1
|
Gallucci Figorelle L, Galvão PT, de Lima FMR, Marimon P, Pentagna N, Milito C, Schaffel R, Carneiro K. Mantle Cell Lymphoma Under the Scope of Personalized Medicine: Perspective and Directions. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2024; 24:433-445. [PMID: 38641485 DOI: 10.1016/j.clml.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/24/2024] [Indexed: 04/21/2024]
Abstract
Mantle cell lymphoma (MCL) is a rare, incurable non-Hodgkin's lymphoma characterized by naive B cells infiltrating the lymphoid follicle's mantle zone. A key feature of MCL is the cytogenetic abnormality t(11;14) (q13:q14), found in 95% of cases, leading to Cyclin D1 overexpression resulting in uncontrolled cell cycle progression and genetic instability. Occasionally, Cyclin D2 or D3 overexpression can substitute for Cyclin D1, causing similar effects. The transcription factor SOX11 is a hallmark of classical Cyclin D1-positive MCL and also in cases without the typical t(11;14) abnormality, making it an important diagnostic marker. MCL's development necessitates secondary genetic changes, including mutations in the ATM, TP53, and NOTCH1 genes, with the TP53 mutation being the only genetic biomarker with established clinical prognostic value. The Mantle Cell Lymphoma International Prognostic Index (MIPI) score, which considers age, performance status, serum LDH levels, and leukocyte count, stratifies patients into risk groups. Histologic variants of MCL, such as classic, blastoid, and pleomorphic, offer additional prognostic information. Recent research highlights new mutations potentially tied to specific populations among MCL patients, suggesting the benefit of personalized management for better predicting outcomes like progression-free survival. This approach could lead to more effective, risk-adapted treatment strategies. However, challenges remain in patient stratification and in developing new therapeutic targets for MCL. This review synthesizes current knowledge on genetic mutations in MCL and their impact on prognosis. It aims to explore the prognostic value of genetic markers related to population traits, emphasizing the importance of tailored molecular medicine in MCL.
Collapse
Affiliation(s)
- Lara Gallucci Figorelle
- Laboratório de Proliferação e Diferenciação Celular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Programa de Pós-graduação em Medicina (Anatomia Patológica), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Peterson Tiago Galvão
- Laboratório de Proliferação e Diferenciação Celular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Programa de Pós-graduação em Medicina (Anatomia Patológica), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Patricia Marimon
- Laboratório de Proliferação e Diferenciação Celular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nathalia Pentagna
- Programa de Pós-graduação em Medicina (Anatomia Patológica), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane Milito
- Programa de Pós-graduação em Medicina (Anatomia Patológica), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rony Schaffel
- Programa de Pós-graduação em Medicina (Anatomia Patológica), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Katia Carneiro
- Programa de Pós-graduação em Medicina (Anatomia Patológica), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| |
Collapse
|
2
|
Liu F, Farris MK, Ververs JD, Hughes RT, Munley MT. Histology-driven hypofractionated radiation therapy schemes for early-stage lung adenocarcinoma and squamous cell carcinoma. Radiother Oncol 2024; 195:110257. [PMID: 38548113 PMCID: PMC11098686 DOI: 10.1016/j.radonc.2024.110257] [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: 01/24/2024] [Revised: 03/06/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND AND PURPOSE Histology was found to be an important prognostic factor for local tumor control probability (TCP) after stereotactic body radiotherapy (SBRT) of early-stage non-small-cell lung cancer (NSCLC). A histology-driven SBRT approach has not been explored in routine clinical practice and histology-dependent fractionation schemes remain unknown. Here, we analyzed pooled histologic TCP data as a function of biologically effective dose (BED) to determine histology-driven fractionation schemes for SBRT and hypofractionated radiotherapy of two predominant early-stage NSCLC histologic subtypes adenocarcinoma (ADC) and squamous cell carcinoma (SCC). MATERIAL AND METHODS The least-χ2 method was used to fit the collected histologic TCP data of 8510 early-stage NSCLC patients to determine parameters for a well-developed radiobiological model per the Hypofractionated Treatment Effects in the Clinic (HyTEC) initiative. RESULTS A fit to the histologic TCP data yielded independent radiobiological parameter sets for radiotherapy of early-stage lung ADC and SCC. TCP increases steeply with BED and reaches an asymptotic maximal plateau, allowing us to determine model-independent optimal fractionation schemes of least doses in 1-30 fractions to achieve maximal tumor control for early-stage lung ADC and SCC, e.g., 30, 44, 48, and 51 Gy for ADC, and 32, 48, 54, and 58 Gy for SCC in 1, 3, 4, and 5 fractions, respectively. CONCLUSION We presented the first determination of histology-dependent radiobiological parameters and model-independent histology-driven optimal SBRT and hypofractionated radiation therapy schemes for early-stage lung ADC and SCC. SCC requires substantially higher radiation doses to maximize tumor control than ADC, plausibly attributed to tumor genetic diversity and microenvironment. The determined optimal SBRT schemes agree well with clinical practice for early-stage lung ADC. These proposed optimal fractionation schemes provide first insights for histology-based personalized radiotherapy of two predominant early-stage NSCLC subtypes ADC and SCC, which require further validation with large-scale histologic TCP data.
Collapse
Affiliation(s)
- Feng Liu
- Department of Radiation Oncology, Wake Forest University School of Medicine and Atrium Health Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA.
| | - Michael K Farris
- Department of Radiation Oncology, Wake Forest University School of Medicine and Atrium Health Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA
| | - James D Ververs
- Department of Radiation Oncology, Wake Forest University School of Medicine and Atrium Health Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA
| | - Ryan T Hughes
- Department of Radiation Oncology, Wake Forest University School of Medicine and Atrium Health Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA
| | - Michael T Munley
- Department of Radiation Oncology, Wake Forest University School of Medicine and Atrium Health Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA
| |
Collapse
|
3
|
Li DM, Li GS, Li JD, Chen F, Huang H, Huang WY, Huang ZG, Dang YW, Tang YL, Tang ZQ, Tang WJ, Chen G, Lu HP. Clinical significance and prospective mechanism of increased CDKN2A expression in small cell lung cancer. Clin Transl Oncol 2024; 26:1519-1531. [PMID: 38206516 PMCID: PMC11108933 DOI: 10.1007/s12094-023-03376-2] [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: 07/12/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Although it has been shown that cyclin dependent kinase inhibitor 2A (CDKN2A) plays a significant role in a number of malignancies, its clinicopathological value and function in small cell lung cancer (SCLC) is unclear and warrants additional research. METHODS The clinical significance of CDKN2A expression in SCLC was examined by multiple methods, including comprehensive integration of mRNA level by high throughput data, Kaplan-Meier survival analysis for prognostic value, and validation of its protein expression using in-house immunohistochemistry. RESULTS The expression of CDKN2A mRNA in 357 cases of SCLC was evidently higher than that in the control group (n = 525) combing the data from 20 research centers worldwide. The standardized mean difference (SMD) was 3.07, and the area under the curve (AUC) of summary receiver operating characteristic curve (sROC) was 0.97 for the overexpression of CDKN2A. ACC, COAD, KICH, KIRC, PCPG, PRAD, UCEC, UVM patients with higher CDKN2A expression had considerably worse overall survival rates than those with lower CDKN2A expression with the hazard ratio (HR) > 1. CONCLUSION CDKN2A upregulation extensively enhances the carcinogenesis and progression of SCLC.
Collapse
Affiliation(s)
- Dong-Ming Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Guo-Sheng Li
- Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Jian-Di Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Feng Chen
- Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Hong Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Wan-Ying Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Yu-Lu Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Zhong-Qing Tang
- Department of Pathology, Wuzhou Gongren Hospital, The Seventh Affiliated Hospital of Guangxi Medical University, No.1, Nansanxiang Gaodi Road, Guangxi Zhuang Autonomous Region, Wuzhou, 543000, People's Republic of China
| | - Wen-Jia Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China
| | - Hui-Ping Lu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, People's Republic of China.
| |
Collapse
|
4
|
Deng C, Li ZX, Xie CJ, Zhang QL, Hu BS, Wang MD, Mei J, Yang C, Zhong Z, Wang KW. Pan-cancer analysis of CDKN2A alterations identifies a subset of gastric cancer with a cold tumor immune microenvironment. Hum Genomics 2024; 18:55. [PMID: 38822443 PMCID: PMC11143690 DOI: 10.1186/s40246-024-00615-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 05/03/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Although CDKN2A alteration has been explored as a favorable factor for tumorigenesis in pan-cancers, the association between CDKN2A point mutation (MUT) and intragenic deletion (DEL) and response to immune checkpoint inhibitors (ICIs) is still disputed. This study aims to determine the associations of CDKN2A MUT and DEL with overall survival (OS) and response to immune checkpoint inhibitors treatment (ICIs) among pan-cancers and the clinical features of CDKN2A-altered gastric cancer. METHODS This study included 45,000 tumor patients that underwent tumor sequencing across 33 cancer types from four cohorts, the MSK-MetTropism, MSK-IMPACT, OrigiMed2020 and TCGA cohorts. Clinical outcomes and genomic factors associated with response to ICIs, including tumor mutational burden, copy number alteration, neoantigen load, microsatellite instability, tumor immune microenvironment and immune-related gene signatures, were collected in pan-cancer. Clinicopathologic features and outcomes were assessed in gastric cancer. Patients were grouped based on the presence of CDKN2A wild type (WT), CDKN2A MUT, CDKN2A DEL and CDKN2A other alteration (ALT). RESULTS Our research showed that CDKN2A-MUT patients had shorter survival times than CDKN2A-WT patients in the MSK MetTropism and TCGA cohorts, but longer OS in the MSK-IMPACT cohort with ICIs treatment, particularly in patients having metastatic disease. Similar results were observed among pan-cancer patients with CDKN2A DEL and other ALT. Notably, CDKN2A ALT frequency was positively related to tumor-specific objective response rates to ICIs in MSK MetTropism and OrigiMed 2020. Additionally, individuals with esophageal carcinoma or stomach adenocarcinoma who had CDKN2A MUT had poorer OS than patients from the MSK-IMPACT group, but not those with adenocarcinoma. We also found reduced levels of activated NK cells, T cells CD8 and M2 macrophages in tumor tissue from CDKN2A-MUT or DEL pan-cancer patients compared to CDKN2A-WT patients in TCGA cohort. Gastric cancer scRNA-seq data also showed that CDKN2A-ALT cancer contained less CD8 T cells but more exhausted T cells than CDKN2A-WT cancer. A crucial finding of the pathway analysis was the inhibition of three immune-related pathways in the CDKN2A ALT gastric cancer patients, including the interferon alpha response, inflammatory response, and interferon gamma response. CONCLUSIONS This study illustrates the CDKN2A MUT and DEL were associated with a poor outcome across cancers. CDKN2A ALT, on the other hand, have the potential to be used as a biomarker for choosing patients for ICI treatment, notably in esophageal carcinoma and stomach adenocarcinoma.
Collapse
Affiliation(s)
- Chao Deng
- Institute of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Rd, Wuxi, Jiangsu Province, 214122, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Zi-Xi Li
- Institute of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Rd, Wuxi, Jiangsu Province, 214122, China
| | - Chen-Jun Xie
- Institute of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Rd, Wuxi, Jiangsu Province, 214122, China
| | - Qing-Lin Zhang
- Departments of Gastroenterology, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Ben-Shun Hu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Mei-Dan Wang
- Institute of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Rd, Wuxi, Jiangsu Province, 214122, China
| | - Jie Mei
- Department of Oncology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Chen Yang
- Institute of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Rd, Wuxi, Jiangsu Province, 214122, China
| | - Zhangfeng Zhong
- Macao Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, Macao SAR 999078, China.
| | - Ke-Wei Wang
- Institute of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Rd, Wuxi, Jiangsu Province, 214122, China.
| |
Collapse
|
5
|
Zhao W, Kepecs B, Mahadevan NR, Segerstolpe A, Weirather JL, Besson NR, Giotti B, Soong BY, Li C, Vigneau S, Slyper M, Wakiro I, Jane-Valbuena J, Ashenberg O, Rotem A, Bueno R, Rozenblatt-Rosen O, Pfaff K, Rodig S, Hata AN, Regev A, Johnson BE, Tsankov AM. A cellular and spatial atlas of TP53 -associated tissue remodeling in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.28.546977. [PMID: 37425718 PMCID: PMC10327017 DOI: 10.1101/2023.06.28.546977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
TP53 is the most frequently mutated gene across many cancers and is associated with shorter survival in lung adenocarcinoma (LUAD). To define how TP53 mutations affect the LUAD tumor microenvironment (TME), we constructed a multi-omic cellular and spatial tumor atlas of 23 treatment-naïve human lung tumors. We found that TP53 -mutant ( TP53 mut ) malignant cells lose alveolar identity and upregulate highly proliferative and entropic gene expression programs consistently across resectable LUAD patient tumors, genetically engineered mouse models, and cell lines harboring a wide spectrum of TP53 mutations. We further identified a multicellular tumor niche composed of SPP1 + macrophages and collagen-expressing fibroblasts that coincides with hypoxic, pro-metastatic expression programs in TP53 mut tumors. Spatially correlated angiostatic and immune checkpoint interactions, including CD274 - PDCD1 and PVR - TIGIT , are also enriched in TP53 mut LUAD tumors, which may influence response to checkpoint blockade therapy. Our methodology can be further applied to investigate mutation-specific TME changes in other cancers.
Collapse
|
6
|
Pan M, Jiang C, Zhang Z, Achacoso N, Solorzano-Pinto AV, Tse P, Chung E, Suga JM, Thomas S, Habel LA. Sex- and Co-Mutation-Dependent Prognosis in Patients with SMARCA4-Mutated Malignancies. Cancers (Basel) 2023; 15:2665. [PMID: 37345003 DOI: 10.3390/cancers15102665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/12/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Whether sex and co-mutations impact prognosis of patients with SMARCA4-mutated (mutSMARCA4) malignancies is not clear. METHODS This cohort included patients from Northern California Kaiser Permanente with next-generation sequencing (NGS) performed from August 2020 to October 2022. We used Cox regression modeling to examine the association between sex and overall survival (OS), adjusting for demographics, performance status, Charlson comorbidity index, receipt of treatment, tumor mutation burden (TMB), and TP53, KRAS, CDKN2A, STK11, and Keap1 co-mutations. RESULTS Out of 9221 cases with NGS performed, 125 cases (1.4%) had a mutSMARCA4. The most common malignancies with a mutSMARCA4 were non-small cell lung cancer (NSCLC, 35.2%), esophageal and stomach adenocarcinoma (12.8%), and cancer of unknown primary (11.2%). The most common co-mutations were p53 (mutp53, 59.2%), KRAS (mutKRAS, 28.8%), CDKN2A (mutCDKN2A, 31.2%), STK11 (mutSTK11, 12.8%), and Keap1 (mutKeap1, 8.8%) mutations. Male patients had substantially worse OS than female patients both among the entire mutSMARCA4 cohort (HR = 1.71, [95% CI 0.92-3.18]) with a median OS of 3.0 versus 43.3 months (p < 0.001), and among the NSCLC subgroup (HR = 14.2, [95% CI 2.76-73.4]) with a median OS of 2.75 months versus un-estimable (p = 0.02). Among all patients with mutSMARCA4, mutp53 versus wtp53 (HR = 2.12, [95% CI 1.04-4.29]) and mutSTK11 versus wtSTK11 (HR = 2.59, [95% CI 0.87-7.73]) were associated with worse OS. Among the NSCLC subgroup, mutp53 versus wtp53 (HR = 0.35, [0.06-1.97]) and mutKRAS versus wtKRAS (HR = 0.04, [0.003-.45]) were associated with better OS, while mutCDKN2A versus wtCDKN2A (HR = 5.04, [1.12-22.32]), mutSTK11 versus wtSTK11 (HR = 13.10, [95% CI 1.16-148.26]), and mutKeap1 versus wtKeap1 (HR = 5.06, [95% CI 0.89-26.61}) were associated with worse OS. CONCLUSION In our cohort of patients with mutSMARCA4, males had substantially worse prognosis than females, while mutTP53, mutKRAS, mutCDKN2A, mutSTK11 and mutKeap1were differentially associated with prognosis among all patients and among the NSCLC subgroup. Our results, if confirmed, could suggest potentially unidentified mechanisms that underly this sex and co-mutation-dependent prognostic disparity among patients whose tumor bears a mutSMARCA4.
Collapse
Affiliation(s)
- Minggui Pan
- Department of Oncology and Hematology, Kaiser Permanente, Santa Clara, CA 94051, USA
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Chen Jiang
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Zheyang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, and National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
| | - Ninah Achacoso
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | | | - Pam Tse
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Elaine Chung
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Jennifer Marie Suga
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Sachdev Thomas
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| |
Collapse
|
7
|
Prazanowska KH, Lim SB. An integrated single-cell transcriptomic dataset for non-small cell lung cancer. Sci Data 2023; 10:167. [PMID: 36973297 PMCID: PMC10042991 DOI: 10.1038/s41597-023-02074-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
As single-cell RNA sequencing (scRNA-seq) has emerged as a great tool for studying cellular heterogeneity within the past decade, the number of available scRNA-seq datasets also rapidly increased. However, reuse of such data is often problematic due to a small cohort size, limited cell types, and insufficient information on cell type classification. Here, we present a large integrated scRNA-seq dataset containing 224,611 cells from human primary non-small cell lung cancer (NSCLC) tumors. Using publicly available resources, we pre-processed and integrated seven independent scRNA-seq datasets using an anchor-based approach, with five datasets utilized as reference and the remaining two, as validation. We created two levels of annotation based on cell type-specific markers conserved across the datasets. To demonstrate usability of the integrated dataset, we created annotation predictions for the two validation datasets using our integrated reference. Additionally, we conducted a trajectory analysis on subsets of T cells and lung cancer cells. This integrated data may serve as a resource for studying NSCLC transcriptome at the single cell level.
Collapse
Affiliation(s)
- Karolina Hanna Prazanowska
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Korea
| | - Su Bin Lim
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea.
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Korea.
| |
Collapse
|
8
|
Ding Z, Liu Y, Huang Q, Cheng C, Song L, Zhang C, Cui X, Wang Y, Han Y, Zhang H. m6A‐ and immune‐related lncRNA signature confers robust predictive power for immune efficacy in lung squamous cell carcinoma. VIEW 2023. [DOI: 10.1002/viw.20220083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
|
9
|
Dias e Silva D, Borba GB, Beal JR, Botrus G, Osawa A, Araújo SEA, Moura F, Guendelmann RAK, Uson Junior PLS. Response to Abemaciclib and Immunotherapy Rechallenge with Nivolumab and Ipilimumab in a Heavily Pretreated TMB-H Metastatic Squamous Cell Lung Cancer with CDKN2A Mutation, PIK3CA Amplification and TPS 80%: A Case Report. Int J Mol Sci 2023; 24:ijms24044209. [PMID: 36835617 PMCID: PMC9963198 DOI: 10.3390/ijms24044209] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Inactivation of the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene is considerably more frequent in squamous cell lung cancer (SqCLC) than in other subtypes of lung cancer and may be a promising target for this histology. Here, we present the course of diagnosis and treatment of a patient with advanced SqCLC, harboring not only CDKN2A mutation but also PIK3CA amplification, Tumor Mutational Burden-High (>10 mutations/megabase), and a Tumor Proportion Score of 80%. After disease progression on multiple lines of chemotherapy and immunotherapy, he responded favorably to treatment with the CDK4/6i Abemaciclib and later achieved a durable partial response to immunotherapy rechallenge with a combination of anti-PD-1 and anti-CTLA-4, nivolumab, and ipilimumab.
Collapse
Affiliation(s)
- Douglas Dias e Silva
- Department of Medical Oncology, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
| | - Guilherme Bes Borba
- Department of Medical Oncology, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
| | - Juliana Rodrigues Beal
- Department of Medical Oncology, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
- Center for Personalized Medicine, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
| | - Gehan Botrus
- Department of Oncology and Hematology, Emory University, Atlanta, GA 30322, USA
| | - Akemi Osawa
- Department of Nuclear Medicine, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
| | - Sérgio Eduardo Alonso Araújo
- Department of Medical Oncology, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
- Center for Personalized Medicine, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
| | - Fernando Moura
- Department of Medical Oncology, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
- Center for Personalized Medicine, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
| | | | - Pedro Luiz Serrano Uson Junior
- Department of Medical Oncology, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
- Center for Personalized Medicine, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil
- Correspondence:
| |
Collapse
|
10
|
Goto K, Ogawa K, Hishima T, Oishi N, Tomita O, Tsuyuki T, Oda T, Iwahashi Y, Inaba Y, Honma K. Seborrheic Keratosis With Malignant Transformation (Invasive or Noninvasive Squamous Cell Carcinoma Arising in Seborrheic Keratosis): A Clinicopathologic and Immunohistochemical Study of 11 Cases. Am J Dermatopathol 2022; 44:891-899. [PMID: 36395445 DOI: 10.1097/dad.0000000000002245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT Seborrheic keratosis is a common benign neoplasm composed of basaloid keratinocytes. However, little is known about the malignant transformation of the tumor. Eleven cases of seborrheic keratosis with malignant transformation were analyzed. The 11 patients included 5 male patients and 6 female patients with a median age of 75 years at diagnosis (68-90 years). The tumors arose at various sites from the scalp (n = 3) to the lower leg (n = 2). The median tumor size was 12 (10-32) and 40 (20-75) mm in 7 noninvasive and 4 invasive cases, respectively. One patient exhibited in-transit skin metastasis. Histopathology of the malignant components resembled porocarcinoma or inverted follicular keratosis. Bowenoid and pagetoid spreading was frequently observed. The malignant components expressed cytokeratin 5/6 (100%) and GATA3 (73%), but not cytokeratin 7 (0%), cytokeratin 19 (9%), BerEP4 (0%), c-kit (0%), and NUT (0%). No significant immunoreactivity of YAP1 was observed in any of the cases. Mutant-type immunostaining of p53 and PTEN was observed in 91% and 82% of the cases, respectively. An increase in p16 expression was seen in 6 (86%) of the 7 cases with noninvasive carcinoma, although a loss of p16 immunoexpression was seen in the invasive carcinoma component in 3 (75%) of the 4 cases. This study demonstrated that seborrheic keratosis can undergo malignant transformation, particularly in large-sized lesions in elderly patients. Malignant components mimic porocarcinoma or inverted follicular keratosis. Malignant transformation induced by TP53 and PTEN mutations and tumor invasion by CDKN2A inactivating mutations are suggested in this study.
Collapse
Affiliation(s)
- Keisuke Goto
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital, Tokyo, Japan
- Department of Pathology, Itabashi Central Clinical Laboratory, Tokyo, Japan
- Department of Anatomic Pathology, Tokyo Medical University, Tokyo, Japan
- Department of Diagnostic Pathology, Shizuoka Cancer Center Hospital, Sunto, Japan
- Department of Clinical Laboratory and Diagnostic Pathology, Osaka National Hospital, Osaka, Japan
- Department of Dermatology, Hyogo Cancer Center, Akashi, Japan
- Department of Dermato-Oncology/Dermatology, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan
| | - Kohei Ogawa
- Department of Dermatology, Nara Medical University School of Medicine, Kashihara, Japan
| | - Tsunekazu Hishima
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital, Tokyo, Japan
| | | | - Ozumi Tomita
- Dermatology, Faculty of Medicine, University of Yamanashi, Chuo, Japan
| | | | - Takao Oda
- Dermatology, Kainan Hospital, Yatomi, Japan ; and
| | | | - Yutaka Inaba
- Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Keiichiro Honma
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
| |
Collapse
|
11
|
Zeng C, Zhou Y, Ye W, Fang Z, Wang K. Exploration and validation of hub genes in lung adenocarcinoma based on bioinformatics analysis. Transl Cancer Res 2022; 11:3814-3826. [PMID: 36388051 PMCID: PMC9641136 DOI: 10.21037/tcr-22-2225] [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: 08/29/2022] [Accepted: 10/12/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Genomic abnormality is a crucial factor for lung cancer development. This study used bioinformatics analysis to explore the hub genes involved in lung adenocarcinoma. METHODS The GeneCards, Comparative Toxicogenomics Database (CTD), and DISEASES databases were used to screen the genes associated with lung adenocarcinoma. The hub genes were then identified using WebGestalt. The Cancer Genome Atlas (TCGA), UALCAN, and the Human Protein Atlas (HPA) were used to validate the expression of hub genes. The predictive effects of hub genes on the risk of lung adenocarcinoma were evaluated using receiver operating characteristic (ROC) curve analysis. The Tumor-Immune System Interaction Database (TISIDB) was used to estimate the correlation between hub genes and immune infiltration. RESULTS A total of 21 genes were defined as common genes associated with lung adenocarcinoma, and from these, AKT1, CD44, and CDKN2A were identified as hub genes. Significant differences in the hub gene mRNA and protein expression were observed between lung adenocarcinoma samples and normal samples derived from the TCGA and UALCAN databases. The area under the ROC curve (AUC) for AKT1, CD44, and CDKN2A in predicting lung adenocarcinoma risk was 0.847, 0.880, and 0.805, respectively, with sensitivity of 89.8%, 93.2%, and 94.9%, respectively. TISIDB analysis indicated that AKT1, CD44, and CDKN2A expression had a strong relationship with immune infiltration in lung adenocarcinoma. CONCLUSIONS These hub genes, AKT1, CD44, and CDKN2A, may represent tumor biomarkers that may contribute to the understanding, diagnosis, and treatment of lung adenocarcinoma.
Collapse
Affiliation(s)
- Changyi Zeng
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China;,Research Centre for Evidence-Based and Translational Medicine, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - You Zhou
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China
| | - Wanqing Ye
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China
| | - Zihan Fang
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China
| | - Ke Wang
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China;,Research Centre for Evidence-Based and Translational Medicine, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| |
Collapse
|