1
|
Matsumoto K, Fujimori N, Ichihara K, Takeno A, Murakami M, Ohno A, Kakehashi S, Teramatsu K, Ueda K, Nakata K, Sugahara O, Yamamoto T, Matsumoto A, Nakayama KI, Oda Y, Nakamura M, Ogawa Y. Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction. J Gastroenterol 2024:10.1007/s00535-024-02103-0. [PMID: 38684511 DOI: 10.1007/s00535-024-02103-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/31/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Recently, two molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) have been proposed: the "Classical" and "Basal-like" subtypes, with the former showing better clinical outcomes than the latter. However, the "molecular" classification has not been applied in real-world clinical practice. This study aimed to establish patient-derived organoids (PDOs) for PDAC and evaluate their application in subtype classification and clinical outcome prediction. METHODS We utilized tumor samples acquired through endoscopic ultrasound-guided fine-needle biopsy and established a PDO library for subsequent use in morphological assessments, RNA-seq analyses, and in vitro drug response assays. We also conducted a prospective clinical study to evaluate whether analysis using PDOs can predict treatment response and prognosis. RESULTS PDOs of PDAC were established at a high efficiency (> 70%) with at least 100,000 live cells. Morphologically, PDOs were classified as gland-like structures (GL type) and densely proliferating inside (DP type) less than 2 weeks after tissue sampling. RNA-seq analysis revealed that the "morphological" subtype (GL vs. DP) corresponded to the "molecular" subtype ("Classical" vs. "Basal-like"). The "morphological" classification predicted the clinical treatment response and prognosis; the median overall survival of patients with GL type was significantly longer than that with DP type (P < 0.005). The GL type showed a better response to gemcitabine than the DP type in vitro, whereas the drug response of the DP type was improved by the combination of ERK inhibitor and chloroquine. CONCLUSIONS PDAC PDOs help in subtype determination and clinical outcome prediction, thereby facilitating the bench-to-bedside precision medicine for PDAC.
Collapse
Affiliation(s)
- Kazuhide Matsumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Nao Fujimori
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Kazuya Ichihara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Ayumu Takeno
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masatoshi Murakami
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akihisa Ohno
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shotaro Kakehashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Katsuhito Teramatsu
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keijiro Ueda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kohei Nakata
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Osamu Sugahara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeo Yamamoto
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masafumi Nakamura
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| |
Collapse
|
2
|
Chen J, Mao M, Ma Z, Liu J, Jiang M, Chen G, Xu Y. Homeobox B2 promotes malignant behavior and contributes to the radioresistance of nasopharyngeal carcinoma by regulating forkhead box protein O1. Int J Med Sci 2024; 21:837-847. [PMID: 38617001 PMCID: PMC11008478 DOI: 10.7150/ijms.93128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/12/2024] [Indexed: 04/16/2024] Open
Abstract
Background: Nasopharyngeal carcinoma (NPC) is an epithelial tumor of the head and neck with heterogeneous racial and geographical distributions. Homeobox B2 (HOXB2) is a tumor promoter in many cancers. However, the biological role of HOXB2 in NPC has not been elucidated. Methods: Bioinformatics analysis was performed to identify the differentially expressed genes (DEGs) between samples of patients with radiosensitive and radioresistant NPC. qRT-PCR, western blotting and immunohistochemistry were used to detect the expression levels of the corresponding mRNA and proteins. Cell viability was detected by CCK-8 assay and colony-forming capability was evaluated using colony formation assays. Further, migration and invasion abilities were examined using wound-healing and transwell chamber assays, respectively. Cellular apoptosis after irradiation was assessed using flow cytometry and terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining. Results: HOXB2 was identified as a potential regulator of radioresistance in NPC. Our in vitro results indicate that HOXB2 overexpression (HOXB2-OE) promoted malignant behaviors including invasion, migration, proliferation, and inhibited the irradiation-induced apoptosis of NPC cells. Consistent with these results, HOXB2 knockdown (HOXB2-sh) exhibited the opposite trends in these biological activities. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were enriched in the FOXO signaling pathway. Mechanistically, western blotting showed that HOXB2-OE inhibited forkhead box protein O1 (FOXO1) expression in NPC cells. Thereafter, we transferred the FOXO1-OE plasmid to HOXB2-OE NPC cells and found that overexpression of FOXO1 reversed cell proliferation, migration, invasion, and radioresistance profiles promoted by HOXB2 overexpression. Conclusion: Our findings showed that HOXB2 acts as a tumor promoter in NPC, activating malignant behaviors and radioresistance of tumors via FOXO1 regulation. Moreover, the inactivation of HOXB2 or activation of FOXO1 are potential strategies to inhibit tumor progression and overcome radioresistance in NPC.
Collapse
Affiliation(s)
- Jinhai Chen
- Department of Otolaryngology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Mao
- Department of Otolaryngology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhaoen Ma
- Department of Otolaryngology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jie Liu
- Department of Anesthesiology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Minqiong Jiang
- Department of Nursing, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guangui Chen
- Department of Otolaryngology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yali Xu
- Department of Otolaryngology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
3
|
Wu H, Ye J, Zhang M, Luo H. A concise review of the regulatory, diagnostic, and prognostic implications of HOXB-AS3 in tumors. J Cancer 2024; 15:714-728. [PMID: 38213732 PMCID: PMC10777036 DOI: 10.7150/jca.91033] [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: 10/12/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024] Open
Abstract
Recent studies have reported that HOXB-AS3 (HOXB Cluster Antisense RNA 3) is an intriguing molecule with dual functionality as a long noncoding RNA (lncRNA) and putative coding peptide in tumorigenesis and progression. The significant expression alterations of HOXB-AS3 were detected in diverse cancer types and closely correlated with clinical stage and patient survival. Furthermore, HOXB-AS3 was involved in a spectrum of biological processes in solid tumors and hematological malignancies, such as stemness, lipid metabolism, migration, invasion, and tumor growth. This review comprehensively analyzes its clinical relevance for diagnosis and prognosis across human tumors and summarizes its functional role and regulatory mechanisms in different malignant tumors, including liver cancer, acute myeloid leukemia, ovarian cancer, lung cancer, endometrial carcinoma, colon cancer, and oral squamous cell carcinoma. Overall, HOXB-AS3 emerges as a promising biomarker and novel therapeutic target in multiple human tumors.
Collapse
Affiliation(s)
- Hongze Wu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, Jiangxi, China
- Department of Traditional Chinese Medicine, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang 332007, Jiangxi, China
| | - Jiarong Ye
- Nanchang University Queen Mary School, Nanchang 330038, Jiangxi, China
| | - Mengqi Zhang
- The Second Clinical Medical College, Nanchang University, Nanchang 330038, Jiangxi, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, Jiangxi, China
| |
Collapse
|
4
|
Cao W, Lan J, Zeng Z, Yu W, Lei S. Gastrodin Induces Ferroptosis of Glioma Cells via Upregulation of Homeobox D10. Molecules 2023; 28:8062. [PMID: 38138552 PMCID: PMC10745471 DOI: 10.3390/molecules28248062] [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: 10/21/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Gastrodin, the primary bioactive compound found in Gastrodia elata, has been shown to exhibit neuroprotective properties in a range of neurological disorders. However, the precise mechanisms through which gastrodin influences glioma cells remain unclear, and there is a scarcity of data regarding its specific effects. To ascertain the viability of glioma cell lines LN229, U251, and T98, the CCK-8 assay, a colony formation assay, and a 3D culture model were employed, utilizing varying concentrations of gastrodin (0, 5, 10, and 20 μM). Gastrodin exhibited a notable inhibitory effect on the growth of glioma cells, as evidenced by its ability to suppress colony formation and spheroid formation. Additionally, gastrodin induced ferroptosis in glioma cells, as it can increase the levels of reactive oxygen species (ROS) and peroxidized lipids, and reduced the levels of glutathione. Using a subcutaneous tumor model, gastrodin was found to significantly inhibit the growth of the T98 glioma cell line in vivo. Using high-throughput sequencing, PPI analysis, and RT-qPCR, we successfully identified Homeobox D10 (HOXD10) as the principal target of gastrodin. Gastrodin administration significantly enhanced the expression of HOXD10 in glioma cells. Furthermore, treatment with gastrodin facilitated the transcription of ACSL4 via HOXD10. Notably, the inhibition of HOXD10 expression impeded ferroptosis in the cells, which was subsequently restored upon rescue with gastrodin treatment. Overall, our findings suggest that gastrodin acts as an anti-cancer agent by inducing ferroptosis and inhibiting cell proliferation in HOXD10/ACSL4-dependent pathways. As a prospective treatment for gliomas, gastrodin will hopefully be effective.
Collapse
Affiliation(s)
- Wenpeng Cao
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China;
- Key Laboratory of Human Brain Bank for Functions and Diseases, Guizhou Medical University, Guiyang 550025, China
| | - Jinzhi Lan
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China; (J.L.); (Z.Z.)
| | - Zhirui Zeng
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China; (J.L.); (Z.Z.)
| | - Wenfeng Yu
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China;
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang 550025, China
- Key Laboratory of Medical Molecular Biology, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China
| | - Shan Lei
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China; (J.L.); (Z.Z.)
| |
Collapse
|
5
|
Parrillo L, Spinelli R, Longo M, Zatterale F, Santamaria G, Leone A, Campitelli M, Raciti GA, Beguinot F. The Transcription Factor HOXA5: Novel Insights into Metabolic Diseases and Adipose Tissue Dysfunction. Cells 2023; 12:2090. [PMID: 37626900 PMCID: PMC10453582 DOI: 10.3390/cells12162090] [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: 06/15/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The transcription factor HOXA5, from the HOX gene family, has long been studied due to its critical role in physiological activities in normal cells, such as organ development and body patterning, and pathological activities in cancer cells. Nonetheless, recent evidence supports the hypothesis of a role for HOXA5 in metabolic diseases, particularly in obesity and type 2 diabetes (T2D). In line with the current opinion that adipocyte and adipose tissue (AT) dysfunction belong to the group of primary defects in obesity, linking this condition to an increased risk of insulin resistance (IR) and T2D, the HOXA5 gene has been shown to regulate adipocyte function and AT remodeling both in humans and mice. Epigenetics adds complexity to HOXA5 gene regulation in metabolic diseases. Indeed, epigenetic mechanisms, specifically DNA methylation, influence the dynamic HOXA5 expression profile. In human AT, the DNA methylation profile at the HOXA5 gene is associated with hypertrophic obesity and an increased risk of developing T2D. Thus, an inappropriate HOXA5 gene expression may be a mechanism causing or maintaining an impaired AT function in obesity and potentially linking obesity to its associated disorders. In this review, we integrate the current evidence about the involvement of HOXA5 in regulating AT function, as well as its association with the pathogenesis of obesity and T2D. We also summarize the current knowledge on the role of DNA methylation in controlling HOXA5 expression. Moreover, considering the susceptibility of epigenetic changes to reversal through targeted interventions, we discuss the potential therapeutic value of targeting HOXA5 DNA methylation changes in the treatment of metabolic diseases.
Collapse
Affiliation(s)
- Luca Parrillo
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Rosa Spinelli
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Michele Longo
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Federica Zatterale
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Gianluca Santamaria
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy;
| | - Alessia Leone
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Michele Campitelli
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Gregory Alexander Raciti
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Francesco Beguinot
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| |
Collapse
|
6
|
Juárez-Rendón KJ, Castro-García MA, Prada-Ortega DG, Rivera G, Ruíz-Godoy LM, Enríquez-Cárcamo VI, Reyes-Lopez MA. Variants Identified in the HOXC13 and HOXD13 Genes Suggest Association with Cervical Cancer in a Cohort of Mexican Women. Genes (Basel) 2023; 14:genes14020358. [PMID: 36833285 PMCID: PMC9957514 DOI: 10.3390/genes14020358] [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: 10/29/2022] [Revised: 01/11/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
HOX genes have been associated with carcinogenesis. However, the molecular mechanism by which tumors are generated remains unclear. The HOXC13 and HOXD13 genes are of interest for their involvement in the development of genitourinary structures. The aim of this first study in the Mexican population was to search for and analyze variants in the coding region of the HOXC13 and HOXD13 genes in women with cervical cancer. Samples from Mexican women with cervical cancer and healthy women were sequenced (50/50). Allelic and genotypic frequencies were compared between groups. The functional impact of the proteins was determined with two bioinformatics servers (SIFT and PolyPhen-2), and the oncogenic potential of the identified nonsynonymous variants was determined using the CGI server. We identified five unreported gene variants: c.895C>A p.(Leu299Ile) and c.777C>T p.(Arg259Arg) in the HOXC13 gene and c.128T>A p.(Phe43Tyr), c.204G>A p.(Ala68Ala), and c.267G>A p.(Ser89Ser) in the HOXD13 gene. In this study, we suggest that the non-synonymous variants c.895C>A p.(Leu299Ile) and c.128T>A p.(Phe43Tyr) could represent a risk factor for the development of the disease, although additional studies in larger patient populations and in different ethnic groups are needed in order to support the results observed.
Collapse
Affiliation(s)
- Karina Janett Juárez-Rendón
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro s/n. Esq. Elías Piña. Col. Narciso Mendoza, Reynosa 88710, Mexico
| | - Manuel Alejandro Castro-García
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro s/n. Esq. Elías Piña. Col. Narciso Mendoza, Reynosa 88710, Mexico
| | - Diddier Giovanni Prada-Ortega
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10027, USA
- Unit for Biomedical Research in Cancer, Instituto Nacional de Cancerología, México City 14080, Mexico
- Department of Biomedical Informatics, Faculty of Medicine, Universidad Nacional Autónoma de México, México City 04510, Mexico
| | - Gildardo Rivera
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro s/n. Esq. Elías Piña. Col. Narciso Mendoza, Reynosa 88710, Mexico
| | | | | | - Miguel Angel Reyes-Lopez
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro s/n. Esq. Elías Piña. Col. Narciso Mendoza, Reynosa 88710, Mexico
- Correspondence: ; Tel.: +52-5557296000 (ext. 87751)
| |
Collapse
|
7
|
HOXA5: A crucial transcriptional factor in cancer and a potential therapeutic target. Biomed Pharmacother 2022; 155:113800. [DOI: 10.1016/j.biopha.2022.113800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/20/2022] Open
|
8
|
Zheng D, Ning J, Xia Y, Ruan Y, Cheng F. Comprehensive analysis of a homeobox family gene signature in clear cell renal cell carcinoma with regard to prognosis and immune significance. Front Oncol 2022; 12:1008714. [PMID: 36387262 PMCID: PMC9660242 DOI: 10.3389/fonc.2022.1008714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/04/2022] [Indexed: 12/30/2022] Open
Abstract
The homeobox (HOX) family genes have been linked to multiple types of tumors, while their effect on malignant behaviors of clear cell renal cell carcinoma (ccRCC) and clinical significance remains largely unknown. Here, we comprehensively analyzed the expression profiles and prognostic value of HOX genes in ccRCC using datasets from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. We developed a prognostic signature comprising eight HOX genes (HOXB1, HOXA7, HOXB5, HOXD8, HOXD9, HOXB9, HOXA9, and HOXA11) for overall survival prediction in ccRCC and it allowed patients to be subdivided into high- and low-risk groups. Kaplan-Meier survival analysis in all the internal and external cohorts revealed significant difference in clinical outcome of patients in different risk groups, indicating the satisfactory predictive power of the signature. Additionally, we constructed a prognostic nomogram by integrating signature-derived risk score and clinical factors such as gender, age, T and M status, which might be helpful for clinical decision-making and designing tailored management schedules. Immunological analysis revealed that the regulatory T cells (Tregs) infiltrated differently between the two subgroups in both TCGA and ICGC cohorts. ssGSEA method showed that the enrichment scores for mast cells were significantly lower in high-risk group compared with the low-risk group, which was consistent in both TCGA and ICGC cohorts. As for the related immune function, the enrichment scores of APC co-inhibition, para-inflammation, and type II IFN response were consistently lower in high-risk group in both cohorts. Of the eight HOX genes, the mRNA and protein levels of HOXD8 were downregulated in ccRCC than that in normal tissues, and decreased expression of HOXD8 was associated with increased tumor grade and stage, and lymph node metastasis. Survival analysis revealed that lower expression of HOXD8 predicted worse overall survival in ccRCC. In conclusion, our HOX gene-based signature was a favorable indicator to predict the prognosis of ccRCC cases and associated with immune cell infiltration. HOXD8 might be a tumor suppressor gene in ccRCC and a potential predictor of tumor progression.
Collapse
Affiliation(s)
| | | | | | - Yuan Ruan
- *Correspondence: Fan Cheng, ; Yuan Ruan,
| | - Fan Cheng
- *Correspondence: Fan Cheng, ; Yuan Ruan,
| |
Collapse
|
9
|
Kabekkodu SP, Chakrabarty S, Varghese VK, Ghosh S, Radhakrishnan R, Mallya SP, Kudva A. Salivary DNA methylation markers for cancer of oral cavity. Cancer Biomark 2022; 35:257-268. [PMID: 36245370 DOI: 10.3233/cbm-220028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
PURPOSE: Aberrant DNA methylation plays a crucial role in oral carcinogenesis. Our previous study demonstrated hypermethylation of DAPK1, LRPPRC, RAB6C, and ZNF471 promoters in patients with tongue squamous cell carcinoma compared with normal samples. Methylation profiling using salivary DNA is considered a non-invasive alternative to tissue samples. Hence, the present study tested the DNA methylation status of these four promoters as indicators of oral cancer progression. METHODS: We performed the bisulfite-based targeted next-generation sequencing of four candidate genes in saliva and tissue DNA from normal, premalignant, and squamous cell carcinoma subjects. The clinicopathological association, diagnostic, and prognostic utility of aberrant DNA methylation were evaluated using the TCGA-HNSCC dataset. Using the Xgboost algorithm and logistic regression, CpG sites were prioritized, and Receiver Operating Characteristic was generated. By Log-rank test and Kaplan-Meier (KM) curves, an association between methylation and overall survival (OS), disease-free interval (DFI), and progression-free interval (PFI) were computed. RESULTS: We identified all four genes as significantly hypermethylation in premalignant and malignant samples compared with normal samples. The methylation levels were comparable between saliva and tissue samples with an r-value of 0.6297 to 0.8023 and 0.7823 to 0.9419 between premalignant tissue vs. saliva and OC vs. saliva, respectively. We identified an inverse correlation between DAPK1, LRPPRC, RAB6C, and ZNF471 promoter methylation with its expression. A classifier of 8 differentially methylated CpG sites belonging to DAPK1, RAB6C, and ZNF471 promoters was constructed, showing an AUC of 0.984 to differentiate tumors from normal samples. The differential methylation status of DAPK1, LRPPRC, and ZNF71 promoters was prognostically important. Abnormal expression of all four genes was associated with immune infiltration. CONCLUSIONS: Thus, methylation analysis of these candidate CpG sites from saliva can be helpful as a non-invasive tool for the clinical management of OC.
Collapse
Affiliation(s)
- Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Centre for DNA repair and Genome Stability (CDRGS), Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Centre for DNA repair and Genome Stability (CDRGS), Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vinay Koshy Varghese
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Supriti Ghosh
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sandeep P. Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Adarsh Kudva
- Department of Oral and Maxillofacial Surgery, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| |
Collapse
|
10
|
Liu Z, Elcheva I. A six-gene prognostic signature for both adult and pediatric acute myeloid leukemia identified with machine learning. Am J Transl Res 2022; 14:6210-6221. [PMID: 36247279 PMCID: PMC9556437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Although it is well-known that adult and pediatric acute myeloid leukemias (AMLs) are genetically distinct diseases, they still share certain gene expression profiles. The age-related genetic heterogeneities of AMLs have been well-studied, but the common prognostic signatures and molecular mechanisms of adult and pediatric AMLs are less investigated. AIM To identify genes and pathways that are associated with both pediatric and adult AMLs and discover a gene signature for overall survival (OS) prediction. METHODS Through mining the transcriptome profiles of The Cancer Genome Atlas (TCGA) data sets of adult cancers and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) data of pediatric cancers, we identified genes that are commonly dysregulated in both pediatric and adult AMLs, further discovered a common gene signature, and built two risk score models for TCGA and TARGET cohorts, respectively with L 0 regularized global AUC (area under the receiver operating characteristic curve) summary maximization. RESULTS We identified 57 genes that are differentially expressed and prognostically significant in both adult and childhood AMLs. The top 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched with those 57 genes include transcriptional misregulation, focal adhesion, PI3K-Akt signaling pathway, and signaling pathways regulating pluripotency of stem cells. We further identified a 6-gene signature including genes of ADAMTS3, DNMT3B, NYNRIN, SORT1, ZFHX3, and ZG16B for risk prediction. We constructed a risk score model with one dataset (either TCGA or TARGET) and evaluated its performance with the other. The test AUCs for the risk prediction of TCGA data with a 2-year and 5-year OS cutoffs are 0.762 (P = 2.33e-13, 95% CI: 0.69-0.83) and 0.759 (P = 7.26e-08, 95% CI: 0.66-0.85), respectively, while the test AUCs of TARGET data with the same cutoffs are 0.71 (P = 3.3e-07, 95% CI: 0.62-0.79) and 0.72 (P= 5.25e-09, 95% CI: 0.65-0.80), respectively. We further stratified patients into 3 equal sized prognostic subtypes with the 6-gene risk scores. The P-values of the tertile partitions are 1.74e-07 and 3.28e-08 for the TARGET and TCGA cohorts, respectively, which are significantly better than the standard cytogenetic risk stratification of both cohorts (TARGET: P = 1.64e-06; TCGA: P = 1.79e-05). When validated with two other independent cohorts, the 6-gene risk score models remain a significant predictor for OS. Investigating the common gene expression program is significant in that we may extrapolate the findings from adults to children and avoid unnecessary pediatric clinical trials.
Collapse
Affiliation(s)
- Zhenqiu Liu
- Department of Public Health Sciences, Pennsylvania State University College of Medicine500 University Drive, Hershey, PA 17033, USA
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine500 University Drive, Hershey, PA 17033, USA
| | - Irina Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine500 University Drive, Hershey, PA 17033, USA
| |
Collapse
|