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Zhang W, Liu J, Ren X, Zhang Z, Zhou M, Li Y, Wang J, Li Q, Zhu Q, Wu G. Identification of the novel markers of PPAR signalling affecting immune microenvironment and immunotherapy response of lung adenocarcinoma patients. J Cell Mol Med 2024; 28:e17877. [PMID: 37556076 PMCID: PMC10902583 DOI: 10.1111/jcmm.17877] [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: 05/21/2023] [Revised: 07/04/2023] [Accepted: 07/19/2023] [Indexed: 08/10/2023] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are essential for cellular physiological processes. However, there is less research on the PPAR-related genes in lung adenocarcinoma (LUAD). Open-access data were get from the cancer genome atlas (TCGA) and gene expression omnibus (GEO) databases. All the analysis were conducted in the R software based on different R packages. In this study, we gauged the PPAR score employing a set of 72 PPAR-associated genes and probed the biological impact of this score on lung adenocarcinoma (LUAD). Subsequently, we established a unique signature composed of eight PPAR-related genes (ANGPTL4, ACSL3, ADIPOQ, FABP1, SLC27A1, ACOX2, PPARD and OLR1) to forecast the prognosis of LUAD. The signature's effectiveness in predicting survival was validated through the receiver operating characteristic curve in the TCGA-LUAD cohort. As per the pathway enrichment analysis, several crucial oncogenic pathways and metabolic processes were enriched in high-risk individuals. Further, we observed that these high-risk patients exhibited heightened genomic instability. Additionally, compared to the low-risk cohort, high-risk patients demonstrated diminished immune components and function. Intriguingly, high-risk patients exhibited a potential heightened sensitivity to immunotherapy and certain drugs, including Gefitinib, Afatinib, Erlotinib, IAP_5620, Sapitinib, LCL161, Lapatinib and AZD3759. The prognosis model based on eight PPAR-related genes has satisfactory prognosis prediction efficiency. Meanwhile, our results can provide direction for future studies in the relevant aspects.
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Affiliation(s)
- Wei Zhang
- Tuberculosis ward No1, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control, Affiliated to Janghan UniversityWuhanChina
| | - Junhui Liu
- Tuberculosis ward No1, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control, Affiliated to Janghan UniversityWuhanChina
| | - Xin Ren
- Department of Tuberculosis Control, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control Affiliated to Janghan UniversityWuhanChina
| | - Zhengbin Zhang
- Department of Tuberculosis Control, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control Affiliated to Janghan UniversityWuhanChina
| | - Meilan Zhou
- Department of Tuberculosis Control, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control Affiliated to Janghan UniversityWuhanChina
| | - Yuehua Li
- Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis ControlWuhanChina
| | - Jianjie Wang
- Department of Tuberculosis Control, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control Affiliated to Janghan UniversityWuhanChina
| | - Quan Li
- Medical department, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control, Affiliated to Janghan UniversityWuhanChina
| | - Qi Zhu
- Tuberculosis ward No1, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control, Affiliated to Janghan UniversityWuhanChina
| | - Gang Wu
- Department of Tuberculosis Control, Wuhan Pulmonary HospitalWuhan Institute for Tuberculosis Control Affiliated to Janghan UniversityWuhanChina
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Miyashita H, Kurzrock R, Bevins NJ, Thangathurai K, Lee S, Pabla S, Nesline M, Glenn ST, Conroy JM, DePietro P, Rubin E, Sicklick JK, Kato S. T-cell priming transcriptomic markers: implications of immunome heterogeneity for precision immunotherapy. NPJ Genom Med 2023; 8:19. [PMID: 37553332 PMCID: PMC10409760 DOI: 10.1038/s41525-023-00359-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/14/2023] [Indexed: 08/10/2023] Open
Abstract
Immune checkpoint blockade is effective for only a subset of cancers. Targeting T-cell priming markers (TPMs) may enhance activity, but proper application of these agents in the clinic is challenging due to immune complexity and heterogeneity. We interrogated transcriptomics of 15 TPMs (CD137, CD27, CD28, CD80, CD86, CD40, CD40LG, GITR, ICOS, ICOSLG, OX40, OX40LG, GZMB, IFNG, and TBX21) in a pan-cancer cohort (N = 514 patients, 30 types of cancer). TPM expression was analyzed for correlation with histological type, microsatellite instability high (MSI-H), tumor mutational burden (TMB), and programmed death-ligand 1 (PD-L1) expression. Among 514 patients, the most common histological types were colorectal (27%), pancreatic (11%), and breast cancer (10%). No statistically significant association between histological type and TPM expression was seen. In contrast, expression of GZMB (granzyme B, a serine protease stored in activated T and NK cells that induces cancer cell apoptosis) and IFNG (activates cytotoxic T cells) were significantly higher in tumors with MSI-H, TMB ≥ 10 mutations/mb and PD-L1 ≥ 1%. PD-L1 ≥ 1% was also associated with significantly higher CD137, GITR, and ICOS expression. Patients' tumors were classified into "Hot", "Mixed", or "Cold" clusters based on TPM expression using hierarchical clustering. The cold cluster showed a significantly lower proportion of tumors with PD-L1 ≥ 1%. Overall, 502 patients (98%) had individually distinct patterns of TPM expression. Diverse expression patterns of TPMs independent of histological type but correlating with other immunotherapy biomarkers (PD-L1 ≥ 1%, MSI-H and TMB ≥ 10 mutations/mb) were observed. Individualized selection of patients based on TPM immunomic profiles may potentially help with immunotherapy optimization.
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Affiliation(s)
- Hirotaka Miyashita
- Department of Hematology and Oncology, Dartmouth Cancer Center, Lebanon, NH, USA.
| | - Razelle Kurzrock
- Worldwide Innovative Network (WIN) for Personalized Cancer Therapy, Paris, France
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nicholas J Bevins
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Kartheeswaran Thangathurai
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Department of Physical Science, University of Vavuniya, Vavuniya, Sri Lanka
| | - Suzanna Lee
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC, San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | | | - Sean T Glenn
- Roswell Park Comprehensive Cancer Center, Center for Personalized Medicine, Buffalo, NY, USA
| | | | | | - Eitan Rubin
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jason K Sicklick
- Division of Surgical Oncology, Department of Surgery, and Center for Personalized Cancer Therapy, University of California, San Diego, La Jolla, CA, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC, San Diego Moores Cancer Center, La Jolla, CA, USA.
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3
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Sun Z, Chen X, Huang X, Wu Y, Shao L, Zhou S, Zheng Z, Lin Y, Chen S. Cuproptosis and Immune-Related Gene Signature Predicts Immunotherapy Response and Prognosis in Lung Adenocarcinoma. Life (Basel) 2023; 13:1583. [PMID: 37511958 PMCID: PMC10381686 DOI: 10.3390/life13071583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Cuproptosis and associated immune-related genes (IRG) have been implicated in tumorigenesis and tumor progression. However, their effects on lung adenocarcinoma (LUAD) have not been elucidated. Therefore, we investigated the impact of cuproptosis-associated IRGs on the immunotherapy response and prognosis of LUAD using a bioinformatical approach and in vitro experiments analyzing clinical samples. Using the cuproptosis-associated IRG signature, we classified LUAD into two subtypes, cluster 1 and cluster 2, and identified three key cuproptosis-associated IRGs, NRAS, TRAV38-2DV8, and SORT1. These three genes were employed to establish a risk model and nomogram, and to classify the LUAD cohort into low- and high-risk subgroups. Biofunctional annotation revealed that cluster 2, remarkably downregulating epigenetic, stemness, and proliferation pathways activity, had a higher overall survival (OS) and immunoinfiltration abundance compared to cluster 1. Real-time quantitative PCR (RT-qPCR) validated the differential expression of these three genes in both subgroups. scRNA-seq demonstrated elevated expression of NRAS and SORT1 in macrophages. Immunity and oncogenic and stromal activation pathways were dramatically enriched in the low-risk subgroup, and patients in this subgroup responded better to immunotherapy. Our data suggest that the cuproptosis-associated IRG signature can be used to effectively predict the immunotherapy response and prognosis in LUAD. Our work provides enlightenment for immunotherapy response assessment, prognosis prediction, and the development of potential prognostic biomarkers for LUAD patients.
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Affiliation(s)
- Zihao Sun
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Xiujing Chen
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Xiaoning Huang
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Yanfen Wu
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Lijuan Shao
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
| | - Suna Zhou
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Zhu Zheng
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Yiguang Lin
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
- Research & Development Division, Guangzhou Anjie Biomedical Technology Co., Ltd., Guangzhou 510535, China
| | - Size Chen
- Department of Immuno-Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Guangdong Provincial Engineering Research Center for Esophageal Cancer Precision Therapy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
- Key Laboratory of Cancer Immunotherapy of Guangdong Higher Education Institutes, Guangzhou 510080, China
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Golbashirzadeh M, Heidari HR, Talebi M, Yari Khosroushahi A. Ferroptosis as a Potential Cell Death Mechanism Against Cisplatin-Resistant Lung Cancer Cell Line. Adv Pharm Bull 2023; 13:176-187. [PMID: 36721820 PMCID: PMC9871276 DOI: 10.34172/apb.2023.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/03/2021] [Accepted: 11/06/2021] [Indexed: 02/03/2023] Open
Abstract
Purpose: Drug resistance is a challenging issue in cancer chemotherapy. Cell death induction is one of the main strategies to overcome chemotherapy resistance. Notably, ferroptosis has been considered a critical cell death mechanism in recent years. Accordingly, in this study, the different cell death strategies focused on ferroptosis have been utilized to overcome cisplatin resistance in an in vitro lung cancer model. Methods: The physiological functions of Akt1 and GPX4, as critical targets for ferroptosis and apoptosis induction, were suppressed by siRNA or antagonistic agents in resistant A549 cells. Afterward, the interventions' impacts on cell viability and reactive oxygen species (ROS) amount were analyzed by flow cytometry. Moreover, the alteration in the relevant gene and protein expression levels were quantified using Real-time PCR and western blot methods. Results: The result showed that the treatment with Akt1 siRNA reversed the cisplatin resistance in the A549 cell line through the induction of apoptosis. Likewise, the combination treatment of the GPX4 siRNA or FIN56 as ferroptosis inducers alongside cisplatin elevated ROS's cellular level, reduced the cellular antioxidant genes level and increased the cisplatin cytotoxic effect. Conclusion: In conclusion, our study indicated that ferroptosis induction can be considered a promising cell death strategy in cisplatin-resistant cancer cells.
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Affiliation(s)
- Morteza Golbashirzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Reza Heidari
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Corresponding Authors: Ahmad Yari Khosroushahi, and Hamid Reza Heidari,
| | - Mehdi Talebi
- Hematology and Oncology Research Center, Department of Applied Cell Sciences, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Yari Khosroushahi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Nanotechnology, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran.,Corresponding Authors: Ahmad Yari Khosroushahi, and Hamid Reza Heidari,
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Emerging function and clinical significance of extracellular vesicle noncoding RNAs in lung cancer. Mol Ther Oncolytics 2022; 24:814-833. [PMID: 35317517 PMCID: PMC8908047 DOI: 10.1016/j.omto.2022.02.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lung cancer (LC) is a commonly diagnosed cancer with an unsatisfactory prognosis. Extracellular vesicles (EVs) are lipid bilayer-delimited particles that mediate cell-cell communication by transporting various biomacromolecules, such as nucleic acids, proteins, and lipids. Noncoding RNAs (ncRNAs), including microRNAs, circular RNAs, and long noncoding RNAs, are important noncoding transcripts that play critical roles in a variety of physiological and pathological processes, especially in cancer. ncRNAs have been verified to be packaged into EVs and transported between LC cells and stromal cells, regulating multiple LC malignant phenotypes, such as proliferation, migration, invasion, epithelial-mesenchymal transition, metastasis, and treatment resistance. Additionally, EVs can be detected in various body fluids and are associated with the stage, grade, and metastasis of LC. Herein, we summarize the biological characteristics and functions of EV ncRNAs in the biological processes of LC, focusing on their potential to serve as diagnostic and prognostic biomarkers of LC as well as their probable role in the clinical treatment of LC. EV ncRNAs provide a new perspective for understanding the mechanism underlying LC pathogenesis and development, which might benefit numerous LC patients in the future.
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Deciphering Tumour Heterogeneity: From Tissue to Liquid Biopsy. Cancers (Basel) 2022; 14:cancers14061384. [PMID: 35326534 PMCID: PMC8946040 DOI: 10.3390/cancers14061384] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Most malignant tumours are highly heterogeneous at molecular and phenotypic levels. Tumour variability poses challenges for the management of patients, as it arises between patients and even evolves in space and time within a single patient. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of tumour diversity in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate tumour heterogeneity. Abstract Human solid malignancies harbour a heterogeneous set of cells with distinct genotypes and phenotypes. This heterogeneity is installed at multiple levels. A biological diversity is commonly observed between tumours from different patients (inter-tumour heterogeneity) and cannot be fully captured by the current consensus molecular classifications for specific cancers. To extend the complexity in cancer, there are substantial differences from cell to cell within an individual tumour (intra-tumour heterogeneity, ITH) and the features of cancer cells evolve in space and time. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity with an emphasis on ITH and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of ITH in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate ITH.
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Xu YF, Du XF, Li ZY, Fang ZP, Zhang FB. Lesion human leukocyte antigen-E is associated with favourable prognosis for patients with oesophageal squamous cell carcinoma. J Int Med Res 2021; 49:3000605211047278. [PMID: 34617814 PMCID: PMC8504691 DOI: 10.1177/03000605211047278] [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: 12/24/2022] Open
Abstract
Objective To investigate the clinical significance of human leukocyte antigen (HLA)-E levels in oesophageal squamous cell carcinoma (ESCC). Methods The levels of HLA-E immunostaining in ESCC lesions and 47 corresponding adjacent normal tissues were measured using immunohistochemistry. The correlation between the levels of immunostaining and clinical parameters was analysed. Results This study analysed 110 paraffin-embedded primary tumour lesions and 47 case–controlled paracancerous tissues that were surgically resected from 110 patients with ESCC. Positive immunostaining for HLA-E was observed in 88.2% (97 of 110) of ESCC lesions and 29.8% (14 of 47) of normal oesophageal tissues. There was no correlation between HLA-E immunostaining in ESCC lesions and clinicopathological characteristics such as lymph node metastasis, tumour–node–metastasis stage and differentiation grade. Kaplan–Meier survival analysis revealed a significantly better prognosis in patients with higher levels of HLA-E immunostaining than in those with lower levels of HLA-E immunostaining; overall survival was 28.6 months (95% confidence interval [CI], 23.2, 34.0) versus 15.3 months (95% CI, 11.5, 19.1), respectively. Furthermore, multivariate analysis showed that the HLA-E level was an independent prognostic factor in patients with ESCC. Conclusion A higher level of HLA-E immunostaining was associated with favourable survival in patients with ESCC.
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Affiliation(s)
- Yong-Fu Xu
- Department of Hepatobiliary Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang Province, China
| | - Xue-Feng Du
- Department of Hepatobiliary Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang Province, China
| | - Zhen-Yu Li
- Department of Hepatobiliary Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang Province, China
| | - Zhe-Ping Fang
- Department of Hepatobiliary Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang Province, China
| | - Fa-Biao Zhang
- Department of Hepatobiliary Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang Province, China
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Xie Y, Olkhov-Mitsel E, Alminawi S, Slodkowska E, Downes MR. Development of a multiplex immuno-oncology biomarker and digital pathology workflow for assessment of urothelial carcinoma. Pathol Res Pract 2021; 226:153607. [PMID: 34509050 DOI: 10.1016/j.prp.2021.153607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/24/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Immune checkpoint inhibitors (ICI) therapies have demonstrated significant benefit in the treatment of many tumors including high grade urothelial cancer (HGUC) of the bladder. However, variability in patients' clinical responses highlights the need for biomarkers to aid patient stratification. ICI relies on an intact host immune response. In this context, we hypothesize that key players in the antitumor immune response such as markers of activated cytotoxic T lymphocytes (CD8, granzyme-B) and immune suppression (FOXP3) may help to identify patients who will derive the greatest therapeutic benefit from ICI. A major obstacle for deployment of such a strategy is the limited quantities of tumor-derived biopsy material. Therefore, in this technical study, we develop a multiplex biomarker with digital workflow. We explored the (1) concordance of conventional single stain results using digital image analysis, and (2) agreement between digital scoring versus manual analysis. METHODS (1) For concordance study of single and multiplex stains, triplicate core tissue microarrays of 207 muscle invasive, HGUC of bladder had sequential 4-micron sections cut and stained with CD8, FOXP3 and granzyme-B. An inhouse developed tri-chromogen multiplex immunohistochemistry (m-IHC) assay consisting of CD8 (green), granzyme B (brown), and FOXP3 (red) was used to stain the next sequential tissue section. (2) Agreement between manual and digital analysis was performed on 19 whole slide sections of HGUC cystectomy specimens. All slides were scanned using Aperio ScanScope AT Digital Scanner at 40X. Quantitative digital image analysis was performed using QuPath version 0.2.3 open-source software. Scores from triplicate cores were averaged for each HGUC specimen for each marker. Intraclass correlation coefficients were used to compare percent positive cells between the single- and multi-plex assays. Lin's concordance correlation coefficients were used for manual versus digital analysis. RESULTS AND CONCLUSIONS m-IHC offers significant advantages in characterizing the host immune microenvironment particularly in limited biopsy tissue material. Utilizing a digital image workflow resulted in significant concordance between m-IHC and individual single stains (p < 0.001 for all assessments). Moderate to good agreements were achieved between manual and digital scoring. Our technical work demonstrated potential uses of multiplex marker in assessing the host immune status and could be used in conjunction with PD-L1 as a predictor of response to ICI therapy.
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Affiliation(s)
- Youheng Xie
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. 1 King's College Circle, 6th Floor, Toronto, ON M 5S 1A8, Canada
| | - Ekaterina Olkhov-Mitsel
- Division of Anatomic Pathology, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada. 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada
| | - Samira Alminawi
- Division of Anatomic Pathology, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada. 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada
| | - Elzbieta Slodkowska
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. 1 King's College Circle, 6th Floor, Toronto, ON M 5S 1A8, Canada; Division of Anatomic Pathology, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada. 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada
| | - Michelle R Downes
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. 1 King's College Circle, 6th Floor, Toronto, ON M 5S 1A8, Canada; Division of Anatomic Pathology, Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada. 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada.
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Zhang Z, Zhang C, Luo Y, Zhang G, Wu P, Sun N, He J. RNA N 6 -methyladenosine modification in the lethal teamwork of cancer stem cells and the tumor immune microenvironment: Current landscape and therapeutic potential. Clin Transl Med 2021; 11:e525. [PMID: 34586737 PMCID: PMC8473646 DOI: 10.1002/ctm2.525] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 12/18/2022] Open
Abstract
N6 -methyladenosine (m6 A), the newest and most prevalent layer of internal epigenetic modification in eukaryotic mRNA, has been demonstrated to play a critical role in cancer biology. Increasing evidence has highlighted that the interaction between cancer stem cells (CSCs) and the tumor immune microenvironment (TIME) is the root cause of tumorigenesis, metastasis, therapy resistance, and recurrence. In recent studies, the m6 A modification has been tightly linked to this CSC-TIME interplay, participating in the regulation of CSCs and TIME remolding. Interestingly, the m6 A modification has also been identified as a novel decisive factor in the efficacy of immunotherapies-particularly anti-PD-1/PD-L1 monotherapies-by changing the plasticity of the TIME. Given the functional importance of the m6 A modification in the crosstalk between CSCs and the TIME, targeting m6 A regulators will open new avenues to overcome therapeutic resistance, especially for immune checkpoint-based immunotherapy. In the present review, we summarize the current landscape of m6 A modifications in CSCs and the TIME, and also prospect the underling role of m6 A modifications at the crossroads of CSCs and the TIME for the first time. Additionally, to provide the possibility of modulating m6 A modifications as an emerging therapeutic strategy, we also explore the burgeoning inhibitors and technologies targeting m6 A regulators. Lastly, considering recent advances in m6 A-seq technologies and cancer drug development, we propose the future directions of m6 A modification in clinical applications, which may not only help to improve individualized monitoring and therapy but also provide enhanced and durable responses in patients with insensitive tumors.
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Affiliation(s)
- Zhihui Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Chaoqi Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yuejun Luo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Guochao Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Peng Wu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Wadowska K, Błasiak P, Rzechonek A, Bil-Lula I, Śliwińska-Mossoń M. New Insights on Old Biomarkers Involved in Tumor Microenvironment Changes and Their Diagnostic Relevance in Non-Small Cell Lung Carcinoma. Biomolecules 2021; 11:1208. [PMID: 34439874 PMCID: PMC8391392 DOI: 10.3390/biom11081208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Lung cancer is a multifactorial disease with a heterogeneous tumor group that hampers diagnostic and therapeutic approaches, as well as understanding of the processes that underlie its pathogenesis. Current research efforts are focused on examining alterations in the tumor microenvironment, which may affect the pathogenesis and further malignant progression in lung cancer. The aim of this study was to investigate changes in the levels of biomarkers involved in the lung tumor microenvironment and their diagnostic utility in differentiating lung cancer subtypes and stages. METHODS This study comprised 112 lung cancer patients, 50 with adenocarcinoma, 35 with squamous cell carcinoma, 13 with other non-small cell lung carcinoma subtypes, and 14 with other lung neoplasms than non-small cell lung carcinoma. Tumor markers (CEA, CYFRA 21-1, and NSE) were measured in the patients' sera and plasmas, along with IL-6, TNF-α, SAA1, CRP, MMP-2, MMP-9, glucose, lactate, and LDH, utilizing enzyme-linked immunosorbent assays, enzyme immunoassays, and automated clinical chemistry and turbidimetry systems. The results were statistically analyzed across patient groups based on the subtype and stage of lung cancer. RESULTS Glucose concentrations showed statistically significant (p < 0.05) differences both between lung cancer subtypes and stages, with the highest levels in patients with other lung neoplasms (me = 130.5 mg/dL) and in patients with stage IIB lung cancer (me = 132.0 mg/dL). In patients with advanced lung cancer, IL-6 and LDH had considerably higher concentration and activity. There was also a significant positive correlation between IL-6 and MMP-9 in adenocarcinoma and SqCC, with correlation coefficients of 0.53 and 0.49, respectively. The ROC analyses showed that the best single biomarkers for distinguishing adenocarcinoma from squamous cell carcinoma are glucose, CRP, and CYFRA 21-1; however, their combination did not significantly improve sensitivity, specificity, and the AUC value. The combinations of IL-6, glucose, LDH and CEA, IL-6, SAA1, MMP-9, and lactate can distinguish patients with stage IIB lung cancer from those with stage IIA with 100% sensitivity, 100% specificity, and with an AUC value of 0.8333 and 1.0000, respectively, whereas the combination of CEA, IL-6, and LDH can identify patients with stage IIIA lung cancer from those with stage IIB with 72.73% sensitivity, 94.44% specificity, and an AUC value of 0.8686. CONCLUSION There is a link between biomarkers of tumor microenvironment changes and tumor markers, and combinations of these markers may be clinically useful in the differential diagnosis of adenocarcinoma and squamous cell carcinoma, as well as lung cancer stages IIB and IIA, and IIIA and IIB.
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Affiliation(s)
- Katarzyna Wadowska
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (I.B.-L.); (M.Ś.-M.)
| | - Piotr Błasiak
- Department and Clinic of Thoracic Surgery, Wroclaw Medical University, Grabiszyńska 105, 53-439 Wroclaw, Poland; (P.B.); (A.R.)
- Department of Thoracic Surgery, Lower Silesian Center for Lung Diseases, Grabiszyńska 105, 53-439 Wroclaw, Poland
| | - Adam Rzechonek
- Department and Clinic of Thoracic Surgery, Wroclaw Medical University, Grabiszyńska 105, 53-439 Wroclaw, Poland; (P.B.); (A.R.)
- Department of Thoracic Surgery, Lower Silesian Center for Lung Diseases, Grabiszyńska 105, 53-439 Wroclaw, Poland
| | - Iwona Bil-Lula
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (I.B.-L.); (M.Ś.-M.)
| | - Mariola Śliwińska-Mossoń
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (I.B.-L.); (M.Ś.-M.)
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Lin J, Wang L, Ji X, Zheng X, Tang K. Characterization of 18F-fluorodeoxyglucose metabolic spatial distribution improves the differential diagnosis of indeterminate pulmonary nodules and masses with high fluorodeoxyglucose uptake. Quant Imaging Med Surg 2021; 11:1543-1553. [PMID: 33816190 DOI: 10.21037/qims-20-768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background The aim of this study was to investigate the value of visual assessment of 18F-fluorodeoxyglucose (18F-FDG) metabolic spatial distribution (V-FMSD) in the diagnosis of indeterminate pulmonary nodules and masses with high 18F-FDG uptake. Methods A total of 301 patients with indeterminate pulmonary nodules or masses who underwent 18F-FDG positron emission tomography/computed tomography (PET/CT) imaging were retrospectively studied. The characteristics of 18F-FDG metabolic spatial distribution (FMSD) in the proximal and distal regions of the lesions were visually analyzed using a 5-point scoring system. The sensitivity, specificity, accuracy, and area under receiver operating characteristic curve (AUC) were compared between V-FMSD and conventional PET/CT methods for the diagnosis of hypermetabolic indeterminate pulmonary nodules and masses. Results The V-FMSD results showed that 180 (92.8%) malignant lesions had a score of ≥3 and 78 (72.9%) benign lesions had a score of ≤2. This indicated that the FMSD in the proximal region of malignant lesions was significantly higher than that of the distal region, and the FMSD in the proximal region of benign lesions was significantly lower than that of the distal region. V-FMSD had a specificity of 72.9%, which was markedly higher than those of the maximum standard uptake value (SUVmax; 0%, P<0.001) and the retention index (RI; 26.2%, P<0.001). The AUC of V-FMSD was 0.886, which was significantly larger than those of the SUVmax (0.626, P<0.001), RI (0.670, P<0.001), and PET/CT (0.788, P<0.05). Conclusions Our study found that pulmonary benign and malignant lesions have distinct FMSD characteristics. V-FMSD can therefore be used as a novel auxiliary marker to improve the diagnostic accuracy of hypermetabolic indeterminate pulmonary nodules and masses.
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Affiliation(s)
- Jie Lin
- Department of PET/CT, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ling Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaowei Ji
- Department of PET/CT, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangwu Zheng
- Department of PET/CT, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kun Tang
- Department of PET/CT, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Ahluwalia P, Ahluwalia M, Mondal AK, Sahajpal N, Kota V, Rojiani MV, Rojiani AM, Kolhe R. Immunogenomic Gene Signature of Cell-Death Associated Genes with Prognostic Implications in Lung Cancer. Cancers (Basel) 2021; 13:E155. [PMID: 33466402 PMCID: PMC7795632 DOI: 10.3390/cancers13010155] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/08/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is one of the leading causes of death worldwide. Cell death pathways such as autophagy, apoptosis, and necrosis can provide useful clinical and immunological insights that can assist in the design of personalized therapeutics. In this study, variations in the expression of genes involved in cell death pathways and resulting infiltration of immune cells were explored in lung adenocarcinoma (The Cancer Genome Atlas: TCGA, lung adenocarcinoma (LUAD), 510 patients). Firstly, genes involved in autophagy (n = 34 genes), apoptosis (n = 66 genes), and necrosis (n = 32 genes) were analyzed to assess the prognostic significance in lung cancer. The significant genes were used to develop the cell death index (CDI) of 21 genes which clustered patients based on high risk (high CDI) and low risk (low CDI). The survival analysis using the Kaplan-Meier curve differentiated patients based on overall survival (40.4 months vs. 76.2 months), progression-free survival (26.2 months vs. 48.6 months), and disease-free survival (62.2 months vs. 158.2 months) (Log-rank test, p < 0.01). Cox proportional hazard model significantly associated patients in high CDI group with a higher risk of mortality (Hazard Ratio: H.R 1.75, 95% CI: 1.28-2.45, p < 0.001). Differential gene expression analysis using principal component analysis (PCA) identified genes with the highest fold change forming distinct clusters. To analyze the immune parameters in two risk groups, cytokines expression (n = 265 genes) analysis revealed the highest association of IL-15RA and IL 15 (> 1.5-fold, p < 0.01) with the high-risk group. The microenvironment cell-population (MCP)-counter algorithm identified the higher infiltration of CD8+ T cells, macrophages, and lower infiltration of neutrophils with the high-risk group. Interestingly, this group also showed a higher expression of immune checkpoint molecules CD-274 (PD-L1), CTLA-4, and T cell exhaustion genes (HAVCR2, TIGIT, LAG3, PDCD1, CXCL13, and LYN) (p < 0.01). Furthermore, functional enrichment analysis identified significant perturbations in immune pathways in the higher risk group. This study highlights the presence of an immunocompromised microenvironment indicated by the higher infiltration of cytotoxic T cells along with the presence of checkpoint molecules and T cell exhaustion genes. These patients at higher risk might be more suitable to benefit from PD-L1 blockade or other checkpoint blockade immunotherapies.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (M.A.); (A.K.M.); (N.S.); (M.V.R.); (A.M.R.)
| | - Meenakshi Ahluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (M.A.); (A.K.M.); (N.S.); (M.V.R.); (A.M.R.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (M.A.); (A.K.M.); (N.S.); (M.V.R.); (A.M.R.)
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (M.A.); (A.K.M.); (N.S.); (M.V.R.); (A.M.R.)
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| | - Mumtaz V. Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (M.A.); (A.K.M.); (N.S.); (M.V.R.); (A.M.R.)
| | - Amyn M. Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (M.A.); (A.K.M.); (N.S.); (M.V.R.); (A.M.R.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (P.A.); (M.A.); (A.K.M.); (N.S.); (M.V.R.); (A.M.R.)
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Aizemaiti R, Wu Z, Tang J, Yan H, Lv X. Heat shock factor 5 correlated with immune infiltration serves as a prognostic biomarker in lung adenocarcinoma. Int J Med Sci 2021; 18:448-458. [PMID: 33390814 PMCID: PMC7757139 DOI: 10.7150/ijms.51297] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the predominant subtype of lung cancer with a relatively poor prognosis. The dramatic improvements of new immunotherapy strategies have shown promising results in lung cancer patients. This study aimed to elucidate the functions of immune-associated genes in LUAD prognosis and pathogenesis by analyzing public databases. We obtained expression profiles of LUAD patients from The Cancer Genome Atlas (TCGA) database and applied the ESTIMATE algorithm to calculate immune scores and stromal scores. A series of microenvironment-related genes with prognostic value was then identified. Of note, heat shock factor 5 (HSF5) was found to be decreased in LUAD patients and positively correlated with overall survival, which was further confirmed in the Gene Expression Omnibus (GEO) database. Moreover, Gene Ontology (GO) analysis based on the correlated genes of HSF5 demonstrated that HSF5 expression was significantly associated with the immune response and inflammatory activities. Based on the Tumor IMmune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA) datasets, HSF5 expression showed strong correlations with various immune cell infiltration and diverse immune marker sets. These findings suggest that HSF5 can be used as a promising biomarker for determining prognosis and immune infiltration in LUAD patients.
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Affiliation(s)
- Rusidanmu Aizemaiti
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhejiang University, Qingchun Road 79, Hangzhou, China, 310009
| | - Zhigang Wu
- Zhejiang University School of Medicine, Yuhangtang Road 866, Hangzhou, China, 310009
| | - Jie Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhejiang University, Qingchun Road 79, Hangzhou, China, 310009
| | - Haimeng Yan
- Bone Marrow Transplantation Center, The First Affiliated Hospital of Zhejiang University, Qingchun Road 79, Hangzhou, China, 310009
| | - Xiayi Lv
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhejiang University, Qingchun Road 79, Hangzhou, China, 310009
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Zhong C, Tao B, Tang F, Yang X, Peng T, You J, Xia K, Xia X, Chen L, Peng L. Remodeling cancer stemness by collagen/fibronectin via the AKT and CDC42 signaling pathway crosstalk in glioma. Am J Cancer Res 2021; 11:1991-2005. [PMID: 33408794 PMCID: PMC7778591 DOI: 10.7150/thno.50613] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer development is a complex set of proliferative progression, which arises in most cases via multistep pathways associated with various factors, including the tumor microenvironment and extracellular matrix. However, the underlying mechanisms of cancer development remain unclear and this study aimed to explore the role of extracellular matrix in glioma progression. Methods: The expression of type I collagen and fibronectin in tumor tissues from glioma patients was examined by immunofluorescence staining. The correlations between collagen/fibronectin and glioma progression were then analyzed. A 3D collagen/fibronectin cultured system was established for tumor cells culture in vitro. Quantitative, real-time PCR and western blot were used to detect PI3K/ATK and CDC42 signals associated proteins expression in glioma. We used in vitro Cell Counting Kit-8, colony formation, and tumorigenesis assays to investigate the function of PI3K/AKT and CDC42 signals associated proteins. A xenograft glioma mice model was also used to study the anticancer effects of integrin inhibitor in vivo. Results: Our study demonstrated that type I collagen and fibronectin collaborate to regulate glioma cell stemness and tumor growth. In a 3D collagen/fibronectin culture model, glioma cells acquired tumorigenic potential and revealed strengthened proliferative characteristics. More significantly, collagen/fibronectin could facilitate the activation of PI3K/AKT/SOX2 and CDC42/YAP-1/NUPR1/Nestin signaling pathways via integrin αvβ3, eliciting sustained tumor growth and cancer relapse. Combination of the integrin signaling pathway inhibitor and the chemotherapeutic agent efficiently suppressed glioma cell proliferation and tumorigenic ability. Conclusion: We demonstrated that type I collagen and fibronectin could collaborate to promote glioma progression through PI3K/AKT/SOX2 and CDC42/YAP-1/NUPR1/Nestin signaling pathways. Blockade of the upstream molecular integrin αvβ3 revealed improved outcome in glioma therapy, which provide new insights for eradicating tumors and reducing glioma cancer relapse.
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Li LB, Yang L, Xie GQ, Zhou XC, Shen XB, Xu QL, Ma ZY, Guo XD. The modulation relationship of genomic pattern of intratumor heterogeneity and immunity microenvironment heterogeneity in hepatocellular carcinoma. Oncol Lett 2020; 20:233. [PMID: 32968455 PMCID: PMC7500054 DOI: 10.3892/ol.2020.12096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/15/2020] [Indexed: 12/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world, with the second highest mortality rate among all cancer types. Growing evidence has demonstrated the notable effects of intratumor heterogeneity (ITH) and tumor immune microenvironment heterogeneity (TIMH) on the biological processes involved in HCC. However, the interactive mechanisms between ITH and TIMH is still unclear. The present study systematically screened the mRNA expression, simple nucleotide variation data and clinical data of samples from The Cancer Genome Atlas (TCGA). The mutant-allele tumor heterogeneity (MATH) score was used to represent ITH, and TCGA cohort was divided into two groups according to the MATH score. Next, different immune-related signaling pathways and enriched immune-related genes were identified using Gene Set Enrichment Analysis of these two groups, and the results revealed that interleukin-1α (IL1A) and serine/threonine-protein kinase PAK4 were associated with prognosis. Furthermore, CIBERSORT was utilized to calculate the fractions of 22 types of leukocytes to represent TIMH, and the fractions of M1 and M2 macrophages were confirmed to be associated with prognosis. Therefore, PAK4, interleukin-1α (IL1A), and M1/M2 ratio were selected as the key factors involved in the interaction between ITH and TIMH. Afterwards, microRNAs (miRNAs) that were linearly related to the M1/M2 ratio and the potential target genes of the miRNAs were screened. Finally, the regulatory network between PAK4, IL1A, and the M1/M2 ratio was established, bridged by the above miRNAs and the target genes. In addition, PAK4, heat shock protein 105 kDa and miRNA-1911 were demonstrated to be a key factor involved in immune response via Weighted Correlation Network Analysis in HCC.
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Affiliation(s)
- Liu-Bo Li
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200080, P.R. China
| | - Lu Yang
- Shanghai Information Center for Life Sciences, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, P.R. China
| | - Guo-Qun Xie
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200080, P.R. China
| | - Xiao-Cui Zhou
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200080, P.R. China
| | - Xu-Bo Shen
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200080, P.R. China
| | - Qiu-Lin Xu
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200080, P.R. China
| | - Zheng-Yuan Ma
- Shanghai Information Center for Life Sciences, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, P.R. China
| | - Xiao-Dong Guo
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200080, P.R. China
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Sun D, Tian L, Bian T, Zhao H, Tao J, Feng L, Liu Q, Hou H. The role of CD28 in the prognosis of young lung adenocarcinoma patients. BMC Cancer 2020; 20:910. [PMID: 32967633 PMCID: PMC7510131 DOI: 10.1186/s12885-020-07412-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/14/2020] [Indexed: 02/22/2023] Open
Abstract
Background The prognosis of lung cancer was found to be associated with a series of biomarkers related to the tumor immune microenvironment (TIME), which can modulate the biological behaviors and consequent outcomes of lung cancer. Therefore, establishing a prognostic model based on the TIME for lung cancer patients, especially young patients with lung adenocarcinoma (LUAD), is urgently needed. Methods In all, 809 lung cancer patients from the TCGA database and 71 young patients with LUAD in our center were involved in this study. Univariate and multivariate analysis based on clinical characteristics and TIME-related expression patterns (as evaluated by IHC) were performed to estimate prognosis and were verified by prognostic nomograms. Results Both LUAD and lung cancer patients with high CD28 expression had shorter disease-free survival (DFS) (P = 0.0011; P = 0.0001) but longer overall survival (OS) (P = 0.0001; P = 0.0282). TIME-related molecules combined with clinical information and genomic signatures could predict the prognosis of young patients with LUAD with robust efficiency and could be verified by the established nomogram based on the Cox regression model. In addition, CD28 expression was correlated with an abundance of lymphocytes and could modulate the TIME. Higher CD28 levels were observed in primary tumors than in metastatic tissues. Conclusion TIME-related molecules were identified as compelling biomarkers for predicting the prognosis of lung cancer, especially in a cohort of young patients. Furthermore, CD28, which is associated with poor DFS but long OS, might participate in the modulation of the TIME and has a different role in the prognosis of young patients with LUAD.
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Affiliation(s)
- Dantong Sun
- Precision Medicine Center of Oncology, the Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, Shandong, China
| | - Lu Tian
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Tiantian Bian
- Breast Disease Center, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, China
| | - Han Zhao
- Department of Pathology, the Affiliated Hospital of Qingdao University, Qingdao, 266000, China
| | - Junyan Tao
- Precision Medicine Center of Oncology, the Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, Shandong, China
| | - Lizong Feng
- Department of General Surgery, Qingdao Eighth People's Hospital, Qingdao, 266041, China
| | - Qiaoling Liu
- Department of Medical Oncology, Qingdao West Coast New Area Central Hospital, Qingdao, 266555, China
| | - Helei Hou
- Precision Medicine Center of Oncology, the Affiliated Hospital of Qingdao University, No. 59 Haier Road, Qingdao, 266000, Shandong, China.
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Xu Y, Xu WH, Shi SN, Yang XL, Ren YR, Zhuang XY, Qu YY, Zhang HL, Zhang XF. Carbonic Anhydrase 4 serves as a Clinicopathological Biomarker for Outcomes and Immune Infiltration in Renal Cell Carcinoma, Lower Grade Glioma, Lung Adenocarcinoma and Uveal Melanoma. J Cancer 2020; 11:6101-6113. [PMID: 32922550 PMCID: PMC7477427 DOI: 10.7150/jca.46902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/26/2020] [Indexed: 01/21/2023] Open
Abstract
Background: Carbonic anhydrase 4 (CA4) maintains homeostasis of carbon dioxide and bicarbonate. It is suggested to be a potential prognostic biomarker, while the correlations between CA4 and different cancers are indistinct. Methods: Differential mRNA expression of CA4 among different cancers and corresponding normal tissues was compared based on datasets on the Cancer Genome Atlas (TCGA) platforms. Then, survival analysis was performed using Tumor-immune system interactionsplatform and TCGA cohort on the basis of distinct comparison expression of CA4 in five kinds of tumors. In addition, molecular penal analysis and functional annotations of CA4-related genes was elaborated. The correlation between CA4 mRNA expression and tumor immune microenvironment were analyzed in detail. Results: Compared with adjacent normal tissues, CA4 mRNA expressions were found significantly lower in various tumors. Moreover, decreased expression of CA4 was significantly related to worse overall survival (OS) and progression-free survival (PFS) in kidney renal clear cell carcinoma (KIRC), brain lower grade glioma (LGG), lung adenocarcinoma (LUAD) and uveal melanoma (UVM), and worse OS of prostate adenocarcinoma (PRAD) (p<0.05). Cox regression analyses indicated that CA4 was a significant prognostic biomarker in KIRC, LGG, LUAD and UVM. Moreover, CA4 showed markedly relationship with tumor immune environment and diverse immune infiltration signatures in KIRC, LGG, LUAD and UVM. Conclusions: Our study revealed that CA4 was a potential biomarker for aggressive progression and poor prognosis in KIRC, LGG, LUAD, PRAD and UVM, correlated with immune infiltration in various tumor environments. These results suggested that CA4 possibly served as a promising prognostic and immune infiltration biomarker in many cancers.
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Affiliation(s)
- Yue Xu
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, 215000, China
- Medical College, Soochow University, Suzhou, 215000, China
| | - Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, China
| | - Shen-Nan Shi
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, China
| | - Xiao-Long Yang
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, 215000, China
- Medical College, Soochow University, Suzhou, 215000, China
| | - Ya-Ru Ren
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, 215000, China
- Medical College, Soochow University, Suzhou, 215000, China
| | - Xin-Yu Zhuang
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, 215000, China
- Medical College, Soochow University, Suzhou, 215000, China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 20032, China
| | - Xiao-Feng Zhang
- Department of Ophthalmology, First Affiliated Hospital of Soochow University, Suzhou, 215000, China
- Medical College, Soochow University, Suzhou, 215000, China
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Zhong R, Chen D, Cao S, Li J, Han B, Zhong H. Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq. Clin Transl Oncol 2020; 23:405-417. [PMID: 32656582 DOI: 10.1007/s12094-020-02435-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Immune cells in the immune microenvironment of lung cancer have a great impact on the development of lung cancer. Our purpose was to analyze the immune cell infiltration features and related marker genes for lung cancer. METHODS Single cell RNA sequencing data of 11,485 lung cancer cells were retrieved from the Gene Expression Omnibus. After quality control and data normalization, cell clustering was performed using the Seurat package. Based on the marker genes of each cell type from the CellMarker database, each cell was divided into G1, G2M, and S phases. Then, differential expression and functional enrichment analyses were performed. CIBERSORT was used to reconstruct immune cell types. RESULTS Following cell filtering, highly variable genes were identified for all cells. 14 cell types were clustered. Among them, CD4 + T cell, B cell, plasma cell, natural killer cell and cancer stem cell were the top five cell types. Up-regulated genes were mainly enriched in immune-related biological processes and pathways. Using CIBERSORT, we identified the significantly higher fractions of naïve B cell, memory CD4 + T cell, T follicular helper cell, T regulatory helper cell and M1 macrophage in lung cancer tissues compared to normal tissues. Furthermore, the fractions of resting NK cell, monocyte, M0 macrophage, resting mast cell, eosinophil and neutrophil were significantly lower in tumor tissues than normal tissues. CONCLUSION Our findings dissected the immune cell infiltration features and related marker genes for lung cancer, which might provide novel insights for the immunotherapy of lung cancer.
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Affiliation(s)
- R Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Huaihai West Road No. 241, Shanghai, 200030, China
| | - D Chen
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Huaihai West Road No. 241, Shanghai, 200030, China
| | - S Cao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Huaihai West Road No. 241, Shanghai, 200030, China
| | - J Li
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Huaihai West Road No. 241, Shanghai, 200030, China
| | - B Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Huaihai West Road No. 241, Shanghai, 200030, China
| | - H Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Huaihai West Road No. 241, Shanghai, 200030, China.
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Zhang L, Chen J, Cheng T, Yang H, Li H, Pan C. Identification of the key genes and characterizations of Tumor Immune Microenvironment in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC). J Cancer 2020; 11:4965-4979. [PMID: 32742444 PMCID: PMC7378909 DOI: 10.7150/jca.42531] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
This study aimed to investigate the key genes and immune microenvironment involved in different TNM stages of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). The gene expression and clinical characteristics data were downloaded from the genomic data commons (GDC) database. After initial data processing, the characteristics of the immune microenvironment were analyzed. The differentially expressed genes (DEGs) in tumor vs. normal, and in early vs. advanced stages were screened, followed by Spearman correlation test for tumor infiltrating immune cells (TIICs) to identify immune-related genes. Finally, functional enrichment, protein-protein interaction, and survival analyses were performed. In LUAD, early stage was with higher immune scores, greater number of memory B cells and M0 macrophages compared to advanced stage. M0 and M2 macrophages, and resting memory CD4+ T cells accounted for a large proportion of TIICs in LUAD. The abundance of M0 macrophage infiltration was significantly correlated with the TNM stage and survival. In LUSC, early stage was with higher cytolytic activity and neoantigen burden compared to advanced stage. M0 and M2 macrophages, and plasma cells accounted for a large proportion of TIICs in LUSC. The abundance of resting and activated mast cells was significantly correlated with TNM stage, while resting dendritic cells, eosinophils, activated memory CD4 T cells, and mast cells were significantly correlated with prognosis. Tumor mutation burden analysis revealed that the median of variants per sample decreased from stage I to IV in LUAD, while it increased in LUSC. Further, 83 and 9 immune-related DEGs were identified in LUAD and LUSC, respectively, of which 23 genes in LUAD and 2 genes in LUSC correlated with survival. In conclusion, we identified the key genes, and characterized the tumor immune microenvironment in LUAD and LUSC which may provide therapeutic targets for the treatment of NSCLC.
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Affiliation(s)
| | - Jianhua Chen
- Thoracic Medicine Department 1, Hunan Cancer Hospital, Changsha, Hunan Province, P.R. China, 410013
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20
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Zhang L, Zhu B, Zeng Y, Shen H, Zhang J, Wang X. Clinical lipidomics in understanding of lung cancer: Opportunity and challenge. Cancer Lett 2019; 470:75-83. [PMID: 31655086 DOI: 10.1016/j.canlet.2019.08.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/01/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022]
Abstract
Disordered lipid metabolisms have been evidenced in lung cancer as well as its subtypes. Lipidomics with in-depth mining is considered as a critical member of the multiple omics family and a lipid-specific tool to understand disease-associated lipid metabolism and disease-specific dysfunctions of lipid species, discover biomarkers and targets for monitoring therapeutic strategies, and provide insights into lipid profiling and pathophysiological mechanisms in lung cancer. The present review describes the characters and patterns of lipidomic profiles in patients with different lung cancer subtypes, important values of comprehensive lipidomic profiles in understanding of lung cancer heterogeneity, urgent needs of standardized methodologies, potential mechanisms by lipid-associated enzymes and proteins, and the importance of integration between clinical phenomes and lipidomic profiles. The characteristics of lipidomic profiles in different lung cancer subtypes are extremely varied among study designs, objects, methods, and analyses. Preliminary data from recent studies demonstrate the specificity of lipidomic profiles specific for lung cancer stage, severity, subtype, and response to drugs. The heterogeneity of lipidomic profiles and lipid metabolism may be part of systems heterogeneity in lung cancer and be responsible for the development of drug resistance, although there are needs for direct evidence to show the existence of intra- or inter-lung cancer heterogeneity of lipidomic profiles. With an increasing understanding of expression profiles of genes and proteins, lipidomic profiles should be associated with activities of enzymes and proteins involved in the processes of lipid metabolism, which can be profiled with genomics and proteomics, and to provide the opportunity for the integration of lipidomic profiles with gene and protein expression profiles. The concept of clinical trans-omics should be emphasized to integrate data of lipidomics with clinical phenomics to identify disease-specific and phenome-specific biomarkers and targets, although there are still a large number of challenges to be overcome in the integration between clinical phenomes and lipidomic profiles.
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Affiliation(s)
- Linlin Zhang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University, Shanghai, China
| | - Bijun Zhu
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University, Shanghai, China
| | - Yiming Zeng
- Department of Respiratory Diseases, Clinical Center for Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Hui Shen
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China.
| | - Jiaqiang Zhang
- Department of Anesthesiology, Clinical Center of Single Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China.
| | - Xiangdong Wang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Fudan University, Shanghai, China.
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21
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Duan X, Chen B, Cui Y, Zhou L, Wu C, Yang Z, Wen Y, Miao X, Li Q, Xiong L, He J. Ready player one? Autophagy shapes resistance to photodynamic therapy in cancers. Apoptosis 2019; 23:587-606. [PMID: 30288638 DOI: 10.1007/s10495-018-1489-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Photodynamic therapy (PDT) is a procedure used in cancer therapy that has been shown to be useful for certain indications. Considerable evidence suggests that PDT might be superior to conventional modalities for some indications. In this report, we examine the relationship between PDT responsiveness and autophagy, which can exert a cytoprotective effect. Autophagy is an essential physiological process that maintains cellular homeostasis by degrading dysfunctional or impaired cellular components and organelles via a lysosome-based pathway. Autophagy, which includes macroautophagy and microautophagy, can be a factor that decreases or abolishes responses to various therapeutic protocols. We systematically discuss the mechanisms underlying cell-fate decisions elicited by PDT; analyse the principles of PDT-induced autophagy, macroautophagy and microautophagy; and present evidence to support the notion that autophagy is a critical mechanism in resistance to PDT. A combined strategy involving autophagy inhibitors may be able to further enhance PDT efficacy. Finally, we provide suggestions for future studies, note where our understanding of the relevant molecular regulators is deficient, and discuss the correlations among PDT-induced resistance and autophagy, especially microautophagy.
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Affiliation(s)
- Xian Duan
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Chen
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yanan Cui
- Department of Respiratory Medicine, Second Xiangya Hospital, Central South University, Changsha, China
| | - Lin Zhou
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Chenkai Wu
- Department of Respiratory Medicine, Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhulin Yang
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yu Wen
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiongying Miao
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Qinglong Li
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Li Xiong
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, China.
| | - Jun He
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, China.
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22
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Wang DC, Wang W, Zhang L, Wang X. A tour of 3D genome with a focus on CTCF. Semin Cell Dev Biol 2019; 90:4-11. [PMID: 30031214 DOI: 10.1016/j.semcdb.2018.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The complex three-dimensional (3D) structure of the genome plays critical roles in the maintenance of genome stability, organization, and dynamics and in regulation of gene expression for understanding molecular mechanisms and diseases. Chromatin maintains biological functions and transcriptional activities through long distance interaction and interactions between loops and enhancers-promoters. We firstly overview the architecture and biology of chromatin and loops, topologically associated domains (TADs) and interactions, and compartments and functions. We specifically focus on CCCTC-binding factor (CTCF) in 3D genome organization and function to furthermore understand the significance of CTCF biology, transcriptional regulations, interactions with cohesin, roles in DNA binding, influences of CTCF degradation, and communication with wings-apart like (Wapl) protein. We also summarize the advanced single cell approaches to further monitor dynamics of CTCF functions and structures in the maintenance of 3D genome organization and function at single cell level.
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Affiliation(s)
- Diane C Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - William Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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23
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Hofman P, Barlesi F. Companion diagnostic tests for treatment of lung cancer patients: what are the current and future challenges? Expert Rev Mol Diagn 2019; 19:429-438. [DOI: 10.1080/14737159.2019.1611426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, and Hospital-integrated Biobank, Côte d’Azur University, Nice, France
| | - Fabrice Barlesi
- CRCM, INSERM, CNRS, AP-HM, Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille University, Marseille, France
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24
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Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:149-158. [PMID: 29943302 DOI: 10.1007/978-981-13-0502-3_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The advent of single-cell omics technology has promoted our understanding of the genomic, epigenomic, and transcriptomic heterogeneity in individual cells. Compared to traditional sequencing studies using bulk cells, single-cell transcriptome technology is naturally more dynamic for in depth analysis of genomic variation resulting from cell division and is useful in unraveling the regulatory mechanisms of gene networks in many diseases. However, there are still some limitations of current single-cell RNA sequencing (scRNA-seq) protocols. Biases that arise during the RNA reverse transcription and cDNA pre-amplification steps are the most common problems and play pivotal roles in limiting the quantitative accuracy of scRNA-seq. In this review, we will describe how these biases emerge and impact scRNA-seq protocols. Moreover, we will introduce several current and convenient modified scRNA-seq methods that allow for bias to be decreased and estimated.
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25
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Detection and Application of RNA Editing in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:159-170. [PMID: 29943303 DOI: 10.1007/978-981-13-0502-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA editing is the process which happened in the post-transcriptional stage that the genetic information contained in an RNA molecule will be changed. RNA editing has been found to be related with many cancers, so through identifying RNA editing sites, we can find useful information on the process of carcinogenesis. In this review, we will discuss the main types of RNA editing and their role in cancers, as well as the current detection methods of RNA editing and the challenges we should overcome.
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26
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Merrick DT, Edwards MG, Franklin WA, Sugita M, Keith RL, Miller YE, Friedman MB, Dwyer-Nield LD, Tennis MA, O'Keefe MC, Donald EJ, Malloy JM, van Bokhoven A, Wilson S, Koch PJ, O'Shea C, Coldren C, Orlicky DJ, Lu X, Baron AE, Hickey G, Kennedy TC, Powell R, Heasley L, Bunn PA, Geraci M, Nemenoff RA. Altered Cell-Cycle Control, Inflammation, and Adhesion in High-Risk Persistent Bronchial Dysplasia. Cancer Res 2018; 78:4971-4983. [PMID: 29997230 PMCID: PMC6147150 DOI: 10.1158/0008-5472.can-17-3822] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/16/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
Persistent bronchial dysplasia is associated with increased risk of developing invasive squamous cell carcinoma (SCC) of the lung. In this study, we hypothesized that differences in gene expression profiles between persistent and regressive bronchial dysplasia would identify cellular processes that underlie progression to SCC. RNA expression arrays comparing baseline biopsies from 32 bronchial sites that persisted/progressed to 31 regressive sites showed 395 differentially expressed genes [ANOVA, FDR ≤ 0.05). Thirty-one pathways showed significantly altered activity between the two groups, many of which were associated with cell-cycle control and proliferation, inflammation, or epithelial differentiation/cell-cell adhesion. Cultured persistent bronchial dysplasia cells exhibited increased expression of Polo-like kinase 1 (PLK1), which was associated with multiple cell-cycle pathways. Treatment with PLK1 inhibitor induced apoptosis and G2-M arrest and decreased proliferation compared with untreated cells; these effects were not seen in normal or regressive bronchial dysplasia cultures. Inflammatory pathway activity was decreased in persistent bronchial dysplasia, and the presence of an inflammatory infiltrate was more common in regressive bronchial dysplasia. Regressive bronchial dysplasia was also associated with trends toward overall increases in macrophages and T lymphocytes and altered polarization of these inflammatory cell subsets. Increased desmoglein 3 and plakoglobin expression was associated with higher grade and persistence of bronchial dysplasia. These results identify alterations in the persistent subset of bronchial dysplasia that are associated with high risk for progression to invasive SCC. These alterations may serve as strong markers of risk and as effective targets for lung cancer prevention.Significance: Gene expression profiling of high-risk persistent bronchial dysplasia reveals changes in cell-cycle control, inflammatory activity, and epithelial differentiation/cell-cell adhesion that may underlie progression to invasive SCC. Cancer Res; 78(17); 4971-83. ©2018 AACR.
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Affiliation(s)
- Daniel T Merrick
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Michael G Edwards
- Department of Medicine/Division of Pulmonary Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Wilbur A Franklin
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Michio Sugita
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Robert L Keith
- Department of Medicine/Division of Pulmonary Medicine, Denver Veterans Affairs Medical Center, Aurora, Colorado
- Department of Medicine/Division of Pulmonary Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - York E Miller
- Department of Medicine/Division of Pulmonary Medicine, Denver Veterans Affairs Medical Center, Aurora, Colorado
- Department of Medicine/Division of Pulmonary Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Micah B Friedman
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Lori D Dwyer-Nield
- Department of Medicine/Division of Pulmonary Medicine, Denver Veterans Affairs Medical Center, Aurora, Colorado
- School of Pharmacy, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Meredith A Tennis
- Department of Medicine/Division of Pulmonary Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Mary C O'Keefe
- Department of Pathology, Denver Health Medical Center, Denver, Colorado
| | - Elizabeth J Donald
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jessica M Malloy
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Adrie van Bokhoven
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Storey Wilson
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Peter J Koch
- Department of Regenerative Medicine and Stem Cell Research, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Charlene O'Shea
- Department of Regenerative Medicine and Stem Cell Research, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - David J Orlicky
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Xian Lu
- Department of Biostatistics and Informatics, Colorado School of Public Health, Denver, Colorado
| | - Anna E Baron
- Department of Biostatistics and Informatics, Colorado School of Public Health, Denver, Colorado
| | - Greg Hickey
- Department of Medicine/Division of Pulmonary Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Timothy C Kennedy
- Department of Medicine/Division of Pulmonary Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Roger Powell
- School of Pharmacy, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Lynn Heasley
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Paul A Bunn
- Department of Medicine/Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Mark Geraci
- Department of Medicine, Indiana University, Bloomington, Indiana
| | - Raphael A Nemenoff
- Department of Medicine/Division of Pulmonary Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Medicine, Division of Renal Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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27
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Hodgson A, Liu SK, Vesprini D, Xu B, Downes MR. Basal-subtype bladder tumours show a ‘hot’ immunophenotype. Histopathology 2018; 73:748-757. [DOI: 10.1111/his.13696] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 05/25/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Anjelica Hodgson
- Department of Anatomic Pathology; Sunnybrook Health Sciences Centre; University of Toronto; Toronto Ontario Canada
- Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Ontario Canada
| | - Stanley K Liu
- Department of Radiation Oncology; University of Toronto; Toronto Ontario Canada
| | - Danny Vesprini
- Department of Radiation Oncology; University of Toronto; Toronto Ontario Canada
| | - Bin Xu
- Department of Anatomic Pathology; Sunnybrook Health Sciences Centre; University of Toronto; Toronto Ontario Canada
- Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Ontario Canada
| | - Michelle R Downes
- Department of Anatomic Pathology; Sunnybrook Health Sciences Centre; University of Toronto; Toronto Ontario Canada
- Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Ontario Canada
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28
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Wang, DC, Wang, W, Zhu, B, Wang X. Lung Cancer Heterogeneity and New Strategies for Drug Therapy. Annu Rev Pharmacol Toxicol 2018; 58:531-546. [PMID: 28977762 DOI: 10.1146/annurev-pharmtox-010716-104523] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Diane C. Wang,
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
| | - William Wang,
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
| | - Bijun Zhu,
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai 200032, China
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29
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Predictive value of different proportion of lesion HLA-G expression in colorectal cancer. Oncotarget 2017; 8:107441-107451. [PMID: 29296176 PMCID: PMC5746078 DOI: 10.18632/oncotarget.22487] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/28/2017] [Indexed: 01/12/2023] Open
Abstract
Differential expression of HLA-G has been observed among cancer types and tumors from individuals with the same type of cancer; however, its clinical significance is rather limited. In this study, expression and predictive relevance of HLA-G expression in 457 primary colorectal cancer (CRC, ncolon = 232, nrectal = 225) patients was investigated. Data showed 70.7% (323/457) of the CRC were HLA-G expression when the above 5% (HLA-GLow) was considered as positive, which wasn't associated with patient survival (p = 0.109). However, HLA-G expression above 55% (HLA-GHigh) was associated with a worse prognosis of CRC patients (p = 0.042). Furthermore, a shorter survival was found for the female (p = 0.042) and elder (p = 0.037) patients whose HLA-G expression was above HLA-GLow level. HLA-G expression above HLA-GHigh level showed a worse prognosis for female (p = 0.013), elder (p = 0.023), colon cancer (p = 0.016), advanced tumor burden (T3+4, p = 0.018), regional lymph node status (N1+2, p = 0.044), and advanced clinical stage patients (AJCC III+IV, p = 0.037). In conclusion, our results demonstrated for the first time that combination of differential lesion HLA-G expression notably improved the value of traditional survival prediction for CRC patients.
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31
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Qian M, Zhu B, Wang X, Liebman M. Drug resistance in ALK-positiveNon-small cell lungcancer patients. Semin Cell Dev Biol 2017; 64:150-157. [DOI: 10.1016/j.semcdb.2016.09.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023]
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32
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Wang DC, Wang X. Systems heterogeneity: An integrative way to understand cancer heterogeneity. Semin Cell Dev Biol 2016; 64:1-4. [PMID: 27552921 DOI: 10.1016/j.semcdb.2016.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/14/2022]
Abstract
The concept of systems heterogeneity was firstly coined and explained in the Special Issue, as a new alternative to understand the importance and complexity of heterogeneity in cancer. Systems heterogeneity can offer a full image of heterogeneity at multi-dimensional functions and multi-omics by integrating gene or protein expression, epigenetics, sequencing, phosphorylation, transcription, pathway, or interaction. The Special Issue starts with the roles of epigenetics in the initiation and development of cancer heterogeneity through the interaction between permanent genetic mutations and dynamic epigenetic alterations. Cell heterogeneity was defined as the difference in biological function and phenotypes between cells in the same organ/tissue or in different organs, as well as various challenges, as exampled in telocytes. The single cell heterogeneity has the value of identifying diagnostic biomarkers and therapeutic targets and clinical potential of single cell systems heterogeneity in clinical oncology. A number of signaling pathways and factors contribute to the development of systems heterogeneity. Proteomic heterogeneity can change the strategy and thinking of drug discovery and development by understanding the interactions between proteins or proteins with drugs in order to optimize drug efficacy and safety. The association of cancer heterogeneity with cancer cell evolution and metastasis was also overviewed as a new alternative for diagnostic biomarkers and therapeutic targets in clinical application.
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Affiliation(s)
- Diane Catherine Wang
- Minghang Hospital of Fudan University, Shanghai Medical College, Shanghai, China
| | - Xiangdong Wang
- Minghang Hospital of Fudan University, Shanghai Medical College, Shanghai, China.
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