknown. Herein, FRLs associated with uterine corpus endometrial carcinoma (UCEC) prognosis were screened to predict treatment response in EC. Methods Samples of EC and adjacent normal tissues were obtained from The Cancer Genome Atlas (TCGA) dataset repository. Limma and survival packages in R software were used to screen FRLs associated with the prognosis of EC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) chord and circle plots of FRLs were also plotted. Next, FRLs screened by the least absolute shrinkage and selection operator (LASSO) method were applied to construct and validate a multivariate Cox proportional risk regression model. Nomogram plots were created to forecast the outcome of UCEC patients, and gene set enrichment analysis (GSEA), principal component analysis (PCA), and immunoassays were performed on the prognostic models. Finally, limma, ggpubr, pRRophetic, and ggplot2 programs were used for drug sensitivity analysis of the prognostic models. Results A signature based on nine FRLs (CFAP58-DT, LINC00443, EMSLR, HYI-AS1, ADIRF-AS1, LINC02474, CDKN2B-AS1, LINC01629, and LINC00942) was constructed. The developed FRL prognostic model effectively discriminated UCEC patients into low-risk and high-risk groups. Immunological checkpoints CD80 and CD40 were strongly expressed in the high-risk group. In addition, the nine FRLs were all more expressed in the high-risk group compared to the low-risk group. Conclusion These findings significantly contribute to the understanding of the function of FRLs in UCEC and provide promising therapeutic strategies for UCEC.
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24
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Tabibzadeh S. Repair, regeneration and rejuvenation require un-entangling pluripotency from senescence. Ageing Res Rev 2022; 80:101663. [PMID: 35690382 DOI: 10.1016/j.arr.2022.101663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/27/2022] [Accepted: 06/04/2022] [Indexed: 11/16/2022]
Abstract
There is a notion that pluripotency and senescence, represent two extremes of life of cells. Pluripotent cells display epigenetic youth, unlimited proliferative capacity and pluripotent differentiating potential whereas cells that reach the Hayflick limit, transit to senescence, undergo permanent inhibition of cell replication and create an aging tissue landscape. However, pluripotency and senescence appear to be intimately linked and are jointly generated in many different contexts such as during embryogenesis or formation of tissue spheroids, in stem cell niches, cancer, or by induction of a pluripotent state (induced pluripotency). Tissue damage and senescence provide signals that are critical to generation of a pluripotent state and, in turn, pluripotency, induces senescence. Thus, it follows, that precisely timed control of senescence is required for harnessing the full benefits of both senescence and its associated pluripotency during tissue regeneration or rejuvenation.
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Affiliation(s)
- Siamak Tabibzadeh
- Frontiers in Bioscience Research Institute in Aging and Cancer, 16471 Scientific Way, Irvine, CA 92618.
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25
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Dai L, Wang X, Bai T, Liu J, Chen B, Yang W. Cellular Senescence-Related Genes: Predicting Prognosis in Gastric Cancer. Front Genet 2022; 13:909546. [PMID: 35719376 PMCID: PMC9198368 DOI: 10.3389/fgene.2022.909546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Our study aimed to explore the effect of cellular senescence and to find potential therapeutic strategies for gastric cancer. Cellular senescence-related genes were acquired from the CellAge database, while gastric cancer data were obtained from GEO and TCGA databases. SMARCA4 had the highest mutation frequency (6%), and it was linked to higher overall survival (OS) and progression-free survival (PFS). The gastric cancer data in TCGA database served as a training set to construct a prognostic risk score signature, and GEO data were used as a testing set to validate the accuracy of the signature. Patients with the low-risk score group had a longer survival time, while the high-risk score group is the opposite. Patients with low-risk scores had higher immune infiltration and active immune-related pathways. The results of drug sensitivity analysis and the TIDE algorithm showed that the low-risk score group was more susceptible to chemotherapy and immunotherapy. Most patients with mutation genes had a lower risk score than the wild type. Therefore, the risk score signature with cellular senescence-related genes can predict gastric cancer prognosis and identify gastric cancer patients who are sensitive to chemotherapy and immunotherapy.
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RB1-Negative Retinal Organoids Display Proliferation of Cone Photoreceptors and Loss of Retinal Differentiation. Cancers (Basel) 2022; 14:cancers14092166. [PMID: 35565295 PMCID: PMC9105736 DOI: 10.3390/cancers14092166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 01/06/2023] Open
Abstract
Simple Summary Retinoblastoma is a tumor of the eye’s retina, which is the very specialized tissue responsible for vision. In 98% of cases, the tumor is caused by inactivation of the RB1 gene. Due to lack of material and models, the understanding of RB1 mutations in tumor development is still unsatisfactory. We aimed to establish a human laboratory model for retinoblastoma. While differentiating stem cells with a mutation in RB1 into retina, we observed reduced differentiation potential but enhanced proliferation—general hallmarks of tumor development. The gene expression signature in the model resembled that of tumor material. This approach now enables research on retinoblastoma and probably therapy in the correct tissue, the human retina. Abstract Retinoblastoma is a tumor of the eye in children under the age of five caused by biallelic inactivation of the RB1 tumor suppressor gene in maturing retinal cells. Cancer models are essential for understanding tumor development and in preclinical research. Because of the complex organization of the human retina, such models were challenging to develop for retinoblastoma. Here, we present an organoid model based on differentiation of human embryonic stem cells into neural retina after inactivation of RB1 by CRISPR/Cas9 mutagenesis. Wildtype and RB1 heterozygous mutant retinal organoids were indistinguishable with respect to morphology, temporal development of retinal cell types and global mRNA expression. However, loss of pRB resulted in spatially disorganized organoids and aberrant differentiation, indicated by disintegration of organoids beyond day 130 of differentiation and depletion of most retinal cell types. Only cone photoreceptors were abundant and continued to proliferate, supporting these as candidate cells-of-origin for retinoblastoma. Transcriptome analysis of RB1 knockout organoids and primary retinoblastoma revealed gain of a retinoblastoma expression signature in the organoids, characterized by upregulation of RBL1 (p107), MDM2, DEK, SYK and HELLS. In addition, genes related to immune response and extracellular matrix were specifically upregulated in RB1-negative organoids. In vitro retinal organoids therefore display some features associated with retinoblastoma and, so far, represent the only valid human cancer model for the development of this disease.
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Abt ER, Le TM, Dann AM, Capri JR, Poddar S, Lok V, Li L, Liang K, Creech AL, Rashid K, Kim W, Wu N, Cui J, Cho A, Lee HR, Rosser EW, Link JM, Czernin J, Wu TT, Damoiseaux R, Dawson DW, Donahue TR, Radu CG. Reprogramming of nucleotide metabolism by interferon confers dependence on the replication stress response pathway in pancreatic cancer cells. Cell Rep 2022; 38:110236. [PMID: 35021095 PMCID: PMC8893345 DOI: 10.1016/j.celrep.2021.110236] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/22/2021] [Accepted: 12/16/2021] [Indexed: 01/19/2023] Open
Abstract
We determine that type I interferon (IFN) response biomarkers are enriched in a subset of pancreatic ductal adenocarcinoma (PDAC) tumors; however, actionable vulnerabilities associated with IFN signaling have not been systematically defined. Integration of a phosphoproteomic analysis and a chemical genomics synergy screen reveals that IFN activates the replication stress response kinase ataxia telangiectasia and Rad3-related protein (ATR) in PDAC cells and sensitizes them to ATR inhibitors. IFN triggers cell-cycle arrest in S-phase, which is accompanied by nucleotide pool insufficiency and nucleoside efflux. In combination with IFN, ATR inhibitors induce lethal DNA damage and downregulate nucleotide biosynthesis. ATR inhibition limits the growth of PDAC tumors in which IFN signaling is driven by stimulator of interferon genes (STING). These results identify a cross talk between IFN, DNA replication stress response networks, and nucleotide metabolism while providing the rationale for targeted therapeutic interventions that leverage IFN signaling in tumors.
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Affiliation(s)
- Evan R Abt
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Thuc M Le
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Amanda M Dann
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Joseph R Capri
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Soumya Poddar
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Vincent Lok
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Luyi Li
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Keke Liang
- Department of General Surgery/Pancreatic and Thyroid Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Amanda L Creech
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Khalid Rashid
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Woosuk Kim
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Nanping Wu
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Jing Cui
- Department of Pancreatic Surgery, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Arthur Cho
- Department of Nuclear Medicine, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Hailey Rose Lee
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Ethan W Rosser
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Jason M Link
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Johannes Czernin
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA; California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA; Department of Bioengineering, Samueli School of Engineering, University of California Los Angeles, Los Angeles, CA, USA
| | - David W Dawson
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Timothy R Donahue
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Caius G Radu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Theranostics Division, University of California Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
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Chen X, Zhu Z, Li X, Yao X, Luo L. The Ferroptosis-Related Noncoding RNA Signature as a Novel Prognostic Biomarker in the Tumor Microenvironment, Immunotherapy, and Drug Screening of Gastric Adenocarcinoma. Front Oncol 2021; 11:778557. [PMID: 34790582 PMCID: PMC8591298 DOI: 10.3389/fonc.2021.778557] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 01/09/2023] Open
Abstract
Background Ferroptosis is a new type of cell death different from apoptosis, necrosis, autophagy, and pyroptosis. This study aimed to explore the relationship between ferroptosis-related noncoding RNA (ncRNA) and gastric adenocarcinoma with regard to immunity and prognosis. Methods Ferroptosis-related ncRNA expression profiles and clinical pathology and overall survival information were collected from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus database. The ferroptosis-related ncRNA signature was identified by Cox regression analysis and the least absolute shrinkage and selection operator analysis. The survival analysis, receiver operating characteristic (ROC) analysis, and decision curve analysis were adopted to evaluate the prognostic prediction performance of the signature. The correlation between risk and multiple clinical characteristics was analyzed using the chi-square test. The Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis were used for mining functions and pathways. The CIBERSORT, ssGSEA, and ESTIMATE algorithms were used to assess immune infiltration and the tumor microenvironment. The response of immunotherapy was predicted using the Submap algorithm, and the Connectivity Map and the ridge regression model were used to screen and evaluate drugs. Results A carcinogenic risk signature was constructed using five ferroptosis-related ncRNAs. It showed an extraordinary ability to predict the prognoses of patients with gastric adenocarcinoma [area under the ROC curve (AUC) after 6 years = 0.689; GSE84426, AUC after 6 years = 0.747]. The lower ferroptosis potential level and lower tumor mutation burden were related to the poor prognoses of patients. The high-risk group had more immune cell recruitment, and the overall effect of the anti-immune checkpoint immunotherapy was not as good as that of the low-risk group. The high- and low-risk groups were enriched in tumor- and immune-related pathways, respectively. The screened antitumor drugs, such as genistein, guanabenz, and betulinic acid, improved the survival of the patients. Conclusions The ferroptosis-related ncRNA signature is a potential carcinogenic prognostic biomarker of gastric adenocarcinoma.
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Affiliation(s)
- Xinming Chen
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Zheng Zhu
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Xiaoling Li
- Experimental Animal Center, Guangdong Medical University, Zhanjiang, China
| | - Xinyue Yao
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China.,The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
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Tumorigenic Aspects of MSC Senescence-Implication in Cancer Development and Therapy. J Pers Med 2021; 11:jpm11111133. [PMID: 34834485 PMCID: PMC8618265 DOI: 10.3390/jpm11111133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022] Open
Abstract
As an organism ages, many physiological processes change, including the immune system. This process, called immunosenescence, characterized by abnormal activation and imbalance of innate and adaptive immunity, leads to a state of chronic low-grade systemic inflammation, termed inflammaging. Aging and inflammaging are considered to be the root of many diseases of the elderly, as infections, autoimmune and chronic inflammatory diseases, degenerative diseases, and cancer. The role of mesenchymal stromal/stem cells (MSCs) in the inflammaging process and the age-related diseases is not completely established, although numerous features of aging MSCs, including altered immunomodulatory properties, impeded MSC niche supporting functions, and senescent MSC secretory repertoire are consistent with inflammaging development. Although senescence has its physiological function and can represent a mechanism of tumor prevention, in most cases it eventually transforms into a deleterious (para-)inflammatory process that promotes tumor growth. In this review we are going through current literature, trying to explore the role of senescent MSCs in making and/or sustaining a microenvironment permissive to tumor development and to analyze the therapeutic options that could target this process.
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30
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Weijiao Y, Fuchun L, Mengjie C, Xiaoqing Q, Hao L, Yuan L, Desheng Y. Immune infiltration and a ferroptosis-associated gene signature for predicting the prognosis of patients with endometrial cancer. Aging (Albany NY) 2021; 13:16713-16732. [PMID: 34170849 PMCID: PMC8266342 DOI: 10.18632/aging.203190] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/04/2021] [Indexed: 04/10/2023]
Abstract
Ferroptosis, a form of programmed cell death induced by excess iron-dependent lipid peroxidation product accumulation, plays a critical role in cancer. However, there are few reports about ferroptosis in endometrial cancer (EC). This article explores the relationship between ferroptosis-related gene (FRG) expression and prognosis in EC patients. One hundred thirty-five FRGs were obtained by mining the literature, retrieving GeneCards and analyzing 552 malignant uterine corpus endometrial carcinoma (UCEC) samples, which were randomly assigned to training and testing groups (1:1 ratio), and 23 normal samples from The Cancer Genome Atlas (TCGA). We established a signature using eight screened FRGs (MDM2, GPX4, PRKAA2, PRNP, SLC11A2, ATP5MC3, PHKG2 and ACO1) related to overall survival using LASSO regression analysis. The samples were divided into low- and high-risk subgroups according to the median risk score. Kaplan-Meier survival curves showed that the low-risk group had better OS. ROC curves showed that this signature performed well in predicting OS (1-, 2-, 3-, and 5-year AUCs of 0.676, 0.775, 0.797, and 0.826, respectively). We systematically analyzed the immune infiltrating profile in UCEC samples from TCGA. Overall, our study identified a novel prognostic signature of 8 FRGs that can potentially predict the prognosis of EC.
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Affiliation(s)
- Yin Weijiao
- Department of Gynecologic Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
- Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Medical College of Henan University of Science and Technology, Luoyang, PR China
| | - Liao Fuchun
- Department of Gynecologic Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Chen Mengjie
- Department of Gynecologic Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Qin Xiaoqing
- Department of Gynecologic Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Lai Hao
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Lin Yuan
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Yao Desheng
- Department of Gynecologic Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
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31
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Li S, Gao J, Xu Q, Zhang X, Huang M, Dai X, Huang K, Liu L. A Signature-Based Classification of Gastric Cancer That Stratifies Tumor Immunity and Predicts Responses to PD-1 Inhibitors. Front Immunol 2021; 12:693314. [PMID: 34177954 PMCID: PMC8232232 DOI: 10.3389/fimmu.2021.693314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 05/28/2021] [Indexed: 12/21/2022] Open
Abstract
Gastric cancer is a leading cause of cancer-related deaths with considerable heterogeneity among patients. Appropriate classifications are essential for prognosis prediction and individualized treatment. Although immunotherapy showed potential efficacy in a portion of patients with gastric cancer, few studies have tried to classify gastric cancer specifically based on immune signatures. In this study, we established a 3-subtype cluster with low (CLIM), medium (CMIM), and high (CHIM) enrichment of immune signatures based on immunogenomic profiling. We validated the classification in multiple independent datasets. The CHIM subtype exhibited a relatively better prognosis and showed features of “hot tumors”, including low tumor purity, high stromal components, overexpression of immune checkpoint molecules, and enriched tumor-infiltrated immune cells (activated T cells and macrophages). In addition, CHIM tumors were also characterized by frequent ARID1A mutation, rare TP53 mutation, hypermethylation status, and altered protein expression (HER2, β-catenin, Cyclin E1, PREX1, LCK, PD-L1, Transglutaminase, and cleaved Caspase 7). By Gene Set Variation Analysis, “TGFβ signaling pathway” and “GAP junction” were enriched in CLIM tumors and inversely correlated with CD8+ and CD4+ T cell infiltration. Of note, the CHIM patients showed a higher response rate to immunotherapy (44.4% vs. 11.1% and 16.7%) and a more prolonged progression-free survival (4.83 vs. 1.86 and 2.75 months) than CMIM and CLIM patients in a microsatellite-independent manner. In conclusion, the new immune signature-based subtypes have potential therapeutic and prognostic implications for gastric cancer management, especially immunotherapy.
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Affiliation(s)
- Song Li
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jing Gao
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qian Xu
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xue Zhang
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Miao Huang
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xin Dai
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Kai Huang
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lian Liu
- Department of Medical Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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Almasabi S, Ahmed AU, Boyd R, Williams BRG. A Potential Role for Integrin-Linked Kinase in Colorectal Cancer Growth and Progression via Regulating Senescence and Immunity. Front Genet 2021; 12:638558. [PMID: 34163519 PMCID: PMC8216764 DOI: 10.3389/fgene.2021.638558] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/08/2021] [Indexed: 01/10/2023] Open
Abstract
Integrin-linked kinase (ILK) has been implicated as a molecular driver and mediator in both inflammation and tumorigenesis of the colon. ILK functions as an adaptor and mediator protein linking the extracellular matrix with downstream signaling pathways. ILK is broadly expressed in many human tissues and cells. It is also overexpressed in many cancers, including colorectal cancer (CRC). Inflammation, as evidenced by inflammatory bowel disease (IBD), is one of the highest risk factors for initiating CRC. This has led to the hypothesis that targeting ILK therapeutically could have potential in CRC, as it regulates different cellular processes associated with CRC development and progression as well as inflammation in the colon. A number of studies have indicated an ILK function in senescence, a cellular process that arrests the cell cycle while maintaining active metabolism and transcription. Senescent cells produce different secretions collectively known as the senescence-associated secretory phenotype (SASP). The SASP secretions influence infiltration of different immune cells, either positively for clearing senescent cells or negatively for promoting tumor growth, reflecting the dual role of senescence in cancer. However, a role for ILK in senescence and immunity in CRC remains to be determined. In this review, we discuss the possible role for ILK in senescence and immunity, paying particular attention to the relevance of ILK in CRC. We also examine how activating Toll-like receptors (TLRs) and their agonists in CRC could trigger immune responses against cancer, as a combination therapy with ILK inhibition.
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Affiliation(s)
- Saleh Almasabi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Cartherics, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Clinical Laboratory Sciences, Applied Medical Sciences, Najran University, Najran, Saudi Arabia.,Department of Molecular and Translational Sciences, Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Afsar U Ahmed
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Richard Boyd
- Cartherics, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Bryan R G Williams
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
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Huang Y, Duanmu J, Liu Y, Yan M, Li T, Jiang Q. Analysis of multi-omics differences in left-side and right-side colon cancer. PeerJ 2021; 9:e11433. [PMID: 34026368 PMCID: PMC8123232 DOI: 10.7717/peerj.11433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/20/2021] [Indexed: 12/22/2022] Open
Abstract
Background Colon cancer is one of the most common tumors in the digestive tract. Studies of left-side colon cancer (LCC) and right-side colon cancer (RCC) show that these two subtypes have different prognoses, outcomes, and clinical responses to chemotherapy. Therefore, a better understanding of the importance of the clinical classifications of the anatomic subtypes of colon cancer is needed. Methods We collected colon cancer patients’ transcriptome data, clinical information, and somatic mutation data from the Cancer Genome Atlas (TCGA) database portal. The transcriptome data were taken from 390 colon cancer patients (172 LCC samples and 218 RCC samples); the somatic mutation data included 142 LCC samples and 187 RCC samples. We compared the expression and prognostic differences of LCC and RCC by conducting a multi-omics analysis of each using the clinical characteristics, immune microenvironment, transcriptomic differences, and mutation differences. The prognostic signatures was validated using the internal testing set, complete set, and external testing set (GSE39582). We also verified the independent prognostic value of the signature. Results The results of our clinical characteristic analysis showed that RCC had a significantly worse prognosis than LCC. The analysis of the immune microenvironment showed that immune infiltration was more common in RCC than LCC. The results of differential gene analysis showed that there were 360 differentially expressed genes, with 142 upregulated genes in LCC and 218 upregulated genes in RCC. The mutation frequency of RCC was generally higher than that of LCC. BRAF and KRAS gene mutations were the dominant genes mutations in RCC, and they had a strong mutual exclusion with APC, while APC gene mutation was the dominant gene mutation in LCC. This suggests that the molecular mechanisms of RCC and LCC differed. The 4-mRNA and 6-mRNA in the prognostic signatures of LCC and RCC, respectively, were highly predictive and may be used as independent prognostic factors. Conclusion The clinical classification of the anatomic subtypes of colon cancer is of great significance for early diagnosis and prognostic risk assessment. Our study provides directions for individualized treatment of left and right colon cancer.
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Affiliation(s)
- Yanyi Huang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Nanchang University, The Second Clinical Medicine College, Nanchang, Jiangxi, China
| | - Jinzhong Duanmu
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yushu Liu
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Nanchang University, The Second Clinical Medicine College, Nanchang, Jiangxi, China
| | - Mengyun Yan
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Nanchang University, The First Clinical Medicine College, Nanchang, Jiangxi, China
| | - Taiyuan Li
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qunguang Jiang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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He C, Hua X, Sun S, Li S, Wang J, Huang X. Integrated Bioinformatic Analysis of SARS-CoV-2 Infection Related Genes ACE2, BSG and TMPRSS2 in Aerodigestive Cancers. J Inflamm Res 2021; 14:791-802. [PMID: 33732005 PMCID: PMC7956868 DOI: 10.2147/jir.s300127] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/23/2021] [Indexed: 12/19/2022] Open
Abstract
Background Cancer patients are more vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than the general population, with lung epithelial cells or enterocytes being the main targets. However, the expressions of SARS-CoV-2 entry-related genes in aerodigestive cancers have not been fully elucidated. Methods In this study, the expressions of SARS-CoV-2 receptors and cofactors, including angiotensin I-converting enzyme 2 (ACE2), basigin (BSG) and transmembrane serine protease 2 (TMPRSS2), were comprehensively assessed. We compared BSG and TMPRSS2 expressions between aerodigestive cancers and matched normal tissues through Gene Expression Profiling Interactive Analysis 2 (GEPIA2). Furthermore, expressions in healthy colon tissues at different anatomical locations were explored using the Genotype-Tissue Expression (GTEx) dataset. In addition, expressions among different tumor stages and the prognostic values were detected through GEPIA2. Moreover, the correlation between gene expression and immune infiltration was explored via Tumor Immune Estimation Resource (TIMER). Finally, expressions in primary colorectal cancer (CRC), lung metastasis and liver metastasis were investigated using the Gene Expression Omnibus (GEO) dataset GSE41258. Results Similar to ACE2, TMPRSS2 and BSG were also highly expressed in the digestive tracts. Intriguingly, BSG/TMPRSS2 expression in adjacent normal colon tissue or lung tissue was higher than that in corresponding healthy tissue, whereas they varied not among different tumor stages and correlated not with prognosis in aerodigestive cancers. Moreover, ACE2 was expressed at higher levels in lung metastases from CRC than in normal lung tissues. Conclusion SARS-CoV-2 entry genes were highly expressed in CRC, and we reported for the first time higher expression of ACE2 in lung metastases from CRC than in normal lung, indicating that these patients may be more susceptible to extrapulmonary or pulmonary SARS-CoV-2 infection. Since our study is a bioinformatic analysis, further experimental evidences and clinical data are urgently needed.
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Affiliation(s)
- Chaobin He
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, People's Republic of China.,Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China.,Department of Pancreatobiliary Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Xin Hua
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, People's Republic of China.,Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China.,Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Shuxin Sun
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, People's Republic of China.,Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China.,Department of Pancreatobiliary Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Shaolong Li
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, People's Republic of China.,Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Jun Wang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, People's Republic of China.,Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China.,Department of Pancreatobiliary Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Xin Huang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, People's Republic of China.,Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China.,Department of Pancreatobiliary Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
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Cai L, Liu H, Huang F, Fujimoto J, Girard L, Chen J, Li Y, Zhang YA, Deb D, Stastny V, Pozo K, Kuo CS, Jia G, Yang C, Zou W, Alomar A, Huffman K, Papari-Zareei M, Yang L, Drapkin B, Akbay EA, Shames DS, Wistuba II, Wang T, Johnson JE, Xiao G, DeBerardinis RJ, Minna JD, Xie Y, Gazdar AF. Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. Commun Biol 2021; 4:314. [PMID: 33750914 PMCID: PMC7943563 DOI: 10.1038/s42003-021-01842-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
Small cell lung cancer (SCLC) is classified as a high-grade neuroendocrine (NE) tumor, but a subset of SCLC has been termed “variant” due to the loss of NE characteristics. In this study, we computed NE scores for patient-derived SCLC cell lines and xenografts, as well as human tumors. We aligned NE properties with transcription factor-defined molecular subtypes. Then we investigated the different immune phenotypes associated with high and low NE scores. We found repression of immune response genes as a shared feature between classic SCLC and pulmonary neuroendocrine cells of the healthy lung. With loss of NE fate, variant SCLC tumors regain cell-autonomous immune gene expression and exhibit higher tumor-immune interactions. Pan-cancer analysis revealed this NE lineage-specific immune phenotype in other cancers. Additionally, we observed MHC I re-expression in SCLC upon development of chemoresistance. These findings may help guide the design of treatment regimens in SCLC. Ling Cai et al. used transcriptomic profiling data of healthy lung, patient-derived small cell lung cancer cell lines, xenografts, and primary tumors to examine a link between neuroendocrine (NE) signatures and immune gene expression. Their findings suggest that cell-autonomous immune gene repression is a shared feature between healthy and tumor cells of NE lineage and may influence tumor-immune cell interaction and response to immunotherapy.
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Affiliation(s)
- Ling Cai
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA. .,Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA. .,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Hongyu Liu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Fang Huang
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luc Girard
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jun Chen
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China.,Department of Lung Cancer Surgery, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yongwen Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yu-An Zhang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Dhruba Deb
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Victor Stastny
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Karine Pozo
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christin S Kuo
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Gaoxiang Jia
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chendong Yang
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wei Zou
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Adeeb Alomar
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kenneth Huffman
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mahboubeh Papari-Zareei
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lin Yang
- Department of Pathology, National Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Benjamin Drapkin
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Esra A Akbay
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - David S Shames
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jane E Johnson
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ralph J DeBerardinis
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - John D Minna
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA. .,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA. .,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Adi F Gazdar
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
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Li MX, Wang HY, Yuan CH, Ma ZL, Jiang B, Li L, Zhang L, Xiu DR. Establishment of a Macrophage Phenotypic Switch Related Prognostic Signature in Patients With Pancreatic Cancer. Front Oncol 2021; 11:619517. [PMID: 33747931 PMCID: PMC7966706 DOI: 10.3389/fonc.2021.619517] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
Introduction Macrophage phenotype switch plays a vital role in the progression of malignancies. We aimed to build a prognostic signature by exploring the expression pattern of macrophage phenotypic switch related genes (MRGs) in the Cancer Genome Atlas (TCGA)—pancreatic adenocarcinoma (PAAD), Genotype-Tissue Expression (GTEx)-Pancreas, and Gene Expression Omnibus (GEO) databases. Methods We identified the differentially expressed genes between the PAAD and normal tissues. We used single factor Cox proportional risk regression analysis, Least Absolute Shrinkage and Selection Operator (LASSO) analysis, and multivariate Cox proportional hazard regression analysis to establish the prognosis risk score by the MRGs. The relationships between the risk score and immune landscape, “key driver” mutations and clinicopathological factors were also analyzed. Gene-set enrichment analysis (GSEA) analysis was also performed. Results We detected 198 differentially expressed MRGs. The risk score was constructed based on 9 genes (KIF23, BIN1, LAPTM4A, ERAP2, ATP8B2, FAM118A, RGS16, ELMO1, RAPGEFL1). The median overall survival time of patients in the low-risk group was significantly longer than that of patients in the high-risk group (P < 0.001). The prognostic value of the risk score was validated in GSE62452 dataset. The prognostic performance of nomogram based on risk score was superior to that of TNM stage. And GSEA analysis also showed that the risk score was closely related with P53 signaling pathway, pancreatic cancer and T cell receptor signaling pathway. qRT-PCR assay showed that the expressions of the 9 MRGs in PDAC cell lines were higher than those in human pancreatic ductal epithelium cell line. Conclusions The nine gene risk score could be used as an independent prognostic index for PAAD patients. Further studies validating the prognostic value of the risk score are warranted.
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Affiliation(s)
- Mu-Xing Li
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Hang-Yan Wang
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Chun-Hui Yuan
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Zhao-Lai Ma
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Bin Jiang
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Lei Li
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Li Zhang
- Department of General Surgery, Peking University Third Hospital, Beijing, China
| | - Dian-Rong Xiu
- Department of General Surgery, Peking University Third Hospital, Beijing, China
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Wang Y, Qiu L, Chen Y, Zhang X, Yang P, Xu F. Screening and Identification of Four Prognostic Genes Related to Immune Infiltration and G-Protein Coupled Receptors Pathway in Lung Adenocarcinoma. Front Oncol 2021; 10:622251. [PMID: 33628734 PMCID: PMC7897677 DOI: 10.3389/fonc.2020.622251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a common malignant tumor with the highest morbidity and mortality worldwide. The degree of tumor immune infiltration and clinical prognosis depend on immune-related genes, but their interaction with the tumor immune microenvironment, the specific mechanism driving immune infiltration and their prognostic value are still not very clear. Therefore, the aim of this work was focused on the elucidation of these unclear aspects. Methods TCGA LUAD samples were divided into three immune infiltration subtypes according to the single sample gene set enrichment analysis (ssGSEA), in which the associated gene modules and hub genes were screened by weighted correlation network analysis (WGCNA). Four key genes related to immune infiltration were found and screened by differential expression analysis, univariate prognostic analysis, and Lasso-COX regression, and their PPI network was constructed. Finally, a Nomogram model based on the four genes and tumor stages was constructed and confirmed in two GEO data sets. Results Among the three subtypes—high, medium, and low immune infiltration subtype—the survival rate of the patients in the high one was higher than the rate in the other two subtypes. The four key genes related to LUAD immune infiltration subtypes were CD69, KLRB1, PLCB2, and P2RY13. The PPI network revealed that the downstream genes of the G-protein coupled receptors (GPCRs) pathway were activated by these four genes through the S1PR1. The risk score signature based on these four genes could distinguish high and low-risk LUAD patients with different prognosis. The Nomogram constructed by risk score and clinical tumor stage showed a good ability to predict the survival rate of LUAD patients. The universality and robustness of the Nomogram was confirmed by two GEO datasets. Conclusions The prognosis of LUAD patients could be predicted by the constructed risk score signature based on the four genes, making this score a potential independent biomarker. The screening, identification, and analysis of these four genes could contribute to the understanding of GPCRs and LUAD immune infiltration, thus guiding the formulation of more effective immunotherapeutic strategies.
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Affiliation(s)
- Yan Wang
- Department of Emergency Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Emergency Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Liwei Qiu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yu Chen
- Department of Emergency Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xia Zhang
- Department of Emergency Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Peng Yang
- Department of Emergency Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Feng Xu
- Department of Emergency Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
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38
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Ahn S, Kim GJ, Do SI, Kim K, Lee H, Do IG, Kim DH, Chae SW, Ryu S, Sohn JH. High-sensitivity C-reactive Protein and Regression of Low-grade Squamous Intraepithelial Lesion: The Role of Low-grade Inflammation in Cervical Carcinogenesis. J Epidemiol 2021; 31:615-620. [PMID: 33536377 PMCID: PMC8593578 DOI: 10.2188/jea.je20200142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Background Inflammation is emerging as a potential mechanism of cervical carcinogenesis. However, few studies have investigated the association between host inflammatory status and the natural course of cervical precursor lesion. The aim of this study was to assess the probability of LSIL regression, associated with an inflammatory biomarker, high-sensitivity C-reactive protein (hs-CRP). Methods In a longitudinal cohort study, female participants were examined annually or biannually using cervical cytology between 2006 and 2015. Incident LSIL cases were included in the analysis, with regression defined as at least one consecutive normal cytologic result. A total of 520 women aged 22–64 years were followed up for LSIL regression. The multivariable-adjusted hazard ratios (HRs) for LSIL regression were estimated using a parametric proportional hazards model. Results During 827.5 person-years of follow-up, 486 out of 520 subjects (93.5%) showed LSIL regression. After adjusting several important potential confounders, a higher quartile of hs-CRP levels was significantly associated with a lower rate of regression (for quartile 4 vs quartile 1, inverse HR 1.33; 95% CI, 1.04–1.69; P for trend = 0.028). Conclusions The low rate of spontaneous regression recorded in women with higher hs-CRP lends support to the role of the perturbated host inflammatory status in cervical carcinogenesis, and suggests that hs-CRP level could help monitor LSIL.
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Affiliation(s)
- Sangjeong Ahn
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - Gi Jeong Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - Sung-Im Do
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - Kyungeun Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - Hyunjoo Lee
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - In-Gu Do
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - Dong-Hoon Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - Seoung Wan Chae
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
| | - Seungho Ryu
- Department of Occupational and Environmental Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine.,Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University, School of Medicine.,Department of Clinical Research Design & Evaluation, SAIHST, Sungkyunkwan University
| | - Jin Hee Sohn
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
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Fu X, Wang X, Duanmu J, Li T, Jiang Q. KRAS mutations are negatively correlated with immunity in colon cancer. Aging (Albany NY) 2020; 13:750-768. [PMID: 33254149 PMCID: PMC7834984 DOI: 10.18632/aging.202182] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
The heterogeneity of colon cancer tumors suggests that therapeutics targeting specific molecules may be effective in only a few patients. It is therefore necessary to explore gene mutations in colon cancer. In this study, we obtained colon cancer samples from The Cancer Genome Atlas, and the International Cancer Genome Consortium. We evaluated the landscape of somatic mutations in colon cancer and found that KRAS mutations, particularly rs121913529, were frequent and had prognostic value. Using ESTIMATE analysis, we observed that the KRAS-mutated group had higher tumor purity, lower immune score, and lower stromal score than the wild-type group. Through single-sample Gene Set Enrichment Analysis and Gene Set Enrichment Analysis, we found that KRAS mutations negatively correlated with enrichment levels of tumor infiltrating lymphocytes, inflammation, and cytolytic activities. HLA gene expression and checkpoint-related genes were also lower in the KRAS-mutated group. Finally, we found 24 immune-related genes that differed in expression between the KRAS-mutated and wild-type samples, which may provide clues to the mechanism of KRAS-related immune alteration. Our findings are indicative of the prognostic and predictive value of KRAS and illustrate the relationship between KRAS mutations and immune activity in colon cancer.
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Affiliation(s)
- Xiaorui Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
- Queen Mary College, Medical Department, Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xinyi Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
- Queen Mary College, Medical Department, Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Jinzhong Duanmu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Taiyuan Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Qunguang Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
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Hurvitz SA, Caswell-Jin JL, McNamara KL, Zoeller JJ, Bean GR, Dichmann R, Perez A, Patel R, Zehngebot L, Allen H, Bosserman L, DiCarlo B, Kennedy A, Giuliano A, Calfa C, Molthrop D, Mani A, Chen HW, Dering J, Adams B, Kotler E, Press MF, Brugge JS, Curtis C, Slamon DJ. Pathologic and molecular responses to neoadjuvant trastuzumab and/or lapatinib from a phase II randomized trial in HER2-positive breast cancer (TRIO-US B07). Nat Commun 2020; 11:5824. [PMID: 33203854 PMCID: PMC7673127 DOI: 10.1038/s41467-020-19494-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
In this multicenter, open-label, randomized phase II investigator-sponsored neoadjuvant trial with funding provided by Sanofi and GlaxoSmithKline (TRIO-US B07, Clinical Trials NCT00769470), participants with early-stage HER2-positive breast cancer (N = 128) were recruited from 13 United States oncology centers throughout the Translational Research in Oncology network. Participants were randomized to receive trastuzumab (T; N = 34), lapatinib (L; N = 36), or both (TL; N = 58) as HER2-targeted therapy, with each participant given one cycle of this designated anti-HER2 therapy alone followed by six cycles of standard combination chemotherapy with the same anti-HER2 therapy. The primary objective was to estimate the rate of pathologic complete response (pCR) at the time of surgery in each of the three arms. In the intent-to-treat population, we observed similar pCR rates between T (47%, 95% confidence interval [CI] 30-65%) and TL (52%, 95% CI 38-65%), and a lower pCR rate with L (25%, 95% CI 13-43%). In the T arm, 100% of participants completed all protocol-specified treatment prior to surgery, as compared to 69% in the L arm and 74% in the TL arm. Tumor or tumor bed tissue was collected whenever possible pre-treatment (N = 110), after one cycle of HER2-targeted therapy alone (N = 89), and at time of surgery (N = 59). Higher-level amplification of HER2 and hormone receptor (HR)-negative status were associated with a higher pCR rate. Large shifts in the tumor, immune, and stromal gene expression occurred after one cycle of HER2-targeted therapy. In contrast to pCR rates, the L-containing arms exhibited greater proliferation reduction than T at this timepoint. Immune expression signatures increased in all arms after one cycle of HER2-targeted therapy, decreasing again by the time of surgery. Our results inform approaches to early assessment of sensitivity to anti-HER2 therapy and shed light on the role of the immune microenvironment in response to HER2-targeted agents.
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Affiliation(s)
- Sara A Hurvitz
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Jennifer L Caswell-Jin
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine L McNamara
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jason J Zoeller
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Gregory R Bean
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Alejandra Perez
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Lee Zehngebot
- Florida Cancer Specialists & Research Institute, Orlando, FL, USA
| | - Heather Allen
- Comprehensive Cancer Centers of Nevada, Las Vegas, NV, USA
| | | | - Brian DiCarlo
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Carmen Calfa
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Molthrop
- Florida Cancer Specialists & Research Institute, Orlando, FL, USA
| | | | - Hsiao-Wang Chen
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Judy Dering
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Brad Adams
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Eran Kotler
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
| | - Dennis J Slamon
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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Wang X, Duanmu J, Fu X, Li T, Jiang Q. Analyzing and validating the prognostic value and mechanism of colon cancer immune microenvironment. J Transl Med 2020; 18:324. [PMID: 32859214 PMCID: PMC7456375 DOI: 10.1186/s12967-020-02491-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/20/2020] [Indexed: 02/08/2023] Open
Abstract
Background Colon cancer is a disease with high malignancy and incidence in the world. Tumor immune microenvironment (TIM) and tumor mutational burden (TMB) have been proved to play crucial roles in predicting clinical outcomes and therapeutic efficacy, but the correlation between them and the underlying mechanism were not completely understood in colon cancer. Methods In this study, we used Single-Sample Gene Set Enrichment Analysis (ssGSEA) and unsupervised consensus clustering analysis to divide patients from the TCGA cohort into three immune subgroups. Then we validated their differences in immune cell infiltration, overall survival outcomes, clinical phenotypes and expression levels of HLA and checkpoint genes by Mann–Whitney tests. We performed weighted correlation network analysis (WGCNA) to obtain immunity-related module and hub genes. Then we explored the underlying mechanism of hub genes by gene set enrichment analysis (GSEA) and gene set evaluation analysis (GSVA). Finally, we gave an overall view of gene variants and verified the correlation between TIM and TMB by comparing microsatellite instability (MSI) and gene mutations among three immune subgroups. Results The colon cancer patients were clustered into low immunity, median immunity and high immunity groups. The median immunity group had a favorable survival probability compared with that of the low and high immunity groups. Three groups had significant differences in immune cell infiltration, tumor stage, living state and T classification. We got 8 hub genes (CCDC69, CLMP, FAM110B, FAM129A, GUCY1B3, PALLD, PLEKHO1 and STY11) and predicted that immunity may correlated with inflammatory response, KRAS signaling pathway and T cell infiltration. With higher immunity, the TMB was higher. The most frequent mutations in low and median immunity groups were APC, TP53 and KRAS, while TTN and MUC16 showed higher mutational frequency in high immunity group. Conclusions We performed a comprehensive evaluation of the immune microenvironment landscape of colon cancer and demonstrated the positive correlation between immunity and TMB. The hub genes and frequently mutated genes were strongly related to immunity and may give suggestion for immunotherapy in the future.
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Affiliation(s)
- Xinyi Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China.,Queen Mary college, Medical Department, Nanchang University, Nanchang, Jiangxi, China
| | - Jinzhong Duanmu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xiaorui Fu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China.,Queen Mary college, Medical Department, Nanchang University, Nanchang, Jiangxi, China
| | - Taiyuan Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Qunguang Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China.
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Huang X, He C, Hua X, Kan A, Sun S, Wang J, Li S. Bioinformatic Analysis of Correlation between Immune Infiltration and COVID-19 in Cancer Patients. Int J Biol Sci 2020; 16:2464-2476. [PMID: 32760213 PMCID: PMC7378636 DOI: 10.7150/ijbs.48639] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 06/20/2020] [Indexed: 01/08/2023] Open
Abstract
In 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused infections worldwide. However, the correlation between the immune infiltration and coronavirus disease 2019 (COVID-19) susceptibility or severity in cancer patients remains to be fully elucidated. ACE2 expressions in normal tissues, cancers and cell lines were comprehensively assessed. Furthermore, we compared ACE2 expression between cancers and matched normal tissues through Gene Expression Profiling Interactive Analysis (GEPIA). In addition, we performed gene set enrichment analysis (GSEA) to investigate the related signaling pathways. Finally, the correlations between ACE2 expression and immune infiltration were investigated via Tumor Immune Estimation Resource (TIMER) and GEPIA. We found that ACE2 was predominantly expressed in both adult and fetal tissues from the digestive, urinary and male reproductive tracts; moreover, ACE2 expressions in corresponding cancers were generally higher than that in matched healthy tissues. GSEA showed that various metabolic and immune-related pathways were significantly associated with ACE2 expression across multiple cancer types. Intriguingly, we found that ACE2 expression correlated significantly with immune cell infiltration in both normal and cancer tissues, especially in the stomach and colon. These findings proposed a possible fecal-oral and maternal-fetal transmission of SARS-CoV-2 and suggested that cancers of the respiratory, digestive or urinary tracts would be more vulnerable to SARS-CoV-2 infection.
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Affiliation(s)
- Xin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Chaobin He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xin Hua
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Anna Kan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Hepatic Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shuxin Sun
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jun Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shengping Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Pancreatobiliary Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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Breast Heterogeneity: Obstacles to Developing Universal Biomarkers of Breast Cancer Initiation and Progression. J Am Coll Surg 2020; 231:85-96. [PMID: 32311464 DOI: 10.1016/j.jamcollsurg.2020.03.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Predicting outcomes and response to therapy through biomarkers is a major challenge in cancer research. In previous studies, we suggested that inappropriate "normal" tissue samples used for comparison with tumors, inter-individual heterogeneity in gene expression, and genetic ancestry all influence biomarker expression in tumors. The aim of this study was to investigate these factors in breast cancer using breast tissues from healthy women and normal tissue adjacent to tumor (NAT) with matrix metalloproteinase 7 (MMP7) as a candidate biomarker. STUDY DESIGN RNA sequencing was performed on primary luminal progenitor cells from healthy breast, NATs, and tumors to identify transcriptomes enriched in NATs and breast cancer. Expression of select genes was validated via quantitative reverse transcription polymerase chain reaction of RNA and via immunohistochemistry of a tissue microarray of normal, NAT, and tumor samples of different genetic ancestry. RESULTS Twenty-six genes were significantly overexpressed in NATs and tumors compared with healthy controls at messenger RNA level and formed a para-inflammatory network. MMP7 had the greatest expression in tumor cells, with upregulation confirmed by quantitative reverse transcription polymerase chain reaction. Tumor-enriched but not NAT-enriched expression of MMP7 compared with healthy controls was reproduced at protein levels. When stratified by genetic ancestry, tumor-specific increase of MMP7 reached statistical significance in women of European ancestry. CONCLUSIONS Transcriptome differences across healthy, NAT, and tumor tissue in breast cancer demonstrate an active para-inflammatory network in NATs and indicate unsuitability of NATs as "normal controls" in biomarker discovery. The discordance between transcriptomic and proteomic MMP7 expression in NATs and the influence of genetic ancestry on its protein expression highlight the complexity in developing universally acceptable biomarkers of breast cancer and the importance of genetic ancestry in biomarker development.
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In silico analyses of the tumor microenvironment highlight tumoral inflammation, a Th2 cytokine shift and a mesenchymal stem cell-like phenotype in advanced in basal cell carcinomas. J Cell Commun Signal 2020; 14:245-254. [PMID: 32198729 DOI: 10.1007/s12079-020-00563-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Basal Cell Carcinoma (BCC) represents the most common form of all cancers. BCC is characteristically surrounded by a fibromyxoid stroma. Previous studies have suggested a shift towards a Th2 response, an increase in T regulatory lymphocytes and the presence of cancer-associated fibroblasts in the BCC tumor microenvironment. In this study, we aimed to further characterize the BCC tumor microenvironment in detail by analyzing BCC RNA-Sequencing data and correlating it with clinically-relevant features via in silico RNA deconvolution. Using immune cell type deconvolution by CIBERSORT, we have identified a brisk lymphocytic infiltration, and more abundant macrophages in BCC tumors compared to normal skin. Using cell type enrichment by xCell, we confirmed the observed immune infiltration in BCC tumors and compared them to normal skin. We observed a shift towards Th2 immunity in advanced and vismodegib-resistant tumors. Tumoral inflammation induced by macrophage activity was associated with advanced BCCs, while lymphocytic infiltration was most significant in non-advanced tumors, likely related to an adaptive anti-tumoral response. In advanced and vismodegib-resistant BCCs, mesenchymal stem cell-like properties were observed. Particularly in vismodegib-resistant BCCs, fibroblasts and adipocytes were found at high number, which ultimately may contribute to the decreased drug delivery to the tumor. In conclusion, this study has revealed notable BCC tumor microenvironment findings associated with important clinical features. Microenvironment-altering agents may be used locally for "routine" BCCs and systematically for advanced or resistant BCCs.
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Greten FR, Grivennikov SI. Inflammation and Cancer: Triggers, Mechanisms, and Consequences. Immunity 2019; 51:27-41. [PMID: 31315034 DOI: 10.1016/j.immuni.2019.06.025] [Citation(s) in RCA: 1913] [Impact Index Per Article: 382.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023]
Abstract
Inflammation predisposes to the development of cancer and promotes all stages of tumorigenesis. Cancer cells, as well as surrounding stromal and inflammatory cells, engage in well-orchestrated reciprocal interactions to form an inflammatory tumor microenvironment (TME). Cells within the TME are highly plastic, continuously changing their phenotypic and functional characteristics. Here, we review the origins of inflammation in tumors, and the mechanisms whereby inflammation drives tumor initiation, growth, progression, and metastasis. We discuss how tumor-promoting inflammation closely resembles inflammatory processes typically found during development, immunity, maintenance of tissue homeostasis, or tissue repair and illuminate the distinctions between tissue-protective and pro-tumorigenic inflammation, including spatiotemporal considerations. Defining the cornerstone rules of engagement governing molecular and cellular mechanisms of tumor-promoting inflammation will be essential for further development of anti-cancer therapies.
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Affiliation(s)
- Florian R Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, 60596 Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Sergei I Grivennikov
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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Zhang Y, Sun C, Song EJ, Liang M, Shi T, Min M, Sun Y. Is periodontitis a risk indicator for gastrointestinal cancers? A meta‐analysis of cohort studies. J Clin Periodontol 2019; 47:134-147. [DOI: 10.1111/jcpe.13217] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 09/26/2019] [Accepted: 10/30/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Yun Zhang
- Department of Epidemiology and Health Statistics School of Public Health Anhui Medical University Hefei China
| | - Chenyu Sun
- AMITA Health Saint Joseph Hospital Chicago Chicago IL USA
| | - Evelyn J. Song
- Department of Medicine Johns Hopkins University School of Medicine Baltimore MD USA
| | - Mingming Liang
- Department of Epidemiology and Health Statistics School of Public Health Anhui Medical University Hefei China
| | - Tingting Shi
- Department of Epidemiology and Health Statistics School of Public Health Anhui Medical University Hefei China
| | - Min Min
- Department of Epidemiology and Health Statistics School of Public Health Anhui Medical University Hefei China
| | - Yehuan Sun
- Department of Epidemiology and Health Statistics School of Public Health Anhui Medical University Hefei China
- Center for Evidence‐Based Practice Anhui Medical University Hefei China
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Calibrated interdental brushing for the prevention of periodontal pathogens infection in young adults - a randomized controlled clinical trial. Sci Rep 2019; 9:15127. [PMID: 31641199 PMCID: PMC6805917 DOI: 10.1038/s41598-019-51938-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/10/2019] [Indexed: 12/29/2022] Open
Abstract
Periodontal disease is clearly correlated with systemic disease. The presence of periodontal pathogens in interdental spaces in young, healthy adults is a strong indicator of the need to introduce daily interdental prophylaxis. Twenty-five subjects (aged 18–35 years), diagnosticated clinically as periodontally healthy, were enrolled in this study. One hundred interdental sites were included. Among these sites, 50 “test” sites were cleaned daily with calibrated interdental brushes (IDBs), whereas the other 50 sites were not cleaned and considered “controls”. The interdental biofilm at these interdental sites was collected at the beginning of the study (basal) and at 1 week, 2 weeks, 3 weeks, 4 weeks, and 3 months. Real-time polymerase chain reaction (PCR) methodology was used to quantify (i) 19 periodontal bacteria, including Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, and (ii) total bacteria. In the test sites, the quantity of total bacteria decreased over time with the use of IDBs. The bacteria from the red and orange Socransky complexes, which are associated with periodontal disease, significantly decreased in the test sites but not in the control sites. Bacteria from the yellow, and purple Socransky complexes, which are associated with periodontal health, increased significantly in both groups whereas bacteria from the blue Socransky complex increased significantly only in the test sites. Furthermore, at basal, 66% of test sites and 68% of control sites bled during interdental brushing. These percentages decreased by 85% in 3 months for the test sites and by 27% in the control sites. In conclusion, the daily use of calibrated IDBs can reduce periodontal pathogens, reestablish symbiotic microbiota and, decrease interdental inflammation in interdental sites of healthy young adults.
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TP53 Mutations Promote Immunogenic Activity in Breast Cancer. JOURNAL OF ONCOLOGY 2019; 2019:5952836. [PMID: 31275382 PMCID: PMC6582869 DOI: 10.1155/2019/5952836] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 03/14/2019] [Accepted: 04/15/2019] [Indexed: 12/25/2022]
Abstract
Background Although immunotherapy has recently achieved clinical successes in a variety of cancers, thus far there is no immunotherapeutic strategy for breast cancer (BC). Thus, it is important to discover biomarkers for identifying BC patients responsive to immunotherapy. TP53 mutations were often associated with worse clinical outcomes in BC whose triple-negative subtype has a high TP53 mutation rate (approximately 80%). To explore a potentially promising therapeutic option for the TP53-mutated BC subtype, we studied the association between TP53 mutations and immunogenic activity in BC. Methods We compared the enrichment levels of 26 immune signatures that indicated activities of diverse immune cells, functions, and pathways between TP53-mutated and TP53-wildtype BCs based on two large-scale BC multiomics datasets. Moreover, we explored the molecular cues associated with the differences in immunogenic activity between TP53-mutated and TP53-wildtype BCs. Furthermore, we performed experimental validation of the findings from bioinformatics analysis. Results Bioinformatics analysis showed that almost all analyzed immune signatures showed significantly higher enrichment levels in TP53-mutated BCs than in TP53-wildtype BCs. Moreover, in vitro experiments confirmed that mutant p53 could increase BC immunogenicity. Both computational and experimental results demonstrated that TP53 mutations could promote BC immunogenicity via regulation of the p53-mediated pathways including cell cycle, apoptosis, Wnt, Jak-STAT, NOD-like receptor, and glycolysis. Furthermore, we found that elevated immune activity was likely associated with a better survival prognosis in TP53-mutated BCs, but not necessarily in TP53-wildtype BCs. Conclusions TP53 mutations may promote immunogenic activity in BC, suggesting that the TP53 mutation status could be a useful biomarker for stratifying BC patients responsive to immunotherapy.
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Todoric J, Karin M. The Fire within: Cell-Autonomous Mechanisms in Inflammation-Driven Cancer. Cancer Cell 2019; 35:714-720. [PMID: 31085174 DOI: 10.1016/j.ccell.2019.04.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/24/2019] [Accepted: 04/04/2019] [Indexed: 02/07/2023]
Abstract
Inflammatory cells are important for tumor initiation and promotion, providing cancer cells with cytokines that enhance cell proliferation and survival. Although malignant epithelial cells were traditionally considered to be on the receiving end of these microenvironmental interactions, recent studies show that epithelial cells can undergo inflammatory reprogramming on their own. Such epigenetic switches are often triggered by chronic tissue injury and play important roles in tissue repair. By converting terminally differentiated cells that harbor even a single oncogenic mutation to a less differentiated state with a higher proliferative potential, cell-autonomous inflammation is an important contributor to tumor initiation.
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Affiliation(s)
- Jelena Todoric
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Laboratory Medicine, Medical University of Vienna, Vienna 1090, Austria
| | - Michael Karin
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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50
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Huynh J, Chand A, Gough D, Ernst M. Therapeutically exploiting STAT3 activity in cancer - using tissue repair as a road map. Nat Rev Cancer 2019; 19:82-96. [PMID: 30578415 DOI: 10.1038/s41568-018-0090-8] [Citation(s) in RCA: 313] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The tightly orchestrated temporal and spatial control of signal transducer and activator of transcription 3 (STAT3) activity in epithelial, immune and stromal cells is critical for wound healing and tissue repair. Excessive STAT3 activation within cancer cells and cells of the tumour microenvironment can be viewed as a neoplastic mimic of an inflammation-driven repair response that collectively promotes tumour progression. In addition to the canonical transcriptional pathways by which STAT3 promotes stem cell-like characteristics, survival, proliferation, metastatic potential and immune evasion, cytoplasmic STAT3 activity fuels tumour growth by metabolic and other non-transcriptional mechanisms. Here, we review the tumour-modulating activities of STAT3 in light of its role as a signalling node integrating inflammatory responses during wound healing. Accordingly, many of the cytokines that contribute to the para-inflammatory state of most solid malignancies converge on and underpin dysregulated STAT3 activity. Targeting of these cytokines, their cognate receptors and associated signalling cascades in clinical trials is beginning to demonstrate therapeutic efficacy, given that interference with STAT3 activity is likely to simultaneously curb the growth of cancer cells and augment antitumour immunity.
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Affiliation(s)
- Jennifer Huynh
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria, Australia
| | - Ashwini Chand
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria, Australia
| | - Daniel Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia.
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria, Australia.
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