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Moutafi MK, Bates KM, Aung TN, Milian RG, Xirou V, Vathiotis IA, Gavrielatou N, Angelakis A, Schalper KA, Salichos L, Rimm DL. High-throughput transcriptome profiling indicates ribosomal RNAs to be associated with resistance to immunotherapy in non-small cell lung cancer (NSCLC). J Immunother Cancer 2024; 12:e009039. [PMID: 38857914 PMCID: PMC11168162 DOI: 10.1136/jitc-2024-009039] [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] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Despite the impressive outcomes with immune checkpoint inhibitor (ICI) in non-small cell lung cancer (NSCLC), only a minority of the patients show long-term benefits from ICI. In this study, we used retrospective cohorts of ICI treated patients with NSCLC to discover and validate spatially resolved protein markers associated with resistance to programmed cell death protein-1 (PD-1) axis inhibition. METHODS Pretreatment samples from 56 patients with NSCLC treated with ICI were collected and analyzed in a tissue microarray (TMA) format in including four different tumor regions per patient using the GeoMx platform for spatially informed transcriptomics. 34 patients had assessable tissue with tumor compartment in all 4 TMA spots, 22 with leukocyte compartment and 12 with CD68 compartment. The patients' tissue that was not assessable in fourfold redundancy in each compartment was designated as the validation cohort; cytokeratin (CK) (N=22), leukocytes CD45 (N=31), macrophages, CD68 (N=43). The human whole transcriptome, represented by~18,000 individual genes assessed by oligonucleotide-tagged in situ hybridization, was sequenced on the NovaSeq platform to quantify the RNAs present in each region of interest. RESULTS 54,000 gene variables were generated per case, from them 25,740 were analyzed after removing targets with expression lower than a prespecified frequency. Cox proportional-hazards model analysis was performed for overall and progression-free survival (OS, PFS, respectively). After identifying genes significantly associated with limited survival benefit (HR>1)/progression per spot per patient, we used the intersection of them across the four TMA spots per patient. This resulted in a list of 12 genes in the tumor-cell compartment (RPL13A, GNL3, FAM83A, CYBA, ACSL4, SLC25A6, EPAS1, RPL5, APOL1, HSPD1, RPS4Y1, ADI1). RPL13A, GNL3 in tumor-cell compartment were also significantly associated with OS and PFS, respectively, in the validation cohort (CK: HR, 2.48; p=0.02 and HR, 5.33; p=0.04). In CD45 compartment, secreted frizzled-related protein 2, was associated with OS in the discovery cohort but not in the validation cohort. Similarly, in the CD68 compartment ARHGAP and PNN interacting serine and arginine rich protein were significantly associated with PFS and OS, respectively, in the majority but not all four spots per patient. CONCLUSION This work highlights RPL13A and GNL3 as potential indicative biomarkers of resistance to PD-1 axis blockade that might help to improve precision immunotherapy strategies for lung cancer.
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Affiliation(s)
- Myrto K Moutafi
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Katherine M Bates
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thazin Nwe Aung
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Rolando Garcia Milian
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, Connecticut, USA
| | - Vasiliki Xirou
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Ioannis A Vathiotis
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Niki Gavrielatou
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Athanasios Angelakis
- Epidemiology and Data Science, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
- Department of Methodology, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Kurt A Schalper
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Leonidas Salichos
- Biomedical Data Science Center Director, Center for Cancer Research, Department of Computational Biology at New York Institute of Technology, New York Institute of Technology, Old Westbury, New York, USA
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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Cui L, Zheng J, Lin Y, Lin P, Lu Y, Zheng Y, Guo B, Zhao X. Decoding the ribosome's hidden language: rRNA modifications as key players in cancer dynamics and targeted therapies. Clin Transl Med 2024; 14:e1705. [PMID: 38797935 PMCID: PMC11128715 DOI: 10.1002/ctm2.1705] [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: 01/22/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Ribosomal RNA (rRNA) modifications, essential components of ribosome structure and function, significantly impact cellular proteomics and cancer biology. These chemical modifications transcend structural roles, critically shaping ribosome functionality and influencing cellular protein profiles. In this review, the mechanisms by which rRNA modifications regulate both rRNA functions and broader cellular physiological processes are critically discussed. Importantly, by altering the translational output, rRNA modifications can shift the cellular equilibrium towards oncogenesis, thus playing a key role in cancer development and progression. Moreover, a special focus is placed on the functions of mitochondrial rRNA modifications and their aberrant expression in cancer, an area with profound implications yet largely uncharted. Dysregulation in these modifications can lead to metabolic dysfunction and apoptosis resistance, hallmark traits of cancer cells. Furthermore, the current challenges and future perspectives in targeting rRNA modifications are highlighted as a therapeutic approach for cancer treatment. In conclusion, rRNA modifications represent a frontier in cancer research, offering novel insights and therapeutic possibilities. Understanding and harnessing these modifications can pave the way for breakthroughs in cancer treatment, potentially transforming the approach to combating this complex disease.
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Affiliation(s)
- Li Cui
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
- Division of Oral Biology and Medicine, School of DentistryUniversity of
California, Los AngelesLos AngelesUSA
| | - Jiarong Zheng
- Department of Dentistry, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Yunfan Lin
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Pei Lin
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Ye Lu
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Yucheng Zheng
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Bing Guo
- Department of Dentistry, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Xinyuan Zhao
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
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Lin L, Huang K, Tu Z, Zhu X, Li J, Lei K, Luo M, Wang P, Gong C, Long X, Wu L. Integrin Alpha-2 as a Potential Prognostic and Predictive Biomarker for Patients With Lower-Grade Glioma. Front Oncol 2021; 11:738651. [PMID: 34778054 PMCID: PMC8578896 DOI: 10.3389/fonc.2021.738651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022] Open
Abstract
Diffuse gliomas are the most common malignant brain tumors with the highest mortality and recurrence rate in adults. Integrin alpha-2 (ITGA2) is involved in a series of biological processes, including cell adhesion, stemness regulation, angiogenesis, and immune/blood cell functions. The role of ITGA2 in lower-grade gliomas (LGGs) is not well defined. Firstly, we downloaded RNA sequencing and relevant clinical information from The Cancer Genome Atlas cohort, the Chinese Glioma Genome Atlas cohort, and related immune cohorts. Next, prognosis analysis, difference analysis, clinical model construction, enrichment analysis, and immune infiltration analysis are performed for this study. These analyses indicated that ITGA2 may have clinical application value and research value in LGG immunotherapy. We also detected the mRNA and protein expression of ITGA2 in three LGG cell lines and normal glial cells using quantitative real-time polymerase chain reaction assay and western blot assay. Our study not only offers a novel target for LGG immunotherapy but also can better comprehend the mechanism of the development and progression of patients with LGG. This study revealed that ITGA2 may be a potential prognostic and predictive biomarker for LGG, which can bring new insights into targeted immunotherapy.
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Affiliation(s)
- Li Lin
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Scientific Research, East China Institute of Digital Medical Engineering, Shangrao, China.,Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Zewei Tu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Jingying Li
- Department of Comprehensive Intensive Care Unit, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kunjian Lei
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Min Luo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Peng Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chuandong Gong
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoyan Long
- Department of Scientific Research, East China Institute of Digital Medical Engineering, Shangrao, China
| | - Lei Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Institute of Neuroscience, Nanchang University, Nanchang, China
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