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Cheng JC, Swarup N, Morselli M, Huang WL, Aziz M, Caggiano C, Kordi M, Patel A, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong DW. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Res 2024; 52:e50. [PMID: 38797520 PMCID: PMC11194076 DOI: 10.1093/nar/gkae276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
Whole-genome bisulfite sequencing (BS-Seq) measures cytosine methylation changes at single-base resolution and can be used to profile cell-free DNA (cfDNA). In plasma, ultrashort single-stranded cfDNA (uscfDNA, ∼50 nt) has been identified together with 167 bp double-stranded mononucleosomal cell-free DNA (mncfDNA). However, the methylation profile of uscfDNA has not been described. Conventional BS-Seq workflows may not be helpful because bisulfite conversion degrades larger DNA into smaller fragments, leading to erroneous categorization as uscfDNA. We describe the '5mCAdpBS-Seq' workflow in which pre-methylated 5mC (5-methylcytosine) single-stranded adapters are ligated to heat-denatured cfDNA before bisulfite conversion. This method retains only DNA fragments that are unaltered by bisulfite treatment, resulting in less biased uscfDNA methylation analysis. Using 5mCAdpBS-Seq, uscfDNA had lower levels of DNA methylation (∼15%) compared to mncfDNA and was enriched in promoters and CpG islands. Hypomethylated uscfDNA fragments were enriched in upstream transcription start sites (TSSs), and the intensity of enrichment was correlated with expressed genes of hemopoietic cells. Using tissue-of-origin deconvolution, we inferred that uscfDNA is derived primarily from eosinophils, neutrophils, and monocytes. As proof-of-principle, we show that characteristics of the methylation profile of uscfDNA can distinguish non-small cell lung carcinoma from non-cancer samples. The 5mCAdpBS-Seq workflow is recommended for any cfDNA methylation-based investigations.
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Affiliation(s)
- Jordan C Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Wei-Lun Huang
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christa Caggiano
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - David Chia
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Zaitlen
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Steve Dubinett
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Zhao F, Su L, Wang X, Luan J, Zhang X, Li Y, Li S, Hu L. Molecular map of disulfidptosis-related genes in lung adenocarcinoma: the perspective toward immune microenvironment and prognosis. Clin Epigenetics 2024; 16:26. [PMID: 38342890 PMCID: PMC10860275 DOI: 10.1186/s13148-024-01632-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024] Open
Abstract
BACKGROUND Disulfidptosis is a recently discovered form of programmed cell death that could impact cancer development. Nevertheless, the prognostic significance of disulfidptosis-related genes (DRGs) in lung adenocarcinoma (LUAD) requires further clarification. METHODS This study systematically explores the genetic and transcriptional variability, prognostic relevance, and expression profiles of DRGs. Clusters related to disulfidptosis were identified through consensus clustering. We used single-sample gene set enrichment analysis and ESTIMATE to assess the tumor microenvironment (TME) in different subgroups. We conducted a functional analysis of differentially expressed genes between subgroups, which involved gene ontology, the Kyoto encyclopedia of genes and genomes, and gene set variation analysis, in order to elucidate their functional status. Prognostic risk models were developed using univariate Cox regression and the least absolute shrinkage and selection operator regression. Additionally, single-cell clustering and cell communication analysis were conducted to enhance the understanding of the importance of signature genes. Lastly, qRT-PCR was employed to validate the prognostic model. RESULTS Two clearly defined DRG clusters were identified through a consensus-based, unsupervised clustering analysis. Observations were made concerning the correlation between changes in multilayer DRG and various clinical characteristics, prognosis, and the infiltration of TME cells. A well-executed risk assessment model, known as the DRG score, was developed to predict the prognosis of LUAD patients. A high DRG score indicates increased TME cell infiltration, a higher mutation burden, elevated TME scores, and a poorer prognosis. Additionally, the DRG score showed a significant correlation with the tumor mutation burden score and the tumor immune dysfunction and exclusion score. Subsequently, a nomogram was established for facilitating the clinical application of the DRG score, showing good predictive ability and calibration. Additionally, crucial DRGs were further validated by single-cell sequencing data. Finally, crucial DRGs were further validated by qRT-PCR and immunohistochemistry. CONCLUSION Our new DRG signature risk score can predict the immune landscape and prognosis of LUAD. It also serves as a reference for LUAD's immunotherapy and chemotherapy.
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Affiliation(s)
- Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Lei Su
- Department of Radiation Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China
| | - Xuefeng Wang
- Department of Radiation Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China
| | - Jiusong Luan
- Pulmonary and Critical Care Medicine, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China
| | - Xin Zhang
- Department of Radiation Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China
| | - Yishuai Li
- Department of Thoracic Surgery, Hebei Chest Hospital, Shijiazhuang, 050000, Hebei, People's Republic of China.
| | - Shujun Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China.
| | - Ling Hu
- Department of Medical Oncology, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, People's Republic of China.
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Zhang Y, Chen J, Tian J, Zhou Y, Liu Y. Role and function of plakophilin 3 in cancer progression and skin disease. Cancer Sci 2024; 115:17-23. [PMID: 38048779 PMCID: PMC10823275 DOI: 10.1111/cas.16019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Plakophilin 3 (PKP3), a component of desmosome, is aberrantly expressed in many kinds of human diseases, especially in cancers. Through direct interaction, PKP3 binds with a series of desmosomal proteins, such as desmoglein, desmocollin, plakoglobin, and desmoplakin, to initiate desmosome aggregation, then promotes its stability. As PKP3 is mostly expressed in the skin, loss of PKP3 promotes the development of several skin diseases, such as paraneoplastic pemphigus, pemphigus vulgaris, and hypertrophic scar. Moreover, accumulated clinical data indicate that PKP3 dysregulates in diverse cancers, including breast, ovarian, colon, and lung cancers. Numerous lines of evidence have shown that PKP3 plays important roles in multiple cellular processes during cancer progression, including metastasis, invasion, tumor formation, autophagy, and proliferation. This review examines the diverse functions of PKP3 in regulating tumor formation and development in various types of cancers and summarizes its detailed mechanisms in the occurrence of skin diseases.
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Affiliation(s)
- Yefei Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Institute of Cancer, Department of Biochemistry, College of Life ScienceNanjing Normal UniversityNanjingChina
| | - Jiahui Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Institute of Cancer, Department of Biochemistry, College of Life ScienceNanjing Normal UniversityNanjingChina
| | - Jia Tian
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Institute of Cancer, Department of Biochemistry, College of Life ScienceNanjing Normal UniversityNanjingChina
| | - Yehui Zhou
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yan Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Institute of Cancer, Department of Biochemistry, College of Life ScienceNanjing Normal UniversityNanjingChina
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Healthcare Engineering JO. Retracted: Analysis of Multiple Human Tumor Cases Reveals the Carcinogenic Effects of PKP3. JOURNAL OF HEALTHCARE ENGINEERING 2023; 2023:9867309. [PMID: 37829397 PMCID: PMC10567387 DOI: 10.1155/2023/9867309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
[This retracts the article DOI: 10.1155/2021/9391104.].
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Reynolds DE, Vallapureddy P, Morales RT, Oh D, Pan M, Chintapula U, Linardi RL, Gaesser AM, Ortved K, Ko J. Equine mesenchymal stem cell derived extracellular vesicle immunopathology biomarker discovery. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e89. [PMID: 38938916 PMCID: PMC11080797 DOI: 10.1002/jex2.89] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/07/2023] [Accepted: 04/25/2023] [Indexed: 06/29/2024]
Abstract
The use of mesenchymal stem cells (MSCs) in human and veterinary clinical applications has become a subject of increasing importance due to their roles in immunomodulation and regenerative processes. MSCs are especially relevant in equine medicine because they may have the ability to treat prevalent musculoskeletal disorders, among other conditions. However, recent evidence suggests that the components secreted by MSCs, particularly extracellular vesicles (EVs), are responsible for these properties. EVs contain proteins and nucleic acids, which possess an active role in intercellular communication and can be used as therapeutics. However, because the intersection of equine veterinary medicine with EVs remains a relatively new field, there is a demand to identify biomarkers that can discern and enrich for therapeutic EVs, progressing their clinical efficacy. In this study, we identified and characterized 84 miRNAs, between three equine donors involved in immunomodulation in cell and EV subjects. We discovered distinct groups of shared miRNAs, like miR-21-5p and miR-451a, that are abundant and enriched between the donors' EVs, respectively. By mapping and comparing the MSC-EV miRNA expression, we discovered many pathways that are involved in immunomodulation and tissue regenerative processes related to equine clinical applications. Therefore, the miRNAs highlighted in this article can be used as valuable biomarkers for screening MSC-derived EVs for potential equine therapy.
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Affiliation(s)
- David E. Reynolds
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Phoebe Vallapureddy
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | | | - Daniel Oh
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Menghan Pan
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Uday Chintapula
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Renata L. Linardi
- Department of Clinical StudiesNew Bolton Center, School of Veterinary Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Angela M. Gaesser
- Department of Clinical StudiesNew Bolton Center, School of Veterinary Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Kyla Ortved
- Department of Clinical StudiesNew Bolton Center, School of Veterinary Medicine, University of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jina Ko
- Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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