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Kurokawa S, Kobori T, Yoneda M, Ogawa Y, Honda Y, Kessoku T, Imajo K, Saito S, Nakajima A, Hotta K. Identification of differentially methylated regions associated with both liver fibrosis and hepatocellular carcinoma. BMC Gastroenterol 2024; 24:57. [PMID: 38302914 PMCID: PMC10832174 DOI: 10.1186/s12876-024-03149-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Liver fibrosis is a major risk factor for hepatocellular carcinoma (HCC). We have previously reported that differentially methylated regions (DMRs) are correlated with the fibrosis stages of metabolic dysfunction-associated steatotic liver disease (MASLD). In this study, the methylation levels of those DMRs in liver fibrosis and subsequent HCC were examined. METHODS The methylation levels of DMRs were investigated using alcoholic cirrhosis and HCC (GSE60753). The data of hepatitis C virus-infected cirrhosis and HCC (GSE60753), and two datasets (GSE56588 and GSE89852) were used for replication analyses. The transcriptional analyses were performed using GSE114564, GSE94660, and GSE142530. RESULTS Hypomethylated DMR and increased transcriptional level of zinc finger and BTB domain containing 38 (ZBTB38) were observed in HCC. Hypermethylated DMRs, and increased transcriptional levels of forkhead box K1 (FOXK1) and zinc finger CCCH-type containing 3 (ZC3H3) were observed in HCC. The methylation levels of DMR of kazrin, periplakin interacting protein (KAZN) and its expression levels were gradually decreased as cirrhosis progressed to HCC. CONCLUSIONS Changes in the methylation and transcriptional levels of ZBTB38, ZC3H3, FOXK1, and KAZN are important for the development of fibrosis and HCC; and are therefore potential therapeutic targets and diagnostic tools for cirrhosis and HCC.
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Affiliation(s)
- Suguru Kurokawa
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Takuro Kobori
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Masato Yoneda
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yuji Ogawa
- Department of Gastroenterology, National Hospital Organization Yokohama Medical Center, 3-60-2 Harajyuku, Totsuka, Yokohama, 245-8675, Japan
| | - Yasushi Honda
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Takaomi Kessoku
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
- Department of Palliative Medicine, International University of Health and Welfare Narita Hospital, 852, Hatakeda, Narita, 286-8520, Japan
| | - Kento Imajo
- Department of Gastroenterology, Shin-yurigaoka General Hospital, 255 Furusawatsuko, Asao, Kawasaki, 2150-0026, Japan
| | - Satoru Saito
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Atsushi Nakajima
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kikuko Hotta
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan.
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Zhu S, Bao H, Zhang MC, Liu H, Wang Y, Lin C, Zhao X, Liu SL. KAZN as a diagnostic marker in ovarian cancer: a comprehensive analysis based on microarray, mRNA-sequencing, and methylation data. BMC Cancer 2022; 22:662. [PMID: 35710397 PMCID: PMC9204993 DOI: 10.1186/s12885-022-09747-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Background Ovarian cancer (OC) is among the deadliest malignancies in women and the lack of appropriate markers for early diagnosis leads to poor prognosis in most cases. Previous studies have shown that KAZN is involved in multiple biological processes during development, such as cell proliferation, differentiation, and apoptosis, so defects or aberrant expression of KAZN might cause queer cell behaviors such as malignancy. Here we evaluated the KAZN expression and methylation levels for possible use as an early diagnosis marker for OC. Methods We used data from Gene Expression Omnibus (GEO) microarrays, The Cancer Genome Atlas (TCGA), and Clinical Proteomic Tumor Analysis Consortium (CPTAC) to investigate the correlations between KAZN expression and clinical characteristics of OC by comparing methylation levels of normal and OC samples. The relationships among differentially methylated sites in the KAZN gene, corresponding KAZN mRNA expression levels and prognosis were analyzed. Results KAZN was up-regulated in ovarian epithelial tumors and the expression of KAZN was correlated with the patients’ survival time. KAZN CpG site cg17657618 was positively correlated with the expression of mRNA and the methylation levels were significantly differential between the group of stage “I and II” and the group of stage “III and IV”. This study also presents a new method to classify tumor and normal tissue in OC using DNA methylation pattern in the KAZN gene body region. Conclusions KAZN was involved in ovarian cancer pathogenesis. Our results demonstrate a new direction for ovarian cancer research and provide a potential diagnostic biomarker as well as a novel therapeutic target for clinical application. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09747-2.
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Affiliation(s)
- Songling Zhu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hongxia Bao
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Meng-Chun Zhang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Huidi Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yao Wang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Caiji Lin
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Xingjuan Zhao
- Physical Examination Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China. .,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China. .,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China. .,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
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Di Giacomo D, Quintini M, Pierini V, Pellanera F, La Starza R, Gorello P, Matteucci C, Crescenzi B, Fiumara PF, Veltroni M, Borlenghi E, Albano F, Forghieri F, Maccaferri M, Bettelli F, Luppi M, Cuneo A, Rossi G, Mecucci C. Genomic and clinical findings in myeloid neoplasms with PDGFRB rearrangement. Ann Hematol 2021; 101:297-307. [PMID: 34859285 PMCID: PMC8742810 DOI: 10.1007/s00277-021-04712-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/08/2022]
Abstract
Platelet-derived growth factor receptor B (PDGFRB) gene rearrangements define a unique subgroup of myeloid and lymphoid neoplasms frequently associated with eosinophilia and characterized by high sensitivity to tyrosine kinase inhibition. To date, various PDGFRB/5q32 rearrangements, involving at least 40 fusion partners, have been reported. However, information on genomic and clinical features accompanying rearrangements of PDGFRB is still scarce. Here, we characterized a series of 14 cases with a myeloid neoplasm using cytogenetic, single nucleotide polymorphism array, and next-generation sequencing. We identified nine PDGFRB translocation partners, including the KAZN gene at 1p36.21 as a novel partner in a previously undescribed t(1;5)(p36;q33) chromosome change. In all cases, the PDGFRB recombination was the sole cytogenetic abnormality underlying the phenotype. Acquired somatic variants were mainly found in clinically aggressive diseases and involved epigenetic genes (TET2, DNMT3A, ASXL1), transcription factors (RUNX1 and CEBPA), and signaling modulators (HRAS). By using both cytogenetic and nested PCR monitoring to evaluate response to imatinib, we found that, in non-AML cases, a low dosage (100–200 mg) is sufficient to induce and maintain longstanding hematological, cytogenetic, and molecular remissions.
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Affiliation(s)
- Danika Di Giacomo
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Martina Quintini
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Valentina Pierini
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Fabrizia Pellanera
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Roberta La Starza
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Paolo Gorello
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy.,Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Caterina Matteucci
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | - Barbara Crescenzi
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy
| | | | - Marinella Veltroni
- Department of Pediatric Oncology-Hematology, Meyer Children's Hospital, Florence, Italy
| | | | - Francesco Albano
- Hematology Unit, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Forghieri
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy
| | - Monica Maccaferri
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy
| | - Francesca Bettelli
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy
| | - Mario Luppi
- Section of Hematology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, AOU Policlinico, Modena, Italy
| | - Antonio Cuneo
- Hematology, Department of Medical Sciences, St. Anna University Hospital, 44124, Ferrara, Italy
| | | | - Cristina Mecucci
- Department of Medicine and Surgery, Center for Hemato-Oncology Research (C.R.E.O.), University of Perugia, Perugia, Italy.
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Yan D, Wu F, Peng C, Wang M. Silencing of LINC00284 inhibits cell proliferation and migration in oral squamous cell carcinoma by the miR-211-3p/MAFG axis and FUS/ KAZN axis. Cancer Biol Ther 2021; 22:149-163. [PMID: 33618612 DOI: 10.1080/15384047.2021.1877864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most common malignancies worldwide. Emerging evidence has suggested that long noncoding RNAs (lncRNAs) play vital roles in various biological processes of cancers, such as cell proliferation, migration, invasion, and apoptosis. As reported previously, long intergenic non-protein coding RNA 284 (LINC00284) is an important regulator in multiple cancers. However, the biological role, as well as regulatory mechanism of LINC00284 in OSCC, has not been investigated. In our study, RT-qPCR results indicated that LINC00284 was significantly upregulated in OSCC tissues and cells. Moreover, loss-of-function experiments demonstrated that LINC00284 downregulation suppressed cell proliferation and migration and facilitated cell apoptosis. Mechanistically, we found that LINC00284 sponged microRNA 211-3p (miR-211-3p) to upregulate MAF bZIP transcription factor G (MAFG) expression in OSCC cells. Additionally, LINC00284 interacted with FUS protein to increase KAZN mRNA stability. Functional assays showed that either MAFG or KAZN overexpression promoted the malignant behaviors of OSCC cells. Through a series of rescue assays, we found that the inhibitory effect of silencing LINC00284 on OSCC cells can be reversed by upregulated MAFG and KAZN. Overall, silencing LINC00284 inhibits the malignant characteristics of OSCC cells by downregulating MAFG and inhibiting the binding of FUS to KAZN mRNA.
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Affiliation(s)
- Dayong Yan
- Department of Oral and Maxillofacial Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Fuhua Wu
- Department of Stomatology, Dezhou People's Hospital, Dezhou, Shandong, China
| | - Caixia Peng
- Department of Oral and Maxillofacial Surgery, Dezhou People's Hospital, Dezhou, Shandong, China
| | - Mei Wang
- Department of Stomatology, Dezhou People's Hospital, Dezhou, Shandong, China
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