1
|
Huang WL, Hsu YC, Luo CW, Chang SJ, Hung YH, Lai CY, Yang YT, Chen YZ, Wu CC, Chen FM, Hou MF, Pan MR. Targeting the CDK7-MDK axis to suppresses irinotecan resistance in colorectal cancer. Life Sci 2024; 353:122914. [PMID: 39004275 DOI: 10.1016/j.lfs.2024.122914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
AIMS Colorectal cancer (CRC) remains a major global health issue, with metastatic cases presenting poor prognosis despite advances in chemotherapy and targeted therapy. Irinotecan, a key drug for advanced CRC treatment, faces challenges owing to the development of resistance. This study aimed to understand the mechanisms underlying irinotecan resistance in colorectal cancer. MAIN METHODS We created a cell line resistant to irinotecan using HT29 cells. These resistant cells were utilized to investigate the role of the CDK7-MDK axis. We employed bulk RNA sequencing, conducted in vivo experiments with mice, and analyzed patient tissues to examine the effects of the CDK7-MDK axis on the cellular response to irinotecan. KEY FINDINGS Our findings revealed that HT29 cells resistant to irinotecan, a crucial colorectal cancer medication, exhibited significant phenotypic and molecular alterations compared to their parental counterparts, including elevated stem cell characteristics and increased levels of cytokines and drug resistance proteins. Notably, CDK7 expression was substantially higher in these resistant cells, and targeting CDK7 effectively decreased their survival and tumor growth, enhancing irinotecan sensitivity. RNA-seq analysis indicated that suppression of CDK7 in irinotecan-resistant HT29 cells significantly reduced Midkine (MDK) expression. Decreased CDK7 and MDK levels, achieved through siRNA and the CDK7 inhibitor THZ1, enhanced the sensitivity of resistant HT29 cells to irinotecan. SIGNIFICANCE Our study sheds light on how CDK7 and MDK influence irinotecan resistance in colorectal and highlights the potential of MDK-targeted therapies. We hypothesized that irinotecan sensitivity and overall treatment efficacy would improve by inhibiting MDK. This finding encourages a careful yet proactive investigation of MDK as a therapeutic target to enhance outcomes in colorectal cancer patients.
Collapse
Affiliation(s)
- Wei-Lun Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | - Yin-Chou Hsu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Department of Emergency Medicine, E-Da Hospital, I-Shou University, Kaohsiung City 824, Taiwan
| | - Chi-Wen Luo
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung City 807, Taiwan; Department of Cosmetic Science, Institute of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan.
| | - Shu-Jyuan Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu-Hsuan Hung
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chiao-Ying Lai
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu-Tzu Yang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yi-Zi Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Fang-Ming Chen
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung City 807, Taiwan
| | - Ming-Feng Hou
- Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung City 807, Taiwan; Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung City 807, Taiwan.
| |
Collapse
|
2
|
Lu Y, Jiang J, He Z, Bao Z, Chen X, Cheng J. Molecular characteristics and oncogenic role of CHD family genes: a pan-cancer analysis based on bioinformatic and biological analysis. Sci Rep 2024; 14:18923. [PMID: 39143142 PMCID: PMC11324730 DOI: 10.1038/s41598-024-68644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 07/25/2024] [Indexed: 08/16/2024] Open
Abstract
Chromodomain helicase DNA-binding protein (CHD) gene family, an ATP (adenosine triphosphate) -dependent chromatin remodeler family, is involved in multiple developmental process and tumor development. However, there have been none pan-cancer analyses of this family. The expression levels, survival profiles, mutation profiles and immune infiltration of the CHD family genes from TCGA and TARGET database were analyzed using online tools or R packages. Interestingly, all types of CHD gene expressions were associated with the prognosis of Neuroblastoma, Acute lymphoblastic leukemia-Phase 3 and Acute Myeloid Leukemia (All P < 0.05). Knock down of CHD7 and CHD9 in K562 (human erythromyeloblastoid leukemia) and HEC-1-B (human endometrial adenocarcinoma) cells significantly inhibit cell proliferation and migration (P < 0.05). Proliferation, colony formation and migration assays were performed in CHD7 and CHD9 knockdown K562 and HBC-1-B cell lines. Mechanisms were also analyzed by PPI and GO ontology for our experiments. Histone modification, especially the methylation of H3K4, might be involved in CHD7 and CHD9 related oncogenesis. Through bioinformatic analysis, we showed CHD genes significantly affected the prognosis of different tumor types, including childhood tumor. Our findings provide new insights into the function and mechanism of CHD gene family, especially in CHD7 and CHD9.
Collapse
Affiliation(s)
- Yujia Lu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiebang Jiang
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Zhihong He
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhouzhou Bao
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xin Chen
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.
- Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University, School of Medicine, Shanghai, China.
| | - Jie Cheng
- Center for Reproductive Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.
| |
Collapse
|
3
|
Shi N, Chen S, Wang D, Wu T, Zhang N, Chen M, Ding X. MDK promotes M2 macrophage polarization to remodel the tumour microenvironment in clear cell renal cell carcinoma. Sci Rep 2024; 14:18254. [PMID: 39107475 PMCID: PMC11303797 DOI: 10.1038/s41598-024-69183-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
The efficacy of immunotherapy for clear cell renal cell carcinoma (ccRCC), especially advanced ccRCC, is limited, presenting a clinical challenge. This limitation is closely tied to the immune regulation network. Understanding the heterogeneity of the tumour microenvironment (TME) is crucial for developing advanced ccRCC therapies. Using publicly available ccRCC data (scRNA-seq, bulk RNA-seq, and somatic mutation data), a multiomics study was performed to explore TME heterogeneity. Three distinct ccRCC immune subtypes were identified through combined scRNA-seq and bulk RNA-seq analysis. A prognostic model based on unique cell signalling molecules in immunosuppressive tumour subtype was validated in the TCGA and CheckMate cohorts. MDK emerged as a critical regulatory gene in the immunosuppressive subtype, predicting a poor ccRCC prognosis and a poor immunotherapy response. MDK promotes M2 macrophage polarization via the MDK-LRP1 interaction, and the inhibition of MDK suppressed M2 polarization. This study revealed the heterogeneity of the ccRCC TME and a reliable prognostic model, shedding light on the vital role of MDK in the immunosuppressive TME and paving the way for optimized ccRCC immunotherapy.
Collapse
Affiliation(s)
- Naipeng Shi
- Department of Urology, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Saisai Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Dong Wang
- Department of Urology, Nantong Tongzhou Hospital of Traditional Chinese Medicine, Nantong, China
| | - Tiange Wu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Nieke Zhang
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Xuefei Ding
- Department of Urology, Northern Jiangsu People's Hospital, Yangzhou, China.
| |
Collapse
|
4
|
Dayati P, Shakhssalim N, Allameh A. Over-expression of KRT17 and MDK genes at mRNA levels in urine-exfoliated cells is associated with early non-invasive diagnosis of non-muscle-invasive bladder cancer. Clin Biochem 2024; 131-132:110808. [PMID: 39069115 DOI: 10.1016/j.clinbiochem.2024.110808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
INTRODUCTION Current diagnostic approaches for bladder cancer (BLCA) are often invasive or lack the required sensitivity and specificity. This underscores the need for an early non-invasive diagnostic test for BLCA. This work aimed to explore the potential of molecular markers in urine-exfoliated cells for the diagnosis of non-muscle-invasive bladder cancer (NMIBC). MATERIALS AND METHODS Urine specimens (n = 140) were collected from NMIBC patients (n = 68) and control subjects (31 healthy volunteers and 41 non-cancer patients with common urological diseases [CUD]. Total RNA was extracted from the cells isolated from urine specimens. mRNA expression of selected genes: CDC20, KRT15, FOXM1, CXCR2, UPK1B, MDK, KRT20, and KRT17 was determined using RT-qPCR. The receiver operating characteristic (ROC) curve was then plotted to obtain the area under the curve (AUC), specificity, and sensitivity of the urinary mRNA markers. RESULTS The expression of CDC20, MDK, UPK1B, FOXM1, KRT17, and KRT20 was up-regulated in samples obtained from low- and high-grade pathological grades of NMIBC compared to that measured in healthy subjects. Notably, MDK and KRT17 mRNA levels in the low- and high-grade cases were substantially higher than in normal and CUD groups. The AUC of the KRT17 and MDK combination in diagnosing NMIBC was 0.92, surpassing that of single genes. The sensitivity and specificity of the KRT17 and MDK combination were 74% and 94%, respectively. In diagnosing low-grade from healthy and CUD groups, analysis of the KRT17 and MDK combination yielded AUCs of 0.94 and 0.95, respectively, with sensitivities of 85% and 97%, and specificities of 93% and 85%. CONCLUSION The findings of this study revealed that KRT17 and MDK together are potential urine-based biomarkers for early diagnosis of NMIBC.
Collapse
Affiliation(s)
- Parisa Dayati
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nasser Shakhssalim
- Urology and Nephrology Research Center, Shahid Labbafinejad Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdolamir Allameh
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
5
|
Fei H, Chen T, Jiang H. Autocrine and paracrine effects of MDK promote lymph node metastasis of cervical squamous cell carcinoma. iScience 2024; 27:110077. [PMID: 39040052 PMCID: PMC11261016 DOI: 10.1016/j.isci.2024.110077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/02/2023] [Accepted: 05/19/2024] [Indexed: 07/24/2024] Open
Abstract
Lymph node metastasis (LNM) is the main metastatic pathway of cervical cancer, which is closely related to 5-year survival rate of cervical squamous cell carcinoma (CSCC), yet the underlying mechanism remains unconfirmed. In this study, we show that midkine (MDK) was highly expressed in CSCC and overexpression of MDK was associated with CSCC LNM. Functional investigations demonstrated that MDK promoted LNM by enhancing proliferation, migration and invasion capacity of cervical cancer cells, facilitating lymphangiogenesis and down-regulating the expression of tight junction proteins of human lymphatic endothelial cells (HLECs). MDK exerted these biological effects by interacting with Syndecan-1 and activating PI3K/AKT and p38 MAPK pathways. A retrospective study showed that s-MDK was related to LNM. s-MDK combined with serum-squamous cell carcinoma antigen(s-SCCA) improved the diagnostic accuracy of CSCC LNM. These findings established a new mechanism of LNM and highlighted MDK as a candidate tumor biomarker and therapeutic target in CSCC.
Collapse
Affiliation(s)
- He Fei
- Department of Gynecology, The Fifth People’s Hospital of Shanghai, Fudan University, Shanghai 200240, China
| | - Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Hua Jiang
- Department of Gynecology, Obstetrics & Gynecology Hospital, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| |
Collapse
|
6
|
Chen S, Liao J, Li J, Wang S. GPC2 promotes prostate cancer progression via MDK-mediated activation of PI3K/AKT signaling pathway. Funct Integr Genomics 2024; 24:127. [PMID: 39014225 PMCID: PMC11252201 DOI: 10.1007/s10142-024-01406-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/13/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024]
Abstract
Prostate cancer is a major medical problem for men worldwide. Advanced prostate cancer is currently incurable. Recently, much attention was paid to the role of GPC2 in the field of oncology. Nevertheless, there have been no investigations of GPC2 and its regulatory mechanism in prostate cancer. Here, we revealed a novel action of GPC2 and a tumor promoting mechanism in prostate cancer. GPC2 was upregulated in prostate cancer tissues and cell lines. Higher expression of GPC2 was correlated with higher Gleason score, lymphatic metastasis, and worse overall survival in prostate cancer patients. Decreased expression of GPC2 inhibited cell proliferation, migration, and invasion in prostate cancer, whereas GPC2 overexpression promoted these properties. Mechanistically, GPC2 promoted the activation of PI3K/AKT signaling pathway through MDK. The rescue assay results in prostate cancer cells demonstrated that overexpression of MDK could attenuate GPC2 knockdown induced inactivation of PI3K/AKT signaling and partly reverse GPC2 knockdown induced inhibition of cell proliferation, migration, and invasion. In all, our study identified GPC2 as an oncogene in prostate cancer. GPC2 promoted prostate cancer cell proliferation, migration, and invasion via MDK-mediated activation of PI3K/AKT signaling pathway. GPC2 might be a promising prognosis predictor and potential therapeutic target in prostate cancer.
Collapse
Affiliation(s)
- Sijin Chen
- Department of Urology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, China
| | - Jiaxing Liao
- Department of Urology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, China
| | - Juhua Li
- Department of Urology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, China
| | - Saihui Wang
- Department of Urology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, China.
| |
Collapse
|
7
|
Yang L, Wang G, Tian H, Jia S, Wang S, Cui R, Zhuang A. RBMS1 reflects a distinct microenvironment and promotes tumor progression in ocular melanoma. Exp Eye Res 2024; 246:109990. [PMID: 38969283 DOI: 10.1016/j.exer.2024.109990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Ocular melanoma, including uveal melanoma (UM) and conjunctival melanoma (CM), is the most common ocular cancer among adults with a high rate of recurrence and poor prognosis. Loss of epigenetic homeostasis disturbed gene expression patterns, resulting in oncogenesis. Herein, we comprehensively analyzed the DNA methylation, transcriptome profiles, and corresponding clinical information of UM patients through multiple machine-learning algorithms, finding that a methylation-driven gene RBMS1 was correlated with poor clinical outcomes of UM patients. RNA-seq and single-cell RNA-seq analyses revealed that RBMS1 reflected diverse tumor microenvironments, where high RBMS1 expression marked an immune active TME. Furthermore, we found that tumor cells were identified to have the higher communication probability in RBMS1+ state. The functional enrichment analysis revealed that RBMS1 was associated with pigment granule and melanosome, participating in cell proliferation as well as apoptotic signaling pathway. Biological experiments were performed and demonstrated that the silencing of RBMS1 inhibited ocular melanoma proliferation and promoted apoptosis. Our study highlighted that RBMS1 reflects a distinct microenvironment and promotes tumor progression in ocular melanoma, contributing to the therapeutic customization and clinical decision-making.
Collapse
Affiliation(s)
- Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, PR China
| | - Gaoming Wang
- Department of Medical Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, PR China
| | - Hao Tian
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, PR China
| | - Shichong Jia
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Nankai University Affiliated Eye Hospital, Tianjin Eye Institute, Tianjin, 300020, PR China
| | - Shaoyun Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, PR China.
| | - Ran Cui
- Department of Medical Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, PR China.
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200011, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, PR China.
| |
Collapse
|
8
|
Liu S, Li G, Yin X, Zhou Y, Luo D, Yang Z, Zhang J, Wang J. Comprehensive investigation of malignant epithelial cell-related genes in clear cell renal cell carcinoma: development of a prognostic signature and exploration of tumor microenvironment interactions. J Transl Med 2024; 22:607. [PMID: 38951896 PMCID: PMC11218120 DOI: 10.1186/s12967-024-05426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a prevalent malignancy with complex heterogeneity within epithelial cells, which plays a crucial role in tumor progression and immune regulation. Yet, the clinical importance of the malignant epithelial cell-related genes (MECRGs) in ccRCC remains insufficiently understood. This research aims to undertake a comprehensive investigation into the functions and clinical relevance of malignant epithelial cell-related genes in ccRCC, providing valuable understanding of the molecular mechanisms and offering potential targets for treatment strategies. Using data from single-cell sequencing, we successfully identified 219 MECRGs and established a prognostic model MECRGS (MECRGs' signature) by synergistically analyzing 101 machine-learning models using 10 different algorithms. Remarkably, the MECRGS demonstrated superior predictive performance compared to traditional clinical features and 92 previously published signatures across six cohorts, showcasing its independence and accuracy. Upon stratifying patients into high- and low-MECRGS subgroups using the specified cut-off threshold, we noted that patients with elevated MECRGS scores displayed characteristics of an immune suppressive tumor microenvironment (TME) and showed worse outcomes after immunotherapy. Additionally, we discovered a distinct ccRCC tumor cell subtype characterized by the high expressions of PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2) and SAA1 (Serum Amyloid A1), which we further validated in the Renji tissue microarray (TMA) cohort. Lastly, 'Cellchat' revealed potential crosstalk patterns between these cells and other cell types, indicating their potential role in recruiting CD163 + macrophages and regulatory T cells (Tregs), thereby establishing an immunosuppressive TME. PLOD2 + SAA1 + cancer cells with intricate crosstalk patterns indeed show promise for potential therapeutic interventions.
Collapse
Affiliation(s)
- Songyang Liu
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ge Li
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaomao Yin
- Department of Gastrointestinal Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yihan Zhou
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dongmei Luo
- Department of Internal Medicine, Shanghai Gongli Hospital, Second Military Medical University, Shanghai, China
| | - Zhenggang Yang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Zhang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianfeng Wang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
9
|
Zvirblyte J, Nainys J, Juzenas S, Goda K, Kubiliute R, Dasevicius D, Kincius M, Ulys A, Jarmalaite S, Mazutis L. Single-cell transcriptional profiling of clear cell renal cell carcinoma reveals a tumor-associated endothelial tip cell phenotype. Commun Biol 2024; 7:780. [PMID: 38942917 PMCID: PMC11213875 DOI: 10.1038/s42003-024-06478-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/21/2024] [Indexed: 06/30/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent form of renal cancer, accounting for over 75% of cases. The asymptomatic nature of the disease contributes to late-stage diagnoses and poor survival. Highly vascularized and immune infiltrated microenvironment are prominent features of ccRCC, yet the interplay between vasculature and immune cells, disease progression and response to therapy remains poorly understood. Using droplet-based single-cell RNA sequencing we profile 50,236 transcriptomes from paired tumor and healthy adjacent kidney tissues. Our analysis reveals significant heterogeneity and inter-patient variability of the tumor microenvironment. Notably, we discover a previously uncharacterized vasculature subpopulation associated with epithelial-mesenchymal transition. The cell-cell communication analysis reveals multiple modes of immunosuppressive interactions within the tumor microenvironment, including clinically relevant interactions between tumor vasculature and stromal cells with immune cells. The upregulation of the genes involved in these interactions is associated with worse survival in the TCGA KIRC cohort. Our findings demonstrate the role of tumor vasculature and stromal cell populations in shaping the ccRCC microenvironment and uncover a subpopulation of cells within the tumor vasculature that is associated with an angiogenic phenotype.
Collapse
Affiliation(s)
- Justina Zvirblyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Juozas Nainys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
- Droplet Genomics, Vilnius, 10257, Lithuania
| | - Simonas Juzenas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Karolis Goda
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Raimonda Kubiliute
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania
| | - Darius Dasevicius
- National Center of Pathology, Affiliate of Vilnius University Hospital Santaros Klinikos, Vilnius, 08406, Lithuania
| | | | - Albertas Ulys
- National Cancer Institute, Vilnius, 08660, Lithuania
| | - Sonata Jarmalaite
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
- National Cancer Institute, Vilnius, 08660, Lithuania.
| | - Linas Mazutis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, 10257, Lithuania.
| |
Collapse
|
10
|
Chien F, Michaud ME, Bakhtiari M, Schroff C, Snuderl M, Velazquez Vega JE, MacDonald TJ, Bhasin MK. Medulloblastoma Spatial Transcriptomics Reveals Tumor Microenvironment Heterogeneity with High-Density Progenitor Cell Regions Correlating with High-Risk Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600684. [PMID: 38979174 PMCID: PMC11230370 DOI: 10.1101/2024.06.25.600684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The tumor microenvironment (TME) of medulloblastoma (MB) influences progression and therapy response, presenting a promising target for therapeutic advances. Prior single-cell analyses have characterized the cellular components of the TME but lack spatial context. To address this, we performed spatial transcriptomic sequencing on sixteen pediatric MB samples obtained at diagnosis, including two matched diagnosis-relapse pairs. Our analyses revealed inter- and intra-tumoral heterogeneity within the TME, comprised of tumor-associated astrocytes (TAAs), macrophages (TAMs), stromal components, and distinct subpopulations of MB cells at different stages of neuronal differentiation and cell cycle progression. We identified dense regions of quiescent progenitor-like MB cells enriched in patients with high-risk (HR) features and an increase in TAAs, TAMs, and dysregulated vascular endothelium following relapse. Our study presents novel insights into the spatial architecture and cellular landscape of the medulloblastoma TME, highlighting spatial patterns linked to HR features and relapse, which may serve as potential therapeutic targets.
Collapse
Affiliation(s)
- Franklin Chien
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
| | - Marina E. Michaud
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Mojtaba Bakhtiari
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Chanel Schroff
- Department of Pathology, NYU Langone Health and Grossman School of Medicine, New York, NY 10016, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health and Grossman School of Medicine, New York, NY 10016, USA
| | - Jose E. Velazquez Vega
- Department of Pathology and Laboratory Medicine, Children’s Healthcare of Atlanta and Emory School of Medicine, Atlanta, GA 30322, USA
| | - Tobey J. MacDonald
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
| | - Manoj K. Bhasin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, GA 30322, USA
- Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
11
|
Zhang M, Zhou K, Wang Z, Liu T, Stevens LE, Lynce F, Chen WY, Peng S, Xie Y, Zhai D, Chen Q, Shi Y, Shi H, Yuan Z, Li X, Xu J, Cai Z, Guo J, Shao N, Lin Y. A Subpopulation of Luminal Progenitors Secretes Pleiotrophin to Promote Angiogenesis and Metastasis in Inflammatory Breast Cancer. Cancer Res 2024; 84:1781-1798. [PMID: 38507720 PMCID: PMC11148543 DOI: 10.1158/0008-5472.can-23-2640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/19/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
Inflammatory breast cancer (IBC) is a highly aggressive subtype of breast cancer characterized by rapidly arising diffuse erythema and edema. Genomic studies have not identified consistent alterations and mechanisms that differentiate IBC from non-IBC tumors, suggesting that the microenvironment could be a potential driver of IBC phenotypes. Here, using single-cell RNA sequencing, multiplex staining, and serum analysis in patients with IBC, we identified enrichment of a subgroup of luminal progenitor (LP) cells containing high expression of the neurotropic cytokine pleiotrophin (PTN) in IBC tumors. PTN secreted by the LP cells promoted angiogenesis by directly interacting with the NRP1 receptor on endothelial tip cells located in both IBC tumors and the affected skin. NRP1 activation in tip cells led to recruitment of immature perivascular cells in the affected skin of IBC, which are correlated with increased angiogenesis and IBC metastasis. Together, these findings reveal a role for cross-talk between LPs, endothelial tip cells, and immature perivascular cells via PTN-NRP1 axis in the pathogenesis of IBC, which could lead to improved strategies for treating IBC. SIGNIFICANCE Nonmalignant luminal progenitor cells expressing pleiotrophin promote angiogenesis by activating NRP1 and induce a prometastatic tumor microenvironment in inflammatory breast cancer, providing potential therapeutic targets for this aggressive breast cancer subtype.
Collapse
Affiliation(s)
- Mengmeng Zhang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaiwen Zhou
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zilin Wang
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ting Liu
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Filipa Lynce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Wendy Y Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sui Peng
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yubin Xie
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Duanyang Zhai
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qianjun Chen
- Department of Breast Oncology, Traditional Chinese Medicine Hospital of Guangdong Province, Guangzhou, Guangdong, China
| | - Yawei Shi
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhongyu Yuan
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoping Li
- Department of Breast Oncology, Jiangmen Central Hospital, Jiangmen, China
| | - Juan Xu
- Department of Breast Oncology, Maternal and Child Health Care Hospital of Guangdong Province, Guangzhou, China
| | - Zhenhai Cai
- Department of Breast Oncology, Jieyang People's Hospital, Jieyang, China
| | - Jianping Guo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Nan Shao
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ying Lin
- Breast Disease Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
12
|
Li K, Zhang R, Wen F, Zhao Y, Meng F, Li Q, Hao A, Yang B, Lu Z, Cui Y, Zhou M. Single-cell dissection of the multicellular ecosystem and molecular features underlying microvascular invasion in HCC. Hepatology 2024; 79:1293-1309. [PMID: 37972953 PMCID: PMC11095903 DOI: 10.1097/hep.0000000000000673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND AIMS Microvascular invasion (MVI) is a crucial pathological hallmark of HCC that is closely associated with poor outcomes, early recurrence, and intrahepatic metastasis following surgical resection and transplantation. However, the intricate tumor microenvironment and transcriptional programs underlying MVI in HCC remain poorly understood. APPROACH AND RESULTS We performed single-cell RNA sequencing of 46,789 individual cells from 10 samples of MVI+ (MVI present) and MVI- (MVI absent) patients with HCC. We conducted comprehensive and comparative analyses to characterize cellular and molecular features associated with MVI and validated key findings using external bulk, single-cell, and spatial transcriptomic datasets coupled with multiplex immunofluorescence assays. The comparison identified specific subtypes of immune and stromal cells critical to the formation of the immunosuppressive and pro-metastatic microenvironment in MVI+ tumors, including cycling T cells, lysosomal associated membrane protein 3+ dendritic cells, triggering receptor expressed on myeloid cells 2+ macrophages, myofibroblasts, and arterial i endothelial cells. MVI+ malignant cells are characterized by high proliferation rates, whereas MVI- malignant cells exhibit an inflammatory milieu. Additionally, we identified the midkine-dominated interaction between triggering receptor expressed on myeloid cells 2+ macrophages and malignant cells as a contributor to MVI formation and tumor progression. Notably, we unveiled a spatially co-located multicellular community exerting a dominant role in shaping the immunosuppressive microenvironment of MVI and correlating with unfavorable prognosis. CONCLUSIONS This study provides a comprehensive single-cell atlas of MVI in HCC, shedding light on the complex multicellular ecosystem and molecular features associated with MVI. These findings deepen our understanding of the underlying mechanisms driving MVI and provide valuable insights for improving clinical diagnosis and developing more effective treatment strategies.
Collapse
Affiliation(s)
- Ke Li
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
| | - Rui Zhang
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Fukai Wen
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Yunzheng Zhao
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Fanshuai Meng
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Qingyu Li
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Aimin Hao
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Bailu Yang
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Zhaoyang Lu
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Yifeng Cui
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Meng Zhou
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, P. R. China
| |
Collapse
|
13
|
Wright GA, Rodriguez-Martinez AC, Conn H, Matarin M, Thompson P, Moore AT, Ba-Abbad R, Webster AR, Moosajee M. Enhanced Learning and Memory in Patients with CRB1 Retinopathy. Genes (Basel) 2024; 15:660. [PMID: 38927596 PMCID: PMC11203261 DOI: 10.3390/genes15060660] [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: 05/04/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Mutations in the CRB1 gene are associated with a diverse spectrum of retinopathies with phenotypic variability causing severe visual impairment. The CRB1 gene has a role in retinal development and is expressed in the cerebral cortex and hippocampus, but its role in cognition has not been described before. This study compares cognitive function in CRB1 retinopathy individuals with subjects with other retinopathies and the normal population. METHODS Neuropsychological tests of cognitive function were used to test individuals with CRB1 and non-CRB1 retinopathies and compare results with a standardised normative dataset. RESULTS CRB1 retinopathy subjects significantly outperformed those with non-CRB1 retinopathy in list learning tasks of immediate (p = 0.001) and delayed memory (p = 0.007), tests of semantic verbal fluency (p = 0.017), verbal IQ digit span subtest (p = 0.037), and estimation test of higher execution function (p = 0.020) but not in the remaining tests of cognitive function (p > 0.05). CRB1 retinopathy subjects scored significantly higher than the normal population in all areas of memory testing (p < 0.05) and overall verbal IQ tests (p = 0.0012). Non-CRB1 retinopathy subjects scored significantly higher than the normal population in story recall, verbal fluency, and overall verbal IQ tests (p = 0.0016). CONCLUSIONS Subjects with CRB1 retinopathy may have enhanced cognitive function in areas of memory and learning. Further work is required to understand the role of CRB1 in cognition.
Collapse
Affiliation(s)
- Genevieve A. Wright
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Ana Catalina Rodriguez-Martinez
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Hanne Conn
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London Hospitals (UCLH), National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK; (H.C.); (M.M.); (P.T.)
| | - Mar Matarin
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London Hospitals (UCLH), National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK; (H.C.); (M.M.); (P.T.)
| | - Pamela Thompson
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London Hospitals (UCLH), National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK; (H.C.); (M.M.); (P.T.)
| | - Anthony T. Moore
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Rola Ba-Abbad
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Andrew R. Webster
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Mariya Moosajee
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| |
Collapse
|
14
|
Younis MA, Harashima H. Understanding Gene Involvement in Hepatocellular Carcinoma: Implications for Gene Therapy and Personalized Medicine. Pharmgenomics Pers Med 2024; 17:193-213. [PMID: 38737776 PMCID: PMC11088404 DOI: 10.2147/pgpm.s431346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/09/2024] [Indexed: 05/14/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the dominant type of liver cancers and is one of the deadliest health threats globally. The conventional therapeutic options for HCC are hampered by low efficiency and intolerable side effects. Gene therapy, however, now offers hope for the treatment of many disorders previously considered incurable, and gene therapy is beginning to address many of the shortcomings of conventional therapies. Herein, we summarize the involvement of genes in the pathogenesis and prognosis of HCC, with a special focus on dysregulated signaling pathways, genes involved in immune evasion, and non-coding RNAs as novel two-edged players, which collectively offer potential targets for the gene therapy of HCC. Herein, the opportunities and challenges of HCC gene therapy are discussed. These include innovative therapies such as genome editing and cell therapies. Moreover, advanced gene delivery technologies that recruit nanomedicines for use in gene therapy for HCC are highlighted. Finally, suggestions are offered for improved clinical translation and future directions in this area of endeavor.
Collapse
Affiliation(s)
- Mahmoud A Younis
- Laboratory of Innovative Nanomedicine, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
- Department of Industrial Pharmacy, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt
| | - Hideyoshi Harashima
- Laboratory of Innovative Nanomedicine, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| |
Collapse
|
15
|
Qin S, Wu H, Li C, Yang J, Yan W, He Z, Xing X, Zhang J, Xu X, Zhao L, Su X. Detection of Naturally occurring abortive transcripts by Base-Stacking Hybridization Assisted Ligation and PCR amplification. Biosens Bioelectron 2024; 251:116099. [PMID: 38330773 DOI: 10.1016/j.bios.2024.116099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Abortive transcripts (ATs) refer to nascent 2-10 nucleotides (nt) RNAs released by RNA polymerases before synthesizing productive RNAs. The quantitative detection of ATs is important for studying transcription initiation and the biological function of ATs; however, no method is available for the qualitative and quantitative assessment of such ultra-short oligonucleotides (typically shorter than 11 nt) in vivo at present, even with the LNA probes, the detection limit can only reach 11 nt. Here, we demonstrated the base stacking hybridization assisted ligation (BSHAL) technique, combined with TaqMan-MGB qPCR, can detect 4-10 nt ATs with a specificity of nucleotide resolution and a sensitivity of approximately 10 pM. By this technique, we detected endogenous ATs in cell lines, mice plasmas, and mice liver tissues, respectively, and proved that naturally occurring ATs do exist. We found that the 8 nt ATs of HMSB and Gapdh could be used as reference ATs for data normalization in Homo and mouse respectively, and 8 nt ATs of Afp and Gpc3 were suitable for use as plasma biomarkers of Hepatocellular carcinoma in mouse, indicate ATs are promising biomarkers. This study offers opportunities to study ATs and other ultra-short oligonucleotides in biological samples.
Collapse
Affiliation(s)
- Shaowei Qin
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Haizhu Wu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Cailin Li
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Jiarui Yang
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, 21218, USA
| | - Weiwei Yan
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Zhigui He
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Xuekun Xing
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Jiayang Zhang
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Xianglin Xu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Lifeng Zhao
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China.
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
16
|
Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T, Mimori K. Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis. EBioMedicine 2024; 103:105102. [PMID: 38614865 PMCID: PMC11121171 DOI: 10.1016/j.ebiom.2024.105102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Cell-cell interaction factors that facilitate the progression of adenoma to sporadic colorectal cancer (CRC) remain unclear, thereby hindering patient survival. METHODS We performed spatial transcriptomics on five early CRC cases, which included adenoma and carcinoma, and one advanced CRC. To elucidate cell-cell interactions within the tumour microenvironment (TME), we investigated the colocalisation network at single-cell resolution using a deep generative model for colocalisation analysis, combined with a single-cell transcriptome, and assessed the clinical significance in CRC patients. FINDINGS CRC cells colocalised with regulatory T cells (Tregs) at the adenoma-carcinoma interface. At early-stage carcinogenesis, cell-cell interaction inference between colocalised adenoma and cancer epithelial cells and Tregs based on the spatial distribution of single cells highlighted midkine (MDK) as a prominent signalling molecule sent from tumour epithelial cells to Tregs. Interaction between MDK-high CRC cells and SPP1+ macrophages and stromal cells proved to be the mechanism underlying immunosuppression in the TME. Additionally, we identified syndecan4 (SDC4) as a receptor for MDK associated with Treg colocalisation. Finally, clinical analysis using CRC datasets indicated that increased MDK/SDC4 levels correlated with poor overall survival in CRC patients. INTERPRETATION MDK is involved in the immune tolerance shown by Tregs to tumour growth. MDK-mediated formation of the TME could be a potential target for early diagnosis and treatment of CRC. FUNDING Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Science Research; OITA Cancer Research Foundation; AMED under Grant Number; Japan Science and Technology Agency (JST); Takeda Science Foundation; The Princess Takamatsu Cancer Research Fund.
Collapse
Affiliation(s)
- Masahiro Hashimoto
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yasuhiro Kojima
- Division of Computational Bioscience, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Takeharu Sakamoto
- Department of Cancer Biology, Institute of Biomedical Science, Kansai Medical University, Hirakata, 573-1010, Japan.
| | - Yuki Ozato
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yusuke Nakano
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Tadashi Abe
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Kiyotaka Hosoda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Hideyuki Saito
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of General Surgical Science, Gastroenterological Surgery, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Satoshi Higuchi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan; Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yuichi Hisamatsu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Takeo Toshima
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Yusuke Yonemura
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Tsuyoshi Hata
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Satoshi Nagayama
- Department of Surgery, Uji-Tokushukai Medical Center, Uji, 611-0041, Japan
| | - Koichi Kagawa
- Department of Gastroenterology, Shin Beppu Hospital, Beppu, 874-8538, Japan
| | - Yasuhiro Goto
- Department of Gastroenterology, Shin Beppu Hospital, Beppu, 874-8538, Japan
| | - Mitsuaki Utou
- Department of Pathology, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Ayako Gamachi
- Department of Pathology, Oita Oka Hospital, Oita, 870-0192, Japan
| | - Kiyomi Imamura
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yuta Kuze
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Junko Zenkoh
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Ayako Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Kazuki Takahashi
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Atsushi Niida
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Shuto Hayashi
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Jun Koseki
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Satoshi Fukuchi
- Department of Gastroenterological Medicine, Almeida Memorial Hospital, Oita, 870-1195, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Hospital, Yufu, 879-5593, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenji Kadomatsu
- Department of Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Taro Tobo
- Department of Pathology, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Kyushu University Hospital, Fukuoka, 812-8582, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, 565-0871, Japan
| | - Masaki Mori
- Tokai University School of Medicine, Isehara, 259-1193, Japan
| | - Masanobu Oshima
- Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan; Department of Computational and Systems Biology, Medical Research Insitute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-0034, Japan.
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, 874-0838, Japan.
| |
Collapse
|
17
|
Pu H, Gao C, Zou Y, Zhao L, Li G, Liu C, Zhao L, Zheng M, Sheng G, Sun X, Hao X, Wang C, He X, Xiao J. Single cell transcriptome profiling of infrapatellar fat pad highlights the role of interstitial inflammatory fibroblasts in osteoarthritis. Int Immunopharmacol 2024; 131:111888. [PMID: 38522139 DOI: 10.1016/j.intimp.2024.111888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
OBJECTIVES Osteoarthritis (OA) is a whole-joint disease in which the role of the infrapatellar fat pad (IFP) in its pathogenesis is unclear. Our study explored the cellular heterogeneity of IFP to understand OA and identify therapeutic targets. METHODS Single-cell and single-nuclei RNA sequencing were used to analyze 10 IFP samples, comprising 5 from OA patients and 5 from healthy controls. Analyses included differential gene expression, enrichment, pseudotime trajectory, and cellular communication, along with comparative studies with visceral and subcutaneous fats. Key subcluster and pathways were validated using multiplex immunohistochemistry. RESULTS The scRNA-seq performed on the IFPs of the OA and control group profiled the gene expressions of over 49,674 cells belonging to 11 major cell types. We discovered that adipose stem and progenitor cells (ASPCs), contributing to the formation of both adipocytes and synovial-lining fibroblasts (SLF). Interstitial inflammatory fibroblasts (iiFBs) were a subcluster of ASPCs that exhibit notable pro-inflammatory and proliferative characteristics. We identified four adipocyte subtypes, with one subtype showing a reduced lipid synthesis ability. Furthermore, iiFBs modulated the activities of macrophages and T cells in the IFP. Compared to subcutaneous and visceral adipose tissues, iiFBs represented a distinctive subpopulation of ASPCs in IFP that regulated cartilage proliferation through the MK pathway. CONCLUSION This study presents a comprehensive single-cell transcriptomic atlas of IFP, uncovering its complex cellular landscape and potential impact on OA progression. Our findings highlight the role of iiFBs in OA, especially through MK pathway, opening new avenues for understanding OA pathogenesis and developing novel targeted therapies.
Collapse
Affiliation(s)
- Hongxu Pu
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chenghao Gao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Zou
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liming Zhao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guanghao Li
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Changyu Liu
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Libo Zhao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meng Zheng
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Gaohong Sheng
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuying Sun
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xingjie Hao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China; Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jun Xiao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| |
Collapse
|
18
|
Wang D, Pu Y, Tan S, Wang X, Zeng L, Lei J, Gao X, Li H. Identification of immune-related biomarkers for glaucoma using gene expression profiling. Front Genet 2024; 15:1366453. [PMID: 38694874 PMCID: PMC11062407 DOI: 10.3389/fgene.2024.1366453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction: Glaucoma, a principal cause of irreversible vision loss, is characterized by intricate optic neuropathy involving significant immune mechanisms. This study seeks to elucidate the molecular and immune complexities of glaucoma, aiming to improve our understanding of its pathogenesis. Methods: Gene expression profiles from glaucoma patients were analyzed to identify immune-related differentially expressed genes (DEGs). Techniques used were weighted gene co-expression network analysis (WGCNA) for network building, machine learning algorithms for biomarker identification, establishment of subclusters related to immune reactions, and single-sample gene set enrichment analysis (ssGSEA) to explore hub genes' relationships with immune cell infiltration and immune pathway activation. Validation was performed using an NMDA-induced excitotoxicity model and RT-qPCR for hub gene expression measurement. Results: The study identified 409 DEGs differentiating healthy individuals from glaucoma patients, highlighting the immune response's significance in disease progression. Immune cell infiltration analysis revealed elevated levels of activated dendritic cells, natural killer cells, monocytes, and immature dendritic cells in glaucoma samples. Three hub genes, CD40LG, TEK, and MDK, were validated as potential diagnostic biomarkers for high-risk glaucoma patients, showing increased expression in the NMDA-induced excitotoxicity model. Discussion: The findings propose the three identified immune-related genes (IRGs) as novel diagnostic markers for glaucoma, offering new insights into the disease's pathogenesis and potential therapeutic targets. The strong correlation between these IRGs and immune responses underscores the intricate role of immunity in glaucoma, suggesting a shift in the approach to its diagnosis and treatment.
Collapse
Affiliation(s)
- Dangdang Wang
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Yanyu Pu
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Sisi Tan
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Xiaochen Wang
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Lihong Zeng
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Junqin Lei
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Xi Gao
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Hong Li
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory for the Prevention and Treatment of Major Blinding Eye Diseases, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| |
Collapse
|
19
|
Xiong K, Fang Y, Qiu B, Chen C, Huang N, Liang F, Huang C, Lu T, Zheng L, Zhao J, Zhu B. Investigation of cellular communication and signaling pathways in tumor microenvironment for high TP53-expressing osteosarcoma cells through single-cell RNA sequencing. Med Oncol 2024; 41:93. [PMID: 38526643 DOI: 10.1007/s12032-024-02318-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Osteosarcoma (OS) stands as the most prevalent primary bone cancer in children and adolescents, and its limited treatment options often result in unsatisfactory outcomes, particularly for metastatic cases. The tumor microenvironment (TME) has been recognized as a crucial determinant in OS progression. However, the intercellular dynamics between high TP53-expressing OS cells and neighboring cell types within the TME are yet to be thoroughly understood. In our study, we harnessed the single-cell RNA sequencing (scRNA-seq) technology in combination with the computational tool-Cellchat, aiming to elucidate the intercellular communication networks present within OS. Through meticulous quantitative inference and subsequent analysis of these networks, we succeeded in identifying significant signaling pathways connecting high TP53-expressing OS cells with proximate cell types, namely Macrophages, Monocytes, Endothelial Cells, and PVLs. This research brings forth a nuanced understanding of the intricate patterns and coordination involved in the TME's intercellular communication signals. These findings not only provide profound insights into the molecular mechanisms underpinning OS but also indicate potential therapeutic targets that could revolutionize treatment strategies.
Collapse
Affiliation(s)
- Kai Xiong
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The Third Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530031, China
| | - Yuqi Fang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
| | - Boyuan Qiu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
| | - Chaotao Chen
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
| | - Nanchang Huang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
| | - Feiyuan Liang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
| | - Chuangming Huang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Nanning, 530021, China
| | - Tiantian Lu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
| | - Li Zheng
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China.
- International Joint Laboratory of Ministry of Education for Regeneration of Bone and Soft Tissues, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
| | - Jinmin Zhao
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China.
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- International Joint Laboratory of Ministry of Education for Regeneration of Bone and Soft Tissues, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
| | - Bo Zhu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
| |
Collapse
|
20
|
Luo C, Peng Y, Gu J, Li T, Wang Q, Qi X, Wei A. Single-cell RNA sequencing reveals critical modulators of extracellular matrix of penile cavernous cells in erectile dysfunction. Sci Rep 2024; 14:5886. [PMID: 38467692 PMCID: PMC10928087 DOI: 10.1038/s41598-024-56428-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
Erectile dysfunction (ED) is a common and difficult to treat disease, and has a high incidence rate worldwide. As a marker of vascular disease, ED usually occurs in cardiovascular disease, 2-5 years prior to cardiovascular disease events. The extracellular matrix (ECM) network plays a crucial role in maintaining cardiac homeostasis, not only by providing structural support, but also by promoting force transmission, and by transducing key signals to intracardiac cells. However, the relationship between ECM and ED remains unclear. To help fill this gap, we profiled single-cell RNA-seq (scRNA-seq) to obtain transcriptome maps of 82,554 cavernous single cells from ED and non-ED samples. Cellular composition of cavernous tissues was explored by uniform manifold approximation and projection. Pseudo-time cell trajectory combined with gene enrichment analysis were performed to unveil the molecular pathways of cell fate determination. The relationship between cavernous cells and the ECM, and the changes in related genes were elucidated. The CellChat identified ligand-receptor pairs (e.g., PTN-SDC2, PTN-NCL, and MDK-SDC2) among the major cell types in the cavernous tissue microenvironment. Differential analysis revealed that the cell type-specific transcriptomic changes in ED are related to ECM and extracellular structure organization, external encapsulating structure organization, and regulation of vasculature development. Trajectory analysis predicted the underlying target genes to modulate ECM (e.g., COL3A1, MDK, MMP2, and POSTN). Together, this study highlights potential cell-cell interactions and the main regulatory factors of ECM, and reveals that genes may represent potential marker features of ED progression.
Collapse
Affiliation(s)
- Chao Luo
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang City, 550004, Guizhou Province, China
| | - Yaqian Peng
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang City, 550004, Guizhou Province, China
| | - Jiang Gu
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Tao Li
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qiang Wang
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education and Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang City, 550004, Guizhou Province, China.
| | - Anyang Wei
- Department of Urology, Nanfang Hospital, Southern Medical University, No.1838 Guangzhou Avenue North, Guangzhou City, Guangdong Province, China.
| |
Collapse
|
21
|
Zhang W, Huang H, Liu X, Zhang L, Li L, Ding Y, Xiao Y, Ali MJ, Sun H, Xiao C. scRNA-Seq: First Atlas and Cellular Landscape of Lacrimal Sac: Implications in Primary Acquired Nasolacrimal Duct Obstruction Pathogenesis. Invest Ophthalmol Vis Sci 2024; 65:38. [PMID: 38551583 PMCID: PMC10981439 DOI: 10.1167/iovs.65.3.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/10/2024] [Indexed: 04/01/2024] Open
Abstract
Purpose The aim of this study was to describe the transcriptional changes of individual cellular components in the lacrimal sac in patients with primary acquired nasolacrimal duct obstruction (PANDO) and attempt to construct the first lacrimal sac cellular atlas to elucidate the potential mechanisms that may drive the disease pathogenesis. Methods Lacrimal sac samples were obtained intra-operatively during the endoscopic dacryocystorhinostomy (EnDCR) procedure from five patients. Single-cell RNA sequencing was performed to analyze each individual cell population including epithelial and immune cells during the early inflammatory and late inflammatory phases of the disease. Results Eleven cell types were identified among 25,791 cells. T cells and B cells were the cell populations with the greatest variation in cell numbers between the two phases and were involved in immune response and epithelium migration-related pathways. The present study showed that epithelial cells highly expressed the genes of senescence-associated secretory phenotype (SASP) and were involved in influencing the inflammation, neutrophil chemotaxis, and migration during the late inflammatory stage. Enhanced activity of CXCLs-CXCRs between the epithelial cells and neutrophils was noted by the cell-cell communication analysis and is suspected to play a role in inflammation by recruiting more neutrophils. Conclusions The study presents a comprehensive single-cell landscape of the lacrimal sac cells in different phases of PANDO. The contribution of T cells, B cells, and epithelial cells to the inflammatory response, and construction of the intercellular signaling networks between the cells within the lacrimal sac has further enhanced the present understanding of the PANDO pathogenesis.
Collapse
Affiliation(s)
- Wenyue Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Huan Huang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xueru Liu
- Ophthalmic Center, Xinjiang 474 Hospital, Urumqi, Xinjiang, China
| | - Leilei Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Lunhao Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Yi Ding
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Yichuan Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mohammad Javed Ali
- Govindram Seksaria Institute of Dacryology, L.V. Prasad Eye Institute, Hyderabad, India
| | - Hao Sun
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Caiwen Xiao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| |
Collapse
|
22
|
Zhou Q, Sun Q, Shen Q, Li X, Qian J. Development and implementation of a prognostic model for clear cell renal cell carcinoma based on heterogeneous TLR4 expression. Heliyon 2024; 10:e25571. [PMID: 38380017 PMCID: PMC10877190 DOI: 10.1016/j.heliyon.2024.e25571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Objective Clear cell renal cell carcinoma (ccRCC) is the most common subtype among renal cell carcinomas and has the worst prognosis, originating from renal tubular epithelial cells. Toll-like receptor 4 (TLR4) plays a crucial role in ccRCC proliferation, infiltration, and metastasis. The aim of this study was to construct a prognostic scoring model for ccRCC based on TLR4 expression heterogeneity and to explore its association with immune infiltration, thereby providing insights for the treatment and prognostic evaluation of ccRCC. Methods Using R software, a differential analysis was conducted on normal samples and ccRCC samples, and in conjunction with the KEGG database, a correlation analysis for the clear cell renal cell carcinoma pathway (hsa05211) was carried out. We observed the expression heterogeneity of TLR4 in the TCGA-KIRC cohort and identified its related differential genes (TRGs). Based on the expression levels of TRGs, consensus clustering was employed to identify TLR4-related subtypes, and further clustering heatmaps, principal component, and single-sample gene set enrichment analyses were conducted. Overlapping differential genes (ODEGs) between subtypes were analysed, and combined with survival data, univariate Cox regression, LASSO, and multivariate Cox regression were used to establish a prognostic risk model for ccRCC. This model was subsequently evaluated through ROC analysis, risk factor correlation analysis, independent prognostic factor analysis, and intergroup differential analysis. The ssGSEA model was employed to explore immune heterogeneity in ccRCC, and the performance of the model in predicting patient prognosis was evaluated using box plots and the oncoPredict software package. Results In the TCGA-KIRC cohort, TLR4 expression was notably elevated in ccRCC samples compared to normal samples, correlating with improved survival in the high-expression group. The study identified distinct TLR4-related differential genes and categorized ccRCC into three subtypes with varied survival outcomes. A risk prognosis model based on overlapping differential genes was established, showing significant associations with immune cell infiltration and key immune checkpoints (PD-1, PD-L1, CTLA4). Additionally, drug sensitivity differences were observed between risk groups. Conclusion In the TCGA-KIRC cohort, the expression of TLR4 in ccRCC samples exhibited significant heterogeneity. Through clustering analysis, we identified that the primary immune cells across subtypes are myeloid-derived suppressor cells, central memory CD4 T cells, and regulatory T cells. Furthermore, we successfully constructed a prognostic risk model for ccRCC composed of 17 genes. This model provides valuable references for the prognosis prediction and treatment of ccRCC patients.
Collapse
Affiliation(s)
- Qingbo Zhou
- Department of Internal Medicine, Shaoxing Yuecheng People's Hospital, Shaoxing, China
| | - Qiang Sun
- Department of Internal Medicine, Shaoxing Yuecheng People's Hospital, Shaoxing, China
| | - Qi Shen
- Department of Internal Medicine, Shaoxing Yuecheng People's Hospital, Shaoxing, China
| | - Xinsheng Li
- Department of Internal Medicine, Shaoxing Yuecheng People's Hospital, Shaoxing, China
| | - Jijiang Qian
- Department of Medical Imaging, Shaoxing Yuecheng People's Hospital, Shaoxing, China
| |
Collapse
|
23
|
Lu P, Xu J, Shen X, Sun J, Liu M, Niu N, Wang Q, Xue J. Spatiotemporal role of SETD2-H3K36me3 in murine pancreatic organogenesis. Cell Rep 2024; 43:113703. [PMID: 38265933 DOI: 10.1016/j.celrep.2024.113703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/11/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Pancreas development is tightly controlled by multilayer mechanisms. Despite years of effort, large gaps remain in understanding how histone modifications coordinate pancreas development. SETD2, a predominant histone methyltransferase of H3K36me3, plays a key role in embryonic stem cell differentiation, whose role in organogenesis remains elusive. Here, by combination of cleavage under targets and tagmentation (CUT&Tag), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing, we show a dramatic increase in the H3K36me3 level from the secondary transition phase and decipher the related transcriptional alteration. Using single-cell RNA sequencing, we define that pancreatic deletion of Setd2 results in abnormalities in both exocrine and endocrine lineages: hyperproliferative tip progenitor cells lead to abnormal differentiation; Ngn3+ endocrine progenitors decline due to the downregulation of Nkx2.2, leading to insufficient endocrine development. Thus, these data identify SETD2 as a crucial player in embryonic pancreas development, providing a clue to understanding the dysregulation of histone modifications in pancreatic disorders.
Collapse
Affiliation(s)
- Ping Lu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Junyi Xu
- Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuqing Shen
- Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiajun Sun
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingzhu Liu
- Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ningning Niu
- Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qidi Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jing Xue
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
24
|
Li Z, Liu G, Yang X, Shu M, Jin W, Tong Y, Liu X, Wang Y, Yuan J, Yang Y. An atlas of cell-type-specific interactome networks across 44 human tumor types. Genome Med 2024; 16:30. [PMID: 38347596 PMCID: PMC10860273 DOI: 10.1186/s13073-024-01303-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Biological processes are controlled by groups of genes acting in concert. Investigating gene-gene interactions within different cell types can help researchers understand the regulatory mechanisms behind human complex diseases, such as tumors. METHODS We collected extensive single-cell RNA-seq data from tumors, involving 563 patients with 44 different tumor types. Through our analysis, we identified various cell types in tumors and created an atlas of different immune cell subsets across different tumor types. Using the SCINET method, we reconstructed interactome networks specific to different cell types. Diverse functional data was then integrated to gain biological insights into the networks, including somatic mutation patterns and gene functional annotation. Additionally, genes with prognostic relevance within the networks were also identified. We also examined cell-cell communications to investigate how gene interactions modulate cell-cell interactions. RESULTS We developed a data portal called CellNetdb for researchers to study cell-type-specific interactome networks. Our findings indicate that these networks can be used to identify genes with topological specificity in different cell types. We also found that prognostic genes can deconvolved into cell types through analyzing network connectivity. Additionally, we identified commonalities and differences in cell-type-specific networks across different tumor types. Our results suggest that these networks can be used to prioritize risk genes. CONCLUSIONS This study presented CellNetdb, a comprehensive repository featuring an atlas of cell-type-specific interactome networks across 44 human tumor types. The findings underscore the utility of these networks in delineating the intricacies of tumor microenvironments and advancing the understanding of molecular mechanisms underpinning human tumors.
Collapse
Affiliation(s)
- Zekun Li
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Gerui Liu
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaoxiao Yang
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Meng Shu
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Wen Jin
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Yang Tong
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaochuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Yuting Wang
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Yang Yang
- Department of Bioinformatics, School of Basic Medical Sciences, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Center for Reproductive Medicine, The Second Hospital of Tianjin Medical University, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Medical University, Tianjin, 300070, China.
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| |
Collapse
|
25
|
Qu C, Yuan H, Tian M, Zhang X, Xia P, Shi G, Hou R, Li J, Jiang H, Yang Z, Chen T, Li Z, Wang J, Yuan Y. Precise Photodynamic Therapy by Midkine Nanobody-Engineered Nanoparticles Remodels the Microenvironment of Pancreatic Ductal Adenocarcinoma and Potentiates the Immunotherapy. ACS NANO 2024; 18:4019-4037. [PMID: 38253029 DOI: 10.1021/acsnano.3c07002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is notorious for its resistance against chemotherapy and immunotherapy due to its dense desmoplastic and immunosuppressive tumor microenvironment (TME). Traditional photodynamic therapy (PDT) was also less effective for PDAC owing to poor selectivity, insufficient penetration, and accumulation of photosensitizers in tumor sites. Here, we designed a light-responsive novel nanoplatform targeting the TME of PDAC through tumor-specific midkine nanobodies (Nbs), which could efficiently deliver semiconducting polymeric nanoparticles (NPs) to the TME of PDAC and locally produce abundant reactive oxygen species (ROS) for precise photoimmunotherapy. The synthesized nanocomposite can not only achieve multimodal imaging of PDAC tumors (fluorescence and photoacoustic imaging) but also lead to apoptosis and immunogenic cell death of tumor cells via ROS under light excitation, ultimately preventing tumor progression and remodeling the immunosuppressive TME with increased infiltration of T lymphocytes. Combined with a PD-1 checkpoint blockade, the targeted PDT platform showed the best antitumor performance and markedly extended mice survival. Conclusively, this work integrating Nbs with photodynamic NPs provides a novel strategy to target formidable PDAC to achieve tumor suppression and activate antitumor immunity, creating possibilities for boosting efficacy of immunotherapy for PDAC tumors through the combination with precise local PDT.
Collapse
Affiliation(s)
- Chengming Qu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, P. R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan 430071, Hubei, P. R. China
| | - Haitao Yuan
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital; First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, Guangdong, P. R. China
| | - Ming Tian
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, P. R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan 430071, Hubei, P. R. China
| | - Xiaodong Zhang
- Department of Medical Imaging, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics· Guangdong Province), Guangzhou 510630, Guangdong, P. R. China
| | - Peng Xia
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, P. R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan 430071, Hubei, P. R. China
| | - Guangwei Shi
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People' s Hospital of Shunde Foshan), Guangzhou 528300, Guangdong, P. R. China
| | - Rui Hou
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital; First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, Guangdong, P. R. China
| | - Ji Li
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands 6009, Western Australia, Australia
| | - Haibo Jiang
- Department of Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong 999077, P. R. China
| | - Zhiyong Yang
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, P. R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan 430071, Hubei, P. R. China
| | - Tengxiang Chen
- Precision Medicine Research Institute of Guizhou Medical University, Affiliated Hospital of Guizhou Medical University, Guiyang 550009, Guizhou, P. R. China
| | - Zhijie Li
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital; First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, Guangdong, P. R. China
| | - Jigang Wang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital; First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, Guangdong, P. R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, P. R. China
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, P. R. China
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng 475004, Henan, P. R. China
| | - Yufeng Yuan
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, P. R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Wuhan 430071, Hubei, P. R. China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, Hubei, P. R. China
| |
Collapse
|
26
|
Győrffy B. Transcriptome-level discovery of survival-associated biomarkers and therapy targets in non-small-cell lung cancer. Br J Pharmacol 2024; 181:362-374. [PMID: 37783508 DOI: 10.1111/bph.16257] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/06/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND AND PURPOSE Survival rate of patients with lung cancer has increased by over 60% in the recent two decades. With longer survival, the identification of genes associated with survival has emerged as an issue of utmost importance to uncover the most promising biomarkers and therapeutic targets. EXPERIMENTAL APPROACH An integrated database was set up by combining multiple independent datasets with clinical data and transcriptome-level gene expression measurements. Univariate and multivariate survival analyses were performed to identify genes with higher expression levels linked to shorter survival. The strongest genes were filtered to include only those with known druggability. KEY RESULTS The entire database includes 2852 tumour specimens from 17 independent cohorts. Of these, 2227 have overall survival data and 1256 samples have progression-free survival time. The most significant genes associated with survival were MIF, UBC and B2M in lung adenocarcinoma and ANXA2, CSNK2A2 and KRT18 in squamous cell carcinoma. We also aimed to reveal the best druggable targets in non-smokers lung cancer. The three most promising hits in this cohort were MDK, THY1 and PADI2. The established lung cancer cohort was added to the Kaplan-Meier plotter (https://www.kmplot.com) enabling the validation of future gene expression-based biomarkers in both the present and yet unexamined subgroups of patients. CONCLUSIONS AND IMPLICATIONS In this study, we established a comprehensive database of transcriptome-level data for lung cancer. The database can be utilized to identify and rank the most promising biomarkers and therapeutic targets for different subtypes of lung cancer.
Collapse
Affiliation(s)
- Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| |
Collapse
|
27
|
Gödicke S, Kresbach C, Ehlert M, Obrecht D, Altendorf L, Hack K, von Hoff K, Carén H, Melcher V, Kerl K, Englinger B, Filbin M, Pajtler KW, Gojo J, Pietsch T, Rutkowski S, Schüller U. Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology. Acta Neuropathol 2024; 147:23. [PMID: 38265527 PMCID: PMC10808473 DOI: 10.1007/s00401-023-02682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/05/2023] [Accepted: 12/30/2023] [Indexed: 01/25/2024]
Abstract
Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell-dense tumor areas. To determine molecular differences in morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Cell-dense areas ranged from 0 to 100% of the tumor area and displayed a higher proportion of proliferating tumor cells (p < 0.01). Clinically, cell density was associated with poor progression-free and overall survival (pPFS = 0.0026, pOS < 0.01). Molecularly, tumor areas with low and high cell density showed diverging DNA methylation profiles regarding their similarity to distinct previously discovered PF-EPN-A subtypes in 9/21 cases. Prognostically relevant chromosomal changes at 1q and 6q showed spatial heterogeneity within single tumors and were significantly enriched in cell-dense tumor areas as shown by single-cell RNA (scRNA)-sequencing as well as copy number profiling and fluorescence in situ hybridization (FISH) analyses of different tumor areas. Finally, spatial transcriptomics revealed cell-dense areas of different tumors to be more similar than various different areas of the same tumor. High-density areas distinctly overexpressed genes encoding histone proteins, WNT5A, TGFB1, or IGF2. Relapsing tumors displayed a higher proportion of cell-dense areas (p = 0.036), a change in PF-EPN-A methylation subtypes (13/32 patients), and novel chromosome 1q gains and 6q losses (12/32 cases) compared to corresponding primary tumors. Our data suggest that PF-EPN-A ependymomas habor a previously unrecognized intratumoral heterogeneity with clinical implications, which has to be accounted for when selecting diagnostic material, inter alia, by histological evaluation of the proportion of cell-dense areas.
Collapse
Affiliation(s)
- Swenja Gödicke
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Catena Kresbach
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Max Ehlert
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Denise Obrecht
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lea Altendorf
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Karoline Hack
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Helena Carén
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Viktoria Melcher
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
- Center for Cancer Research and Comprehensive Cancer Center, Medical University Vienna, 1090, Vienna, Austria
| | - Mariella Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| |
Collapse
|
28
|
Christou C, Stylianou A, Gkretsi V. Midkine (MDK) in Hepatocellular Carcinoma: More than a Biomarker. Cells 2024; 13:136. [PMID: 38247828 PMCID: PMC10814326 DOI: 10.3390/cells13020136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/02/2024] [Accepted: 01/06/2024] [Indexed: 01/23/2024] Open
Abstract
Midkine (MDK) is a multifunctional secreted protein that can act as a cytokine or growth factor regulating multiple signaling pathways and being implicated in fundamental cellular processes, such as survival, proliferation, and migration. Although its expression in normal adult tissues is barely detectable, MDK serum levels are found to be elevated in several types of cancer, including hepatocellular carcinoma (HCC). In this review, we summarize the findings of recent studies on the role of MDK in HCC diagnosis and progression. Overall, studies show that MDK is a powerful biomarker for HCC early diagnosis, as it can differentiate not only between HCC patients and normal individuals but also between HCC patients and patients with other liver pathologies. It is correlated with high recurrence rates and was shown to be valuable for the diagnosis of early-stage HCC, even in patients negative for α-fetoprotein (AFP), the most commonly used biomarker for HCC diagnosis. A comparison with AFP reveals that MDK is inferior to AFP with regard to specificity but significantly superior with regard to sensitivity, which further indicates the need for using both biomarkers for more effective HCC diagnosis.
Collapse
Affiliation(s)
- Christiana Christou
- Cancer Metastasis and Adhesion Laboratory, Basic and Translational Cancer Research Center (BTCRC), European University Cyprus, Nicosia 2404, Cyprus;
- European University Cyprus Research Centre Ltd., Nicosia 2404, Cyprus;
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
| | - Andreas Stylianou
- European University Cyprus Research Centre Ltd., Nicosia 2404, Cyprus;
- Cancer Mechanobiology and Applied Biophysics Laboratory, Basic and Translational Cancer Research Center (BTCRC), European University Cyprus, Nicosia 2404, Cyprus
| | - Vasiliki Gkretsi
- Cancer Metastasis and Adhesion Laboratory, Basic and Translational Cancer Research Center (BTCRC), European University Cyprus, Nicosia 2404, Cyprus;
- European University Cyprus Research Centre Ltd., Nicosia 2404, Cyprus;
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
| |
Collapse
|
29
|
Luu JK, Johnson FD, Jajarmi J, Sihota T, Shi R, Lu D, Farnsworth D, Spencer SE, Negri GL, Morin GB, Lockwood WW. Characterizing the secretome of EGFR mutant lung adenocarcinoma. Front Oncol 2024; 13:1286821. [PMID: 38260835 PMCID: PMC10801028 DOI: 10.3389/fonc.2023.1286821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Background Lung cancer is the leading cause of cancer related death worldwide, mainly due to the late stage of disease at the time of diagnosis. Non-invasive biomarkers are needed to supplement existing screening methods to enable earlier detection and increased patient survival. This is critical to EGFR-driven lung adenocarcinoma as it commonly occurs in individuals who have never smoked and do not qualify for current screening protocols. Methods In this study, we performed mass spectrometry analysis of the secretome of cultured lung cells representing different stages of mutant EGFR driven transformation, from normal to fully malignant. Identified secreted proteins specific to the malignant state were validated using orthogonal methods and their clinical activity assessed in lung adenocarcinoma patient cohorts. Results We quantified 1020 secreted proteins, which were compared for differential expression between stages of transformation. We validated differentially expressed proteins at the transcriptional level in clinical tumor specimens, association with patient survival, and absolute concentration to yield three biomarker candidates: MDK, GDF15, and SPINT2. These candidates were validated using ELISA and increased levels were associated with poor patient survival specifically in EGFR mutant lung adenocarcinoma patients. Conclusions Our study provides insight into changes in secreted proteins during EGFR driven lung adenocarcinoma transformation that may play a role in the processes that promote tumor progression. The specific candidates identified can harnessed for biomarker use to identify high risk individuals for early detection screening programs and disease management for this molecular subgroup of lung adenocarcinoma patients.
Collapse
Affiliation(s)
- Jennifer K. Luu
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Fraser D. Johnson
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Jana Jajarmi
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Tianna Sihota
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rocky Shi
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Daniel Lu
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dylan Farnsworth
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Sandra E. Spencer
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Gian Luca Negri
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Gregg B. Morin
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William W. Lockwood
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| |
Collapse
|
30
|
Jia C, Liu M, Yao L, Zhao F, Liu S, Li Z, Han Y. Multi-omics analysis reveals cuproptosis and mitochondria-based signature for assessing prognosis and immune landscape in osteosarcoma. Front Immunol 2024; 14:1280945. [PMID: 38250070 PMCID: PMC10796547 DOI: 10.3389/fimmu.2023.1280945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Background Osteosarcoma (OSA), the most common primary mesenchymal bone tumor, is a health threat to children and adolescents with a dismal prognosis. While cuproptosis and mitochondria dysfunction have been demonstrated to exert a crucial role in tumor progression and development, the mechanisms by which they are regulated in OSA still await clarification. Methods Two independent OSA cohorts containing transcriptome data and clinical information were collected from public databases. The heterogeneity of OSA were evaluated by single cell RNA (scRNA) analysis. To identify a newly molecular subtype, unsupervised consensus clustering was conducted. Cox relevant regression methods were utilized to establish a prognostic gene signature. Wet lab experiments were performed to confirm the effect of model gene in OSA cells. Results We determined 30 distinct cell clusters and assessed OSA heterogeneity and stemness scRNA analysis. Then, univariate Cox analysis identified 24 candidate genes which were greatly associated with the prognosis of OSA. Based on these prognostic genes, we obtained two molecular subgroups. After conducting step Cox regression, three model genes were selected to construct a signature showing a favorable performance to forecast clinical outcome. Our proposed signature could also evaluate the response to chemotherapy and immunotherapy of OSA cases. Conclusion We generated a novel risk model based on cuproptosis and mitochondria-related genes in OSA with powerful predictive ability in prognosis and immune landscape.
Collapse
Affiliation(s)
- Chenguang Jia
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Orthopedics, Hebei Chest Hospital, Shijiazhuang, China
| | - Mei Liu
- Molecular Biology Laboratory, Hebei Chest Hospital, Shijiazhuang, China
| | - Liming Yao
- Department of Orthopedics, Hebei Chest Hospital, Shijiazhuang, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Shuren Liu
- Department of Orthopedics, Hebei Chest Hospital, Shijiazhuang, China
| | - Zhuo Li
- Department of Orthopedics, Hebei Chest Hospital, Shijiazhuang, China
| | - Yongtai Han
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
31
|
Yang T, Liu J, Liu F, Lei J, Chen S, Ma Z, Ke P, Yang Q, Wen J, He Y, Duan J, Zeng X. Integrative analysis of disulfidptosis and immune microenvironment in hepatocellular carcinoma: a putative model and immunotherapeutic strategies. Front Immunol 2024; 14:1294677. [PMID: 38235128 PMCID: PMC10791859 DOI: 10.3389/fimmu.2023.1294677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a malignant tumor with a high rate of recurrence and m metastasis that does not respond well to current therapies and has a very poor prognosis. Disulfidptosis is a novel mode of cell death that has been analyzed as a novel therapeutic target for HCC cells. Methods This study integrated bulk ribonucleic acid (RNA) sequencing datasets, spatial transcriptomics (ST), and single-cell RNA sequencing to explore the landscape of disulfidptosis and the immune microenvironment of HCC cells. Results We developed a novel model to predict the prognosis of patients with HCC based on disulfidptosis. The model has good stability, applicability, and prognostic and immune response prediction abilities. N-myc downregulated gene1 (NDRG1) may contribute to poor prognosis by affecting macrophage differentiation, thus allowing HCC cells to evade the immune system. Conclusion Our study explores the disulfidptosis of HCC cells through multi-omics and establishes a new putative model that explores possible targets for HCC treatment.
Collapse
Affiliation(s)
- Ti Yang
- Department of Hepatobiliary-pancreatic&hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Junhao Liu
- Department of Hepatobiliary-pancreatic&hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Fang Liu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiashun Lei
- Department of Hepatobiliary-pancreatic&hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Siliang Chen
- Department of Interventional Radiology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Zengxin Ma
- Department of Hepatobiliary-pancreatic&hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Peifeng Ke
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Qiaolan Yang
- Department of Hepatobiliary-pancreatic&hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Jianfan Wen
- Department of Hepatobiliary-pancreatic&hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Yifeng He
- Department of General Management, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Juan Duan
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiancheng Zeng
- Department of Hepatobiliary-pancreatic&hernia Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
32
|
Hohlstein P, Abu Jhaisha S, Yagmur E, Wawer D, Pollmanns MR, Adams JK, Wirtz TH, Brozat JF, Bündgens L, Hamesch K, Weiskirchen R, Tacke F, Trautwein C, Koch A. Elevated Midkine Serum Levels Are Associated with Long-Term Survival in Critically Ill Patients. Int J Mol Sci 2023; 25:454. [PMID: 38203625 PMCID: PMC10779074 DOI: 10.3390/ijms25010454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Midkine (Mdk) is a multifunctional protein involved in inflammatory processes. Hence, circulating Mdk is increased in sepsis and has been previously suggested as a potential biomarker in these patients. The aim of this study was to elucidate the role of Mdk serum concentrations in critical illness and sepsis and to verify its value as a prognostic biomarker. Thus, we analyzed the Mdk serum concentrations of 192 critically ill patients on admission to the medical intensive care unit (ICU). While the serum levels of Mdk at admission were similar in septic and nonseptic critical illness (362 vs. 337 ng/L, p = 0.727), we found several interesting correlations of Mdk to laboratory and clinical markers associated with ischemia or hypoxia, e.g., to renal failure and hepatic injury. Mdk serum concentrations at admission did not differ between various causes of sepsis or other critical illness. Most noticeable, we observed upregulated Mdk serum concentrations at admission in patients surviving in the long-term, which was only seen in nonseptic critical illness but not in sepsis. Our study suggests a relevant role of Mdk in critically ill patients in general and highlights the possible protective features of Mdk in critical illness.
Collapse
Affiliation(s)
- Philipp Hohlstein
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Samira Abu Jhaisha
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Eray Yagmur
- Institute of Laboratory Medicine, Western Palatinate Hospital, 67655 Kaiserslautern, Germany;
| | - Dennis Wawer
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Maike R. Pollmanns
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Jule K. Adams
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Theresa H. Wirtz
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Jonathan F. Brozat
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Augustenburger Platz 1, 13353 Berlin, Germany;
| | - Lukas Bündgens
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Karim Hamesch
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany;
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Augustenburger Platz 1, 13353 Berlin, Germany;
| | - Christian Trautwein
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| | - Alexander Koch
- Department for Gastroenterology, Metabolic Disorders and Intensive Care Medicine, RWTH-University Hospital Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (P.H.); (S.A.J.); (D.W.); (M.R.P.); (J.K.A.); (T.H.W.); (J.F.B.); (L.B.); (K.H.); (C.T.)
| |
Collapse
|
33
|
Wen S, Lv X, Li P, Li J, Qin D. Analysis of cancer-associated fibroblasts in cervical cancer by single-cell RNA sequencing. Aging (Albany NY) 2023; 15:15340-15359. [PMID: 38157264 PMCID: PMC10781451 DOI: 10.18632/aging.205353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/10/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE Since scRNA-seq is an effective tool to study tumor heterogeneity, this paper intends to reveal the differences of cervical cancer in patients at the individual cell level by scRNA-seq, and focus on the biological functions of cancer-associated fibroblasts (CAFs) in cervical cancer, facilitating the provision of a new interpretation of the heterogeneity of the microenvironment of cervical cancer, and an in-depth exploration of the pathogenesis of cervical cancer as well as pursuit of effective means of treatment intake. METHODS 3 cervical cancer specimens were collected by clinical surgery for single-cell RNA sequencing. Cell suspensions of fresh cervical cancer tissues were prepared, and cDNA libraries were created and sequenced on the machine. Furthermore, the sequencing data were analyzed using bioinformatics, including descending clustering of cells, identification of cell populations, mimetic time series analysis, inferCNV, cell communication analysis, and identification of transcription factors. RESULTS A total of 9 cell types were identified, encompassing T cells, epithelial cells, smooth muscle cells, CAFs, endothelial cells, macrophages, B cells, lymphocytes, and plasma cells. CAFs were further divided into three cell subtypes, named type1 cells, type2 cells, and type3 cells. With key transcription factors for the three cells, TCF21, ZC3H11A, and MYEF2 obtained, this research revealed the communication relationship between CAFs and several other cells, and found an important role of CAFs in the MK signaling pathway. CONCLUSIONS scRNA-seq technology contributed to exploring the tumor heterogeneity of cervical cancer more deeply, and also further gaining insight into the biological functions of CAFs in cervical cancer.
Collapse
Affiliation(s)
- Shuang Wen
- Reproductive Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xuefeng Lv
- Department of Laboratory Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Pengxiang Li
- Henan Provincial Chest Hospital, Zhengzhou, Henan, China
| | - Jinpeng Li
- Department of Laboratory Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Dongchun Qin
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
34
|
Yakubovich E, Cook DP, Rodriguez GM, Vanderhyden BC. Mesenchymal ovarian cancer cells promote CD8 + T cell exhaustion through the LGALS3-LAG3 axis. NPJ Syst Biol Appl 2023; 9:61. [PMID: 38086828 PMCID: PMC10716312 DOI: 10.1038/s41540-023-00322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Cancer cells often metastasize by undergoing an epithelial-mesenchymal transition (EMT). Although abundance of CD8+ T-cells in the tumor microenvironment correlates with improved survival, mesenchymal cancer cells acquire greater resistance to antitumor immunity in some cancers. We hypothesized the EMT modulates the immune response to ovarian cancer. Here we show that cancer cells from infiltrated/inflamed tumors possess more mesenchymal cells, than excluded and desert tumors. We also noted high expression of LGALS3 is associated with EMT in vivo, a finding validated with in vitro EMT models. Dissecting the cellular communications among populations in the tumor revealed that mesenchymal cancer cells in infiltrated tumors communicate through LGALS3 to LAG3 receptor expressed by CD8+ T cells. We found CD8+ T cells express high levels of LAG3, a marker of T cell exhaustion. The results indicate that EMT in ovarian cancer cells promotes interactions between cancer cells and T cells through the LGALS3 - LAG3 axis, which could increase T cell exhaustion in infiltrated tumors, dampening antitumor immunity.
Collapse
Affiliation(s)
- Edward Yakubovich
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada.
| | - David P Cook
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Galaxia M Rodriguez
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Barbara C Vanderhyden
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
35
|
Song B, Wang K, Peng Y, Zhu Y, Cui Z, Chen L, Yu Z, Song B. Combined signature of G protein-coupled receptors and tumor microenvironment provides a prognostic and therapeutic biomarker for skin cutaneous melanoma. J Cancer Res Clin Oncol 2023; 149:18135-18160. [PMID: 38006451 DOI: 10.1007/s00432-023-05486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/19/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND G protein-coupled receptors (GPCRs) have been shown to have an important role in tumor development and metastasis, and abnormal expression of GPCRs is significantly associated with poor prognosis of tumor patients. In this study, we analyzed the GPCRs-related gene (GPRGs) and tumor microenvironment (TME) in skin cutaneous melanoma (SKCM) to construct a prognostic model to help SKCM patients obtain accurate clinical treatment strategies. METHODS SKCM expression data and clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Differential expression analysis, LASSO algorithm, and univariate and multivariate cox regression analysis were used to screen prognosis-related genes (GPR19, GPR146, S1PR2, PTH1R, ADGRE5, CXCR3, GPR143, and OR2I1P) and multiple prognosis-good immune cells; the data set was analyzed according to above results and build up a GPR-TME classifier. The model was further subjected to immune infiltration, functional enrichment, tumor mutational load, immunotherapy prediction, and scRNA-seq data analysis. Finally, cellular experiments were conducted to validate the functionality of the key gene GPR19 in the model. RESULTS The findings indicate that high expression of GPRGs is associated with a poor prognosis in patients with SKCM, highlighting the significant role of GPRGs and the tumor microenvironment (TME) in SKCM development. Notably, the group characterized by low GPR expression and a high TME exhibited the most favorable prognosis and immunotherapeutic efficacy. Furthermore, cellular assays demonstrated that knockdown of GPR19 significantly reduced the proliferation, migration, and invasive capabilities of melanoma cells in A375 and A2058 cell lines. CONCLUSION This study provides novel insights for the prognosis evaluation and treatment of melanoma, along with the identification of a new biomarker, GPR19.
Collapse
Affiliation(s)
- Binyu Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Kai Wang
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Yixuan Peng
- School of Basic Medicine, The Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China
| | - Yuhan Zhu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Zhiwei Cui
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China
| | - Lin Chen
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China.
| | - Zhou Yu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China.
| | - Baoqiang Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi Province, China.
| |
Collapse
|
36
|
Wang Y, Song W, Li Y, Liu Z, Zhao K, Jia L, Wang X, Jiang R, Tian Y, He X. Integrated analysis of tumor microenvironment features to establish a diagnostic model for papillary thyroid cancer using bulk and single-cell RNA sequencing technology. J Cancer Res Clin Oncol 2023; 149:16837-16850. [PMID: 37733241 PMCID: PMC10645658 DOI: 10.1007/s00432-023-05420-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND Characterizing tumor microenvironment using single-cell RNA sequencing has been a promising strategy for cancer diagnosis and treatment. However, a few studies have focused on diagnosing papillary thyroid cancer (PTC) through this technology. Therefore, our study explored tumor microenvironment (TME) features and identified potential biomarkers to establish a diagnostic model for papillary thyroid cancer. METHODS The cell types were identified using the markers from the CellMarker database and published research. The CellChat package was conducted to analyze the cell-cell interaction. The SCEVAN package was used to identify malignant thyroid cells. The SCP package was used to perform multiple single-cell downstream analyses, such as GSEA analysis, enrichment analysis, pseudotime trajectory analysis, and differential expression analysis. The diagnostic model of PTC was estimated using the calibration curves, receiver operating characteristic curves, and decision curve analysis. RT-qPCR was performed to validate the expression of candidate genes in human papillary thyroid samples. RESULTS Eight cell types were identified in the scRNA-seq dataset by published cell markers. Extensive cell-cell interactions like FN1/ITGB1 existed in PTC tissues. We identified 26 critical genes related to PTC progression. Further, eight subgroups of PTC tumor cells were identified and exhibited high heterogeneity. The MDK/LRP1, MDK/ALK, GAS6/MERTK, and GAS6/AXL were identified as potential ligand-receptor pairs involved in the interactions between fibroblasts/endothelial cells and tumor cells. Eventually, the diagnostic model constructed by TRPC5, TENM1, NELL2, DMD, SLC35F3, and AUTS2 showed a good efficiency for distinguishing the PTC and normal tissues. CONCLUSIONS Our study comprehensively characterized the tumor microenvironment in papillary thyroid cancer. Through combined analysis with bulk RNA-seq, six potential diagnostic biomarkers were identified and validated. The diagnostic model we constructed was a promising tool for PTC diagnosis. Our findings provide new insights into the heterogeneity of thyroid cancer and the theoretical basis for diagnosing thyroid cancer.
Collapse
Affiliation(s)
- Yizeng Wang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Wenbin Song
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Yingxi Li
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Zhaoyi Liu
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Ke Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Lanning Jia
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Xiaoning Wang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Ruoyu Jiang
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China
| | - Yao Tian
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
| | - Xianghui He
- Department of General Surgery, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, People's Republic of China.
| |
Collapse
|
37
|
Farisoğullari N, Tanaçan A, Sakcak B, Denizli R, Özkavak OO, Turgut E, Kara Ö, Yazihan N, Şahin D. The Association of Serum Midkine Level with Invasion in Placenta Previa: A Case-Control Study from a Tertiary Reference Center. J Interferon Cytokine Res 2023; 43:557-564. [PMID: 38126935 DOI: 10.1089/jir.2023.0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
We aimed to examine the relationship between serum midkine levels and placental invasion in pregnant women with placenta previa. The study group consisted of 43 pregnant women diagnosed with placenta previa, whereas the control group consisted of 60 healthy pregnant women. Serum midkine levels were compared between pregnant women with placenta previa and the control group in this study's first part. Thereafter, the utility of midkine in the prediction of the abnormally invasive placenta (AIP) was investigated and optimal cutoff values were calculated. Significantly higher serum midkine level was observed in placenta previa cases than in the controls (1.16 ng/mL vs. 0.18 ng/mL, P < 0.001). Serum midkine level was also significantly higher in the AIP group among the placenta previa cases (P = 0.004). In the receiver operating characteristic analysis, the cutoff value of the midkine level in predicting AIP was 1.19 ng/mL. This study revealed that the serum midkine level is higher in pregnant women with AIP. Maternal serum midkine level may be used as a complementary biomarker to the radiological and clinical findings for the prediction of the AIP in placenta previa cases.
Collapse
Affiliation(s)
- Nihat Farisoğullari
- Division of Perinatology, Department of Obstetrics and Gynecology, Turkish Ministry of Health Ankara City Hospital, Cankaya, Turkey
| | - Atakan Tanaçan
- Division of Perinatology, Department of Obstetrics and Gynecology, Turkish Ministry of Health Ankara City Hospital, Cankaya, Turkey
| | - Bedri Sakcak
- Division of Perinatology, Department of Obstetrics and Gynecology, Turkish Ministry of Health Ankara City Hospital, Cankaya, Turkey
| | - Ramazan Denizli
- Division of Perinatology, Department of Obstetrics and Gynecology, Turkish Ministry of Health Ankara City Hospital, Cankaya, Turkey
| | - Osman Onur Özkavak
- Division of Perinatology, Department of Obstetrics and Gynecology, Turkish Ministry of Health Ankara City Hospital, Cankaya, Turkey
| | - Ezgi Turgut
- Division of Perinatology, Department of Obstetrics and Gynecology, Turkish Ministry of Health Ankara City Hospital, Cankaya, Turkey
| | - Özgür Kara
- Division of Perinatology, Department of Obstetrics and Gynecology, Turkish Ministry of Health Ankara City Hospital, Cankaya, Turkey
| | - Nuray Yazihan
- Department of Pathophysiology, Internal Medicine, Ankara University Medical School, Cankaya, Turkey
| | - Dilek Şahin
- Division of Perinatology, Department of Obstetrics and Gynecology, University of Health Sciences, Turkish Ministry of Health Ankara City Hospital, Ankara, Turkey
| |
Collapse
|
38
|
de Paz JL, García-Jiménez MJ, Jafari V, García-Domínguez M, Nieto PM. Synthesis and interaction with growth factors of sulfated oligosaccharides containing an anomeric fluorinated tail. Bioorg Chem 2023; 141:106929. [PMID: 37879181 DOI: 10.1016/j.bioorg.2023.106929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Compounds that mimic the biological properties of glycosaminoglycans (GAGs) and can be more easily prepared than the native GAG oligosaccharides are highly demanded. Here, we present the synthesis of sulfated oligosaccharides displaying a perfluorinated aliphatic tag at the reducing end as GAG mimetics. The preparation of these molecules was greatly facilitated by the presence of the fluorinated tail since the reaction intermediates were isolated by simple fluorous solid-phase extraction. Fluorescence polarization competition assays indicated that the synthesized oligosaccharides interacted with two heparin-binding growth factors, midkine (MK) and FGF-2, showing higher binding affinities than the natural oligosaccharides, and can be therefore considered as useful GAG mimetics. Moreover, NMR experiments showed that the 3D structure of these compounds is similar to that of the native sequences, in terms of sugar ring and glycosidic linkage conformations. Finally, we also demonstrated that these derivatives are able to block the MK-stimulating effect on NIH3T3 cells growth.
Collapse
Affiliation(s)
- José L de Paz
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC and Universidad de Sevilla, Americo Vespucio, 49, 41092 Sevilla, Spain.
| | - María José García-Jiménez
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC and Universidad de Sevilla, Americo Vespucio, 49, 41092 Sevilla, Spain
| | - Vahid Jafari
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Américo Vespucio, 24, 41092 Sevilla, Spain
| | - Mario García-Domínguez
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Américo Vespucio, 24, 41092 Sevilla, Spain
| | - Pedro M Nieto
- Glycosystems Laboratory, Instituto de Investigaciones Químicas (IIQ), cicCartuja, CSIC and Universidad de Sevilla, Americo Vespucio, 49, 41092 Sevilla, Spain.
| |
Collapse
|
39
|
Wang J, Harwood CA, Bailey E, Bewicke-Copley F, Anene CA, Thomson J, Qamar MJ, Laban R, Nourse C, Schoenherr C, Treanor-Taylor M, Healy E, Lai C, Craig P, Moyes C, Rickaby W, Martin J, Proby C, Inman GJ, Leigh IM. Transcriptomic analysis of cutaneous squamous cell carcinoma reveals a multigene prognostic signature associated with metastasis. J Am Acad Dermatol 2023; 89:1159-1166. [PMID: 37586461 DOI: 10.1016/j.jaad.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Metastasis of cutaneous squamous cell carcinoma (cSCC) is uncommon. Current staging methods are reported to have sub-optimal performances in metastasis prediction. Accurate identification of patients with tumors at high risk of metastasis would have a significant impact on management. OBJECTIVE To develop a robust and validated gene expression profile signature for predicting primary cSCC metastatic risk using an unbiased whole transcriptome discovery-driven approach. METHODS Archival formalin-fixed paraffin-embedded primary cSCC with perilesional normal tissue from 237 immunocompetent patients (151 nonmetastasizing and 86 metastasizing) were collected retrospectively from four centers. TempO-seq was used to probe the whole transcriptome and machine learning algorithms were applied to derive predictive signatures, with a 3:1 split for training and testing datasets. RESULTS A 20-gene prognostic model was developed and validated, with an accuracy of 86.0%, sensitivity of 85.7%, specificity of 86.1%, and positive predictive value of 78.3% in the testing set, providing more stable, accurate prediction than pathological staging systems. A linear predictor was also developed, significantly correlating with metastatic risk. LIMITATIONS This was a retrospective 4-center study and larger prospective multicenter studies are now required. CONCLUSION The 20-gene signature prediction is accurate, with the potential to be incorporated into clinical workflows for cSCC.
Collapse
Affiliation(s)
- Jun Wang
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Catherine A Harwood
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK; Department of Dermatology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Emma Bailey
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Chinedu Anthony Anene
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK; Centre for Biomedical Science Research, School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, UK
| | - Jason Thomson
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK; Department of Dermatology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Mah Jabeen Qamar
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK; Department of Dermatology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Rhiannon Laban
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK; Department of Dermatology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Craig Nourse
- Cancer Research UK Beatson Institute, Glasgow, Scotland, UK
| | | | - Mairi Treanor-Taylor
- Cancer Research UK Beatson Institute, Glasgow, Scotland, UK; School of Cancer Sciences, University of Glasgow, Scotland, UK
| | - Eugene Healy
- Dermatopharmacology, University of Southampton, Southampton General Hospital, Southampton, UK; Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Chester Lai
- Dermatopharmacology, University of Southampton, Southampton General Hospital, Southampton, UK; Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Paul Craig
- Cellular Pathology, Gloucestershire Hospitals NHS Foundation Trust, Cheltenham General Hospital, Cheltenham, UK
| | - Colin Moyes
- Queen Elizabeth University Hospital, Glasgow, Scotland
| | | | - Joanne Martin
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Charlotte Proby
- Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, Scotland
| | - Gareth J Inman
- Cancer Research UK Beatson Institute, Glasgow, Scotland, UK; School of Cancer Sciences, University of Glasgow, Scotland, UK
| | - Irene M Leigh
- Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| |
Collapse
|
40
|
Neumaier EE, Rothhammer V, Linnerbauer M. The role of midkine in health and disease. Front Immunol 2023; 14:1310094. [PMID: 38098484 PMCID: PMC10720637 DOI: 10.3389/fimmu.2023.1310094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Midkine (MDK) is a neurotrophic growth factor highly expressed during embryogenesis with important functions related to growth, proliferation, survival, migration, angiogenesis, reproduction, and repair. Recent research has indicated that MDK functions as a key player in autoimmune disorders of the central nervous system (CNS), such as Multiple Sclerosis (MS) and is a promising therapeutic target for the treatment of brain tumors, acute injuries, and other CNS disorders. This review summarizes the modes of action and immunological functions of MDK both in the peripheral immune compartment and in the CNS, particularly in the context of traumatic brain injury, brain tumors, neuroinflammation, and neurodegeneration. Moreover, we discuss the role of MDK as a central mediator of neuro-immune crosstalk, focusing on the interactions between CNS-infiltrating and -resident cells such as astrocytes, microglia, and oligodendrocytes. Finally, we highlight the therapeutic potential of MDK and discuss potential therapeutic approaches for the treatment of neurological disorders.
Collapse
Affiliation(s)
| | - Veit Rothhammer
- Department of Neurology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | | |
Collapse
|
41
|
Zhang S, Zhang L, Wang L, Wang H, Wu J, Cai H, Mo C, Yang J. Machine learning identified MDK score has prognostic value for idiopathic pulmonary fibrosis based on integrated bulk and single cell expression data. Front Genet 2023; 14:1246983. [PMID: 38075691 PMCID: PMC10704369 DOI: 10.3389/fgene.2023.1246983] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/10/2023] [Indexed: 03/09/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease that poses a significant challenge to medical professionals due to its increasing incidence and prevalence coupled with the limited understanding of its underlying molecular mechanisms. In this study, we employed a novel approach by integrating five expression datasets from bulk tissue with single-cell datasets; they underwent pseudotime trajectory analysis, switch gene selection, and cell communication analysis. Utilizing the prognostic information derived from the GSE47460 dataset, we identified 22 differentially expressed switch genes that were correlated with clinical indicators as important genes. Among these genes, we found that the midkine (MDK) gene has the potential to serve as a marker of Idiopathic pulmonary fibrosis because its cellular communicating genes are differentially expressed in the epithelial cells. We then utilized midkine and its cellular communication-related genes to calculate the midkine score. Machine learning models were further constructed through midkine and related genes to predict Idiopathic pulmonary fibrosis disease through the bulk gene expression datasets. The midkine score demonstrated a correlation with clinical indexes, and the machine learning model achieved an AUC of 0.94 and 0.86 in the Idiopathic pulmonary fibrosis classification task based on lung tissue samples and peripheral blood mononuclear cell samples, respectively. Our findings offer valuable insights into the pathogenesis of Idiopathic pulmonary fibrosis, providing new therapeutic directions and target genes for further investigation.
Collapse
Affiliation(s)
- Shichen Zhang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lanlan Zhang
- State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Wang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongqiu Wang
- Systems Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
| | - Jiaxin Wu
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jian Yang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
42
|
Yuemaierabola A, Guo J, Sun L, Yeerkenbieke B, Liu F, Ye D, Zhai X, Guo W, Cao Y. Comprehensive analysis of CPSF4-related alternative splice genes in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:13955-13971. [PMID: 37542549 PMCID: PMC10590311 DOI: 10.1007/s00432-023-05178-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND An important stage in controlling gene expression is RNA alternative splicing (AS), and aberrant AS can trigger the development and spread of malignancies, including hepatocellular carcinoma (HCC). A crucial component of AS is cleavage and polyadenylation-specific factor 4 (CPSF4), a component of the CPSF complex, but it is unclear how CPSF4-related AS molecules describe immune cell infiltration in the total tumor microenvironment (TME). METHODS Using RNA-sequencing data and clinical data from TCGA-LIHC from the Cancer Genome Atlas (TCGA) database, the AS genes with differential expression were found. The univariate Cox analysis, KM analysis, and Spearman analysis were used to identify the AS genes related to prognosis. Screening of key AS genes that are highly correlated with CPSF4. Key genes were screened using Cox regression analysis and stepwise regression analysis, and prognosis prediction models and the topography of TME cell infiltration were thoroughly analyzed. RESULTS A model consisting of seven AS genes (STMN1, CLSPN, MDK, RNFT2, PRR11, RNF157, GHR) was constructed that was aimed to predict prognostic condition. The outcomes of the HCC samples in the high-risk group were considerably worse than those in the lower risk group (p < 0.0001), and different risk patient groups were formed. According to the calibration curves and the area under the ROC curve (AUC) values for survival at 1, 2, and 3 years, the clinical nomogram performs well in predicting survival in HCC patients. These values were 0.76, 0.70, and 0.69, respectively. Moreover, prognostic signature was markedly related to immune infiltration and immune checkpoint genes expression. CONCLUSION By shedding light on the function of CPSF4 and the seven AS genes in the formation and progression of HCC, this research analysis contributes to the development of more useful prognostic, diagnostic, and possibly therapeutic biomarkers.
Collapse
Affiliation(s)
- Anwaier Yuemaierabola
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Jun Guo
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Lili Sun
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Buerlan Yeerkenbieke
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Fuzhong Liu
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Dilinaer Ye
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Xiaoyi Zhai
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Wenjia Guo
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China.
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China.
| | - Yan Cao
- Cancer Hospital of Xinjiang Uygur Autonomous Region (Affiliated Cancer Hospital of Xinjiang Medical University), Urumqi, 830011, China.
- Nursing School of Xinjiang Medical University, Urumqi, 830011, China.
| |
Collapse
|
43
|
Sebastian A, Martin KA, Peran I, Hum NR, Leon NF, Amiri B, Wilson SP, Coleman MA, Wheeler EK, Byers SW, Loots GG. Loss of Cadherin-11 in pancreatic ductal adenocarcinoma alters tumor-immune microenvironment. Front Oncol 2023; 13:1286861. [PMID: 37954069 PMCID: PMC10639148 DOI: 10.3389/fonc.2023.1286861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the top five deadliest forms of cancer with very few treatment options. The 5-year survival rate for PDAC is 10% following diagnosis. Cadherin 11 (Cdh11), a cell-to-cell adhesion molecule, has been suggested to promote tumor growth and immunosuppression in PDAC, and Cdh11 inhibition significantly extended survival in mice with PDAC. However, the mechanisms by which Cdh11 deficiency influences PDAC progression and anti-tumor immune responses have yet to be fully elucidated. To investigate Cdh11-deficiency induced changes in PDAC tumor microenvironment (TME), we crossed p48-Cre; LSL-KrasG12D/+; LSL-Trp53R172H/+ (KPC) mice with Cdh11+/- mice and performed single-cell RNA sequencing (scRNA-seq) of the non-immune (CD45-) and immune (CD45+) compartment of KPC tumor-bearing Cdh11 proficient (KPC-Cdh11+/+) and Cdh11 deficient (KPC-Cdh11+/-) mice. Our analysis showed that Cdh11 is expressed primarily in cancer-associated fibroblasts (CAFs) and at low levels in epithelial cells undergoing epithelial-to-mesenchymal transition (EMT). Cdh11 deficiency altered the molecular profile of CAFs, leading to a decrease in the expression of myofibroblast markers such as Acta2 and Tagln and cytokines such as Il6, Il33 and Midkine (Mdk). We also observed a significant decrease in the presence of monocytes/macrophages and neutrophils in KPC-Cdh11+/- tumors while the proportion of T cells was increased. Additionally, myeloid lineage cells from Cdh11-deficient tumors had reduced expression of immunosuppressive cytokines that have previously been shown to play a role in immune suppression. In summary, our data suggests that Cdh11 deficiency significantly alters the fibroblast and immune microenvironments and contributes to the reduction of immunosuppressive cytokines, leading to an increase in anti-tumor immunity and enhanced survival.
Collapse
Affiliation(s)
- Aimy Sebastian
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
| | - Kelly A. Martin
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
| | - Ivana Peran
- Georgetown-Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC, United States
| | - Nicholas R. Hum
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
| | - Nicole F. Leon
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
| | - Beheshta Amiri
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
| | - Stephen P. Wilson
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
| | - Matthew A. Coleman
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
| | - Elizabeth K. Wheeler
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
| | - Stephen W. Byers
- Georgetown-Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University Medical Center, Washington, DC, United States
| | - Gabriela G. Loots
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, United States
- University of California Davis Health, Department of Orthopaedic Surgery, Sacramento, CA, United States
| |
Collapse
|
44
|
He CC, Song TC, Qi RQ, Gao XH. Integrated single-cell and spatial transcriptomics reveals heterogeneity of fibroblast and pivotal genes in psoriasis. Sci Rep 2023; 13:17134. [PMID: 37816883 PMCID: PMC10564713 DOI: 10.1038/s41598-023-44346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023] Open
Abstract
Psoriasis, which is one of the most common skin diseases, involves an array of complex immune constituents including T cells, dendritic cells and monocytes. Particularly, the cytokine IL17A, primarily generated by TH17 cells, assumes a crucial function in the etiology of psoriasis. In this study, a comprehensive investigation utilizing bulk RNA analysis, single-cell RNA sequencing, and spatial transcriptomics was employed to elucidate the underlying mechanisms of psoriasis. Our study revealed that there is an overlap between the genes that are differentially expressed in psoriasis patients receiving three anti-IL17A monoclonal antibody drugs and the genes that are differentially expressed in lesion versus non-lesion samples in these patients. Further analysis using single-cell and spatial data from psoriasis samples confirmed the expression of hub genes that had low expressions in psoriasis tissue but were up-regulated after anti-IL17A treatments. These genes were found to be associated with the treatment effects of brodalumab and methotrexate, but not adalimumab, etanercept, and ustekinumab. Additionally, these genes were predominantly expressed in fibroblasts. In our study, fibroblasts were categorized into five clusters. Notably, hub genes exhibited predominant expression in cluster 3 fibroblasts, which were primarily engaged in the regulation of the extracellular matrix and were predominantly located in the reticular dermis. Subsequent analysis unveiled that cluster 3 fibroblasts also established communication with epithelial cells and monocytes via the ANGPTL-SDC4 ligand-receptor configuration, and their regulation was governed by the transcription factor TWIST1. Conversely, cluster 4 fibroblasts, responsible for vascular endothelial regulation, were predominantly distributed in the papillary dermis. Cluster 4 predominantly engaged in interactions with endothelial cells via MDK signals and was governed by the distinctive transcription factor, ERG. By means of an integrated analysis encompassing bulk transcriptomics, single-cell RNA sequencing, and spatial transcriptomics, we have discerned genes and clusters of fibroblasts that potentially contribute to the pathogenesis of psoriasis.
Collapse
Affiliation(s)
- Cong-Cong He
- Department of Dermatology, The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, 110001, Liaoning, People's Republic of China
| | - Tian-Cong Song
- Department of Nuclear Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Rui-Qun Qi
- Department of Dermatology, The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, 110001, Liaoning, People's Republic of China
| | - Xing-Hua Gao
- Department of Dermatology, The First Hospital of China Medical University and Key Laboratory of Immunodermatology, Ministry of Health and Ministry of Education, No.155 Nanjing Bei Street, Heping District, Shenyang, 110001, Liaoning, People's Republic of China.
| |
Collapse
|
45
|
Said EA, Al-Dughaishi S, Al-Hatmi W, Al-Reesi I, Al-Balushi MS, Al-Bimani A, Al-Busaidi JZ, Al-Riyami M, Al-Khabori M, Al-Kindi S, Procopio FA, Al-Sinawi S, Al-Ansari A, Koh CY, Al-Naamani K, Al-Jabri AA. Differential Production of Midkine and Pleiotrophin by Innate APCs upon Stimulation through Nucleic Acid-Sensing TLRs. J Immunol Res 2023; 2023:7944102. [PMID: 37850119 PMCID: PMC10578979 DOI: 10.1155/2023/7944102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/26/2023] [Accepted: 08/26/2023] [Indexed: 10/19/2023] Open
Abstract
Midkine (MK) and pleiotrophin (PTN) belong to the same family of cytokines. They have similar sequences and functions. Both have important roles in cellular proliferation, tumors, and diseases. They regulate and are expressed by some immune cells. We have recently demonstrated MK production by some human innate antigen-presenting cells (iAPCs), i.e., monocyte-derived dendritic cells (MDDCs) and macrophages stimulated through Toll-like receptor (TLR)-4, and plasmacytoid dendritic cells (pDCs) stimulated through TLR 7. While PTN production was only documented in tissue macrophages. TLRs 3, 7, 8, and 9 are nucleic acid sensing (NAS) TLRs that detect nucleic acids from cell damage and infection and induce iAPC responses. We investigated whether NAS TLRs can induce MK and PTN production by human iAPCs, namely monocytes, macrophages, MDDCs, myeloid dendritic cells (mDCs), and pDCs. Our results demonstrated for the first time that PTN is produced by all iAPCs upon TLR triggering (p < 0.01). IAPCs produced more PTN than MK (p < 0.01). NAS TLRs and iAPCs had differential abilities to induce the production of MK, which was induced in monocytes and pDCs by all NAS TLRs (p < 0.05) and in MDDCs by TLRs 7/8 (p < 0.05). TLR4 induced a stronger MK production than NAS TLRs (p ≤ 0.05). Monocytes produced higher levels of PTN after differentiation to macrophages and MDDCs (p < 0.05). The production of MK and PTN differs among iAPCs, with a higher production of PTN and a selective induction of MK production by NAS TLR. This highlights the potentially important role of iAPCs in angiogenesis, tumors, infections, and autoimmunity through the differential production of MK and PTN upon TLR triggering.
Collapse
Affiliation(s)
- Elias A. Said
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Sumaya Al-Dughaishi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Wadha Al-Hatmi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Iman Al-Reesi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Mohammed S. Al-Balushi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Atika Al-Bimani
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Juma Z. Al-Busaidi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Marwa Al-Riyami
- Department of Pathology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Murtadha Al-Khabori
- Department of Hematology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Salam Al-Kindi
- Department of Hematology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Francesco A. Procopio
- Service of Immunology and Allergy, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Shadia Al-Sinawi
- Department of Pathology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Aliyaa Al-Ansari
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Crystal Y. Koh
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Ali A. Al-Jabri
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| |
Collapse
|
46
|
Ko KP, Huang Y, Zhang S, Zou G, Kim B, Zhang J, Jun S, Martin C, Dunbar KJ, Efe G, Rustgi AK, Nakagawa H, Park JI. Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion. Gastroenterology 2023; 165:613-628.e20. [PMID: 37257519 PMCID: PMC10527250 DOI: 10.1053/j.gastro.2023.05.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND & AIMS Despite recent progress in identifying aberrant genetic and epigenetic alterations in esophageal squamous cell carcinoma (ESCC), the mechanism of ESCC initiation remains unknown. METHODS Using CRISPR/Cas 9-based genetic ablation, we targeted 9 genes (TP53, CDKN2A, NOTCH1, NOTCH3, KMT2D, KMT2C, FAT1, FAT4, and AJUBA) in murine esophageal organoids. Transcriptomic phenotypes of organoids and chemokine released by organoids were analyzed by single-cell RNA sequencing. Tumorigenicity and immune evasion of organoids were monitored by allograft transplantation. Human ESCC single-cell RNA sequencing data sets were analyzed to classify patients and find subsets relevant to organoid models and immune evasion. RESULTS We established 32 genetically engineered esophageal organoids and identified key genetic determinants that drive ESCC initiation. A single-cell transcriptomic analysis uncovered that Trp53, Cdkn2a, and Notch1 (PCN) triple-knockout induces neoplastic features of ESCC by generating cell lineage heterogeneity and high cell plasticity. PCN knockout also generates an immunosuppressive niche enriched with exhausted T cells and M2 macrophages via the CCL2-CCR2 axis. Mechanistically, CDKN2A inactivation transactivates CCL2 via nuclear factor-κB. Moreover, comparative single-cell transcriptomic analyses stratified patients with ESCC and identified a specific subtype recapitulating the PCN-type ESCC signatures, including the high expression of CCL2 and CD274/PD-L1. CONCLUSIONS Our study unveils that loss of TP53, CDKN2A, and NOTCH1 induces esophageal neoplasia and immune evasion for ESCC initiation and proposes the CCL2 blockade as a viable option for targeting PCN-type ESCC.
Collapse
Affiliation(s)
- Kyung-Pil Ko
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuanjian Huang
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shengzhe Zhang
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gengyi Zou
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bongjun Kim
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jie Zhang
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sohee Jun
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cecilia Martin
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
| | - Karen J Dunbar
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
| | - Gizem Efe
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
| | - Anil K Rustgi
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
| | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; The University of Texas MD Anderson Cancer Center, UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas; Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
47
|
Li L, Shucheng H, Fu L, Pei B, Xu W, Jiang X. Overexpression and potential roles of midkine via regulation of vascular endothelial growth factor A in psoriasis. Exp Dermatol 2023; 32:1383-1393. [PMID: 37218430 DOI: 10.1111/exd.14836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Midkine plays a critical role in angiogenesis by regulating the vascular endothelial growth factor (VEGF) signalling pathway, which is known to be associated with psoriasis pathogenesis. However, research on midkine-psoriasis relationship remains limited. The objective of this study was to detect midkine expression in psoriasis and investigate its potential role in the disease. Midkine expression was measured using immunohistochemistry and ELISA. Effects of midkine on HaCaT cell proliferation, VEGF-A production and signalling pathways were assessed using CCK8, RT-PCR and WB. Scratch and in vitro tube formation tests were used to evaluate the effects of HaCaT-cell-activated midkine on the migration and tube formation of human dermal microvascular endothelial cells. Murine psoriasiform models were injected with midkine recombinant protein and midkine monoclonal antibody to investigate skin lesions, tissue sections and dermal microvessel density. Levels of midkine significantly increased in both lesions and serum of patients with psoriasis. Serum expression of midkine decreased after treatment and a positive correlation was found between midkine and disease severity. Midkine promoted HaCaT cell proliferation and VEGF-A production. The Notch2/HES1/JAK2-STAT5A pathway expression increased after midkine treatment of HaCaT cells. The supernatant of HaCaT cells treated with midkine promoted HMEC-1 migration and angiogenesis in vitro. Recombinant midkine protein exacerbated psoriasiform lesions with increased expressions of VEGF-A and microvessel density, while midkine monoclonal antibody alleviated psoriasis lesions. Midkine may have a significant impact on psoriasis angiogenesis by regulating VEGF-A expression through the Notch2/HES1/JAK2-STAT5A pathway, highlighting a potential therapeutic target for psoriasis treatment.
Collapse
Affiliation(s)
- Lin Li
- Department of Dermatology and Venereology, West China Hospital, Sichuan University, Chengdu, China
- Department of Dermatology, Chengdu Second People's Hospital, Chengdu, China
| | - Huidi Shucheng
- Department of Dermatology and Venereology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Lixin Fu
- Department of Dermatology, Chengdu Second People's Hospital, Chengdu, China
| | - Baoqiang Pei
- Department of Dermatology, Chengdu Second People's Hospital, Chengdu, China
| | - Wen Xu
- Department of Dermatology, Chengdu Second People's Hospital, Chengdu, China
| | - Xian Jiang
- Department of Dermatology and Venereology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
48
|
Saikia M, Cheung N, Singh AK, Kapoor V. Role of Midkine in Cancer Drug Resistance: Regulators of Its Expression and Its Molecular Targeting. Int J Mol Sci 2023; 24:ijms24108739. [PMID: 37240085 DOI: 10.3390/ijms24108739] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Molecules involved in drug resistance can be targeted for better therapeutic efficacies. Research on midkine (MDK) has escalated in the last few decades, which affirms a positive correlation between disease progression and MDK expression in most cancers and indicates its association with multi-drug resistance in cancer. MDK, a secretory cytokine found in blood, can be exploited as a potent biomarker for the non-invasive detection of drug resistance expressed in various cancers and, thereby, can be targeted. We summarize the current information on the involvement of MDK in drug resistance, and transcriptional regulators of its expression and highlight its potential as a cancer therapeutic target.
Collapse
Affiliation(s)
- Minakshi Saikia
- Department of Radiation Oncology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Nathan Cheung
- Department of Radiation Oncology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Abhay Kumar Singh
- Department of Radiation Oncology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Vaishali Kapoor
- Department of Radiation Oncology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
- Siteman Cancer Center, St. Louis, MO 63108, USA
| |
Collapse
|
49
|
Rüland L, Andreatta F, Massalini S, Chuva de Sousa Lopes S, Clevers H, Hendriks D, Artegiani B. Organoid models of fibrolamellar carcinoma mutations reveal hepatocyte transdifferentiation through cooperative BAP1 and PRKAR2A loss. Nat Commun 2023; 14:2377. [PMID: 37137901 PMCID: PMC10156813 DOI: 10.1038/s41467-023-37951-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 04/06/2023] [Indexed: 05/05/2023] Open
Abstract
Fibrolamellar carcinoma (FLC) is a lethal primary liver cancer, affecting young patients in absence of chronic liver disease. Molecular understanding of FLC tumorigenesis is limited, partly due to the scarcity of experimental models. Here, we CRISPR-engineer human hepatocyte organoids to recreate different FLC backgrounds, including the predominant genetic alteration, the DNAJB1-PRKACA fusion, as well as a recently reported background of FLC-like tumors, encompassing inactivating mutations of BAP1 and PRKAR2A. Phenotypic characterizations and comparisons with primary FLC tumor samples revealed mutant organoid-tumor similarities. All FLC mutations caused hepatocyte dedifferentiation, yet only combined loss of BAP1 and PRKAR2A resulted in hepatocyte transdifferentiation into liver ductal/progenitor-like cells that could exclusively grow in a ductal cell environment. BAP1-mutant hepatocytes represent primed cells attempting to proliferate in this cAMP-stimulating environment, but require concomitant PRKAR2A loss to overcome cell cycle arrest. In all analyses, DNAJB1-PRKACAfus organoids presented with milder phenotypes, suggesting differences between FLC genetic backgrounds, or for example the need for additional mutations, interactions with niche cells, or a different cell-of-origin. These engineered human organoid models facilitate the study of FLC.
Collapse
Affiliation(s)
- Laura Rüland
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Simone Massalini
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Hans Clevers
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| |
Collapse
|
50
|
Hosseini SA, Haddadi MH, Fathizadeh H, Nemati F, Aznaveh HM, Taraj F, Aghabozorgizadeh A, Gandomkar G, Bazazzadeh E. Long non-coding RNAs and gastric cancer: An update of potential biomarkers and therapeutic applications. Biomed Pharmacother 2023; 163:114407. [PMID: 37100014 DOI: 10.1016/j.biopha.2023.114407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 04/28/2023] Open
Abstract
The frequent metastasis of gastric cancer (GC) complicates the cure and therefore the development of effective diagnostic and therapeutic approaches is urgently necessary. In recent years, lncRNA has emerged as a drug target in the treatment of GC, particularly in the areas of cancer immunity, cancer metabolism, and cancer metastasis. This has led to the demonstration of the importance of these RNAs as prognostic, diagnostic and therapeutic agents. In this review, we provide an overview of the biological activities of lncRNAs in GC development and update the latest pathological activities, prognostic and diagnostic strategies, and therapeutic options for GC-related lncRNAs.
Collapse
Affiliation(s)
- Sayedeh Azimeh Hosseini
- Department of Medical Biotechnology, School of Advanced Technology, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran; USERN office, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Hadis Fathizadeh
- Student Research Committee, Sirjan School of Medical Sciences, Sirjan, Iran; Department of Laboratory sciences, Sirjan School of Medical Sciences, Sirjan, Iran
| | - Foroogh Nemati
- Department of Microbiology, Kashan University of Medical Sciences, Kashan, Iran
| | - Hooman Mahmoudi Aznaveh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-154, Tehran, Iran
| | - Farima Taraj
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - AmirArsalan Aghabozorgizadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Isfahan, Iran
| | - Golmaryam Gandomkar
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Elaheh Bazazzadeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-154, Tehran, Iran
| |
Collapse
|