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Sun H, Chang Z, Li H, Tang Y, Liu Y, Qiao L, Feng G, Huang R, Han D, Yin DT. Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier. Transl Oncol 2024; 43:101889. [PMID: 38382228 PMCID: PMC10900934 DOI: 10.1016/j.tranon.2024.101889] [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: 10/11/2023] [Revised: 01/02/2024] [Accepted: 01/21/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND The reclassification of Papillary Thyroid Carcinoma (PTC) is an area of research that warrants attention. The connection between thyroid cancer, inflammation, and immune responses necessitates considering the mechanisms of differential prognosis of thyroid tumors from an immunological perspective. Given the high adaptability of macrophages to environmental stimuli, focusing on the differentiation characteristics of macrophages might offer a novel approach to address the issues related to PTC subtyping. METHODS Single-cell RNA sequencing data of medullary cells infiltrated by papillary thyroid carcinoma obtained from public databases was subjected to dimensionality reduction clustering analysis. The RunUMAP and FindAllMarkers functions were utilized to identify the gene expression matrix of different clusters. Cell differentiation trajectory analysis was conducted using the Monocle R package. A complex regulatory network for the classification of Immune status and Macrophage differentiation-associated Papillary Thyroid Cancer Classification (IMPTCC) was constructed through quantitative multi-omics analysis. Immunohistochemistry (IHC) staining was utilized for pathological histology validation. RESULTS Through the integration of single-cell RNA and bulk sequencing data combined with multi-omics analysis, we identified crucial transcription factors, immune cells/immune functions, and signaling pathways. Based on this, regulatory networks for three IMPTCC clusters were established. CONCLUSION Based on the co-expression network analysis results, we identified three subtypes of IMPTCC: Immune-Suppressive Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (ISMPTCC), Immune-Neutral Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (INMPTCC), and Immune-Activated Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (IAMPTCC). Each subtype exhibits distinct metabolic, immune, and regulatory characteristics corresponding to different states of macrophage differentiation.
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Affiliation(s)
- Hanlin Sun
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Zhengyan Chang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Hongqiang Li
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Yifeng Tang
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Yihao Liu
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Lixue Qiao
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Guicheng Feng
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China
| | - Runzhi Huang
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China.
| | - Dongyan Han
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, PR China.
| | - De-Tao Yin
- Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China; Engineering Research Center of Multidisciplinary Diagnosis and Treatment of Thyroid Cancer of Henan Province, Zhengzhou 450052, Henan, PR China; Key Medicine Laboratory of Thyroid Cancer of Henan Province, Zhengzhou 450052, Henan, PR China.
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D'Amico AE, Wong AC, Zajd CM, Zhang X, Murali A, Trebak M, Lennartz MR. PKC-ε regulates vesicle delivery and focal exocytosis for efficient IgG-mediated phagocytosis. J Cell Sci 2021; 134:jcs258886. [PMID: 34622926 PMCID: PMC8627556 DOI: 10.1242/jcs.258886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/27/2021] [Indexed: 11/20/2022] Open
Abstract
Protein kinase C (PKC)-ε is required for membrane addition during IgG-mediated phagocytosis, but its role in this process is ill defined. Here, we performed high-resolution imaging, which reveals that PKC-ε exits the Golgi and enters phagosomes on vesicles that then fuse. TNF and PKC-ε colocalize at the Golgi and on vesicles that enter the phagosome. Loss of PKC-ε and TNF delivery upon nocodazole treatment confirmed vesicular transport on microtubules. That TNF+ vesicles were not delivered in macrophages from PKC-ε null mice, or upon dissociation of the Golgi-associated pool of PKC-ε, implies that Golgi-tethered PKC-ε is a driver of Golgi-to-phagosome trafficking. Finally, we established that the regulatory domain of PKC-ε is sufficient for delivery of TNF+ vesicles to the phagosome. These studies reveal a novel role for PKC-ε in focal exocytosis - its regulatory domain drives Golgi-derived vesicles to the phagosome, whereas catalytic activity is required for their fusion. This is one of the first examples of a PKC requirement for vesicular trafficking and describes a novel function for a PKC regulatory domain. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Anna E. D'Amico
- Albany Medical College, 47 New Scotland Ave MC-165, Albany, NY 12208, USA
| | - Alexander C. Wong
- Albany Medical College, 47 New Scotland Ave MC-165, Albany, NY 12208, USA
| | - Cheryl M. Zajd
- Albany Medical College, 47 New Scotland Ave MC-165, Albany, NY 12208, USA
| | - Xuexin Zhang
- Penn State College of Medicine, 500 University Dr., Hershey, PA 17033, USA
| | - Ananya Murali
- Albany Medical College, 47 New Scotland Ave MC-165, Albany, NY 12208, USA
| | - Mohamed Trebak
- University of Pittsburgh School of Medicine, 2550 Terrace Street, Pittsburgh, PA 15231, USA
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Papadaki A, Tziouvara O, Kotopouli A, Koumarianou P, Doukas A, Rios P, Tardieux I, Köhn M, Boleti H. The Leishmania donovani LDBPK_220120.1 Gene Encodes for an Atypical Dual Specificity Lipid-Like Phosphatase Expressed in Promastigotes and Amastigotes; Substrate Specificity, Intracellular Localizations, and Putative Role(s). Front Cell Infect Microbiol 2021; 11:591868. [PMID: 33842381 PMCID: PMC8027504 DOI: 10.3389/fcimb.2021.591868] [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: 08/05/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
The intracellular protozoan parasites of the Leishmania genus are responsible for Leishmaniases, vector borne diseases with a wide range of clinical manifestations. Leishmania (L.) donovani causes visceral leishmaniasis (kala azar), the most severe of these diseases. Along their biological cycle, Leishmania parasites undergo distinct developmental transitions including metacyclogenesis and differentiation of metacyclic promastigotes (MPs) to amastigotes. Metacyclogenesis inside the phlebotomine sandfly host's midgut converts the procyclic dividing promastigotes to non-dividing infective MPs eventually injected into the skin of mammalian hosts and phagocytosed by macrophages where the MPs are converted inside modified phagolysosomes to the intracellular amastigotes. These developmental transitions involve dramatic changes in cell size and shape and reformatting of the flagellum requiring thus membrane and cytoskeleton remodeling in which phosphoinositide (PI) signaling and metabolism must play central roles. This study reports on the LDBPK_220120.1 gene, the L. donovani ortholog of LmjF.22.0250 from L. major that encodes a phosphatase from the "Atypical Lipid Phosphatases" (ALPs) enzyme family. We confirmed the expression of the LDBPK_220120.1 gene product in both L. donovani promastigotes and axenic amastigotes and showed that it behaves in vitro as a Dual Specificity P-Tyr and monophosphorylated [PI(3)P and PI(4)P] PI phosphatase and therefore named it LdTyrPIP_22 (Leishmaniad onovani Tyrosine PI Phosphatase, gene locus at chromosome 22). By immunofluorescence confocal microscopy we localized the LdTyrPIP_22 in several intracellular sites in the cell body of L. donovani promastigotes and amastigotes and in the flagellum. A temperature and pH shift from 25°C to 37°C and from pH 7 to 5.5, induced a pronounced recruitment of LdTyrPIP_22 epitopes to the flagellar pocket and a redistribution around the nucleus. These results suggest possible role(s) for this P-Tyr/PI phosphatase in the regulation of processes initiated or upregulated by this temperature/pH shift that contribute to the developmental transition from MPs to amastigotes inside the mammalian host macrophages.
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Affiliation(s)
- Amalia Papadaki
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Olympia Tziouvara
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Anastasia Kotopouli
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Petrina Koumarianou
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece.,Light Microscopy Unit, Hellenic Pasteur Institute, Athens, Greece
| | - Anargyros Doukas
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Pablo Rios
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Isabelle Tardieux
- Team «Biomechanics of Host Parasite Interactions», Institut for Advanced BioSciences, Univ. Grenoble Alpes, Inserm U1209 - CNRS UMR 5309, 38700 La Tronche, France
| | - Maja Köhn
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Haralabia Boleti
- Intracellular Parasitism Laboratory, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece.,Light Microscopy Unit, Hellenic Pasteur Institute, Athens, Greece
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Li Y, Zhou Y, Zhao M, Zou J, Zhu Y, Yuan X, Liu Q, Cai H, Chu CQ, Liu Y. Differential Profile of Plasma Circular RNAs in Type 1 Diabetes Mellitus. Diabetes Metab J 2020; 44:854-865. [PMID: 32662258 PMCID: PMC7801755 DOI: 10.4093/dmj.2019.0151] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/30/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND No currently available biomarkers or treatment regimens fully meet therapeutic needs of type 1 diabetes mellitus (T1DM). Circular RNA (circRNA) is a recently identified class of stable noncoding RNA that have been documented as potential biomarkers for various diseases. Our objective was to identify and analyze plasma circRNAs altered in T1DM. METHODS We used microarray to screen differentially expressed plasma circRNAs in patients with new onset T1DM (n=3) and age-/gender-matched healthy controls (n=3). Then, we selected six candidates with highest fold-change and validated them by quantitative real-time polymerase chain reaction in independent human cohort samples (n=12). Bioinformatic tools were adopted to predict putative microRNAs (miRNAs) sponged by these validated circRNAs and their downstream messenger RNAs (mRNAs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to gain further insights into T1DM pathogenesis. RESULTS We identified 68 differentially expressed circRNAs, with 61 and seven being up- and downregulated respectively. Four of the six selected candidates were successfully validated. Curations of their predicted interacting miRNAs revealed critical roles in inflammation and pathogenesis of autoimmune disorders. Functional relations were visualized by a circRNA-miRNA-mRNA network. GO and KEGG analyses identified multiple inflammation-related processes that could be potentially associated with T1DM pathogenesis, including cytokine-cytokine receptor interaction, inflammatory mediator regulation of transient receptor potential channels and leukocyte activation involved in immune response. CONCLUSION Our study report, for the first time, a profile of differentially expressed plasma circRNAs in new onset T1DM. Further in silico annotations and bioinformatics analyses supported future application of circRNAs as novel biomarkers of T1DM.
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Affiliation(s)
- Yangyang Li
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, China
| | - Ying Zhou
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Minghui Zhao
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, China
| | - Jing Zou
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Yuxiao Zhu
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Xuewen Yuan
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Qianqi Liu
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hanqing Cai
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, China
| | - Cong-Qiu Chu
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University School of Medicine, Portland, OR, USA
- Section of Rheumatology, VA Portland Health Care System, Portland, OR, USA
| | - Yu Liu
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
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Zajd CM, Ziemba AM, Miralles GM, Nguyen T, Feustel PJ, Dunn SM, Gilbert RJ, Lennartz MR. Bone Marrow-Derived and Elicited Peritoneal Macrophages Are Not Created Equal: The Questions Asked Dictate the Cell Type Used. Front Immunol 2020; 11:269. [PMID: 32153579 PMCID: PMC7047825 DOI: 10.3389/fimmu.2020.00269] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/03/2020] [Indexed: 12/18/2022] Open
Abstract
Macrophages are a heterogeneous and plastic population of cells whose phenotype changes in response to their environment. Macrophage biologists utilize peritoneal (pMAC) and bone marrow-derived macrophages (BMDM) for in vitro studies. Given that pMACs mature in vivo while BMDM are ex vivo differentiated from stem cells, it is likely that their responses differ under experimental conditions. Surprisingly little is known about how BMDM and pMACs responses compare under the same experimental conditionals. While morphologically similar with respect to forward and side scatter by flow cytometry, reports in the literature suggest that pMACs are more mature than their BMDM counterparts. Given the dearth of information comparing BMDM and pMACs, this work was undertaken to test the hypothesis that elicited pMACs are more responsive to defined conditions, including phagocytosis, respiratory burst, polarization, and cytokine and chemokine release. In all cases, our hypothesis was disproved. At steady state, BMDM are more phagocytic (both rate and extent) than elicited pMACs. In response to polarization, they upregulate chemokine and cytokine gene expression and release more cytokines. The results demonstrate that BMDM are generally more responsive and poised to respond to their environment, while pMAC responses are, in comparison, less pronounced. BMDM responses are a function of intrinsic differences, while pMAC responses reflect their differentiation in the context of the whole animal. This distinction may be important in knockout animals, where the pMAC phenotype may be influenced by the absence of the gene of interest.
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Affiliation(s)
- Cheryl M Zajd
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Alexis M Ziemba
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Grace M Miralles
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Terry Nguyen
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
| | - Paul J Feustel
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY, United States
| | - Stanley M Dunn
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Ryan J Gilbert
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Michelle R Lennartz
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States
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Nelson NLJ, Zajd CM, Lennartz MR, Gosselin EJ. Fcγ receptors and toll-like receptor 9 synergize to drive immune complex-induced dendritic cell maturation. Cell Immunol 2019; 345:103962. [PMID: 31582169 DOI: 10.1016/j.cellimm.2019.103962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/30/2019] [Accepted: 08/03/2019] [Indexed: 12/11/2022]
Abstract
Previous in vivo studies established that inactivated Francisella tularensis immune complexes (mAb-iFt) are a more protective vaccine against lethal tularemia than iFt alone. Subsequent in vitro studies revealed enhanced DC maturation marker expression with mAb-iFt stimulation. The goal of this study was to determine the mechanism of enhanced DC maturation. Multiparameter analysis of surface marker expression and cytokine secretion demonstrates a requirement for FcγR signaling in enhanced DC maturation. MyD88 was also found to be essential for heightened DC maturation, implicating MyD88-dependent TLRs in DC maturation. Upon further study, we discovered that TLRs 2 & 4 drive cytokine secretion, but surprisingly TLR9 is required for DC maturation marker upregulation. These studies reveal a separation of DC cytokine and maturation marker induction pathways and demonstrate that FcγR-TLR/MyD88 synergy underlies the enhanced dendritic cell maturation in response to the mAb-iFt vaccine.
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Affiliation(s)
- Nicole L J Nelson
- Department of Immunology and Microbial Disease, Albany Medical College, 47 New Scotland Avenue, Albany, NY 12208, United States.
| | - Cheryl M Zajd
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Avenue, Albany, NY 12208, United States
| | - Michelle R Lennartz
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Avenue, Albany, NY 12208, United States
| | - Edmund J Gosselin
- Department of Immunology and Microbial Disease, Albany Medical College, 47 New Scotland Avenue, Albany, NY 12208, United States.
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D’Amico AE, Lennartz MR. Protein Kinase C-epsilon in Membrane Delivery during Phagocytosis. JOURNAL OF IMMUNOLOGICAL SCIENCES 2018; 2:26-32. [PMID: 30112519 PMCID: PMC6089528 DOI: 10.29245/2578-3009/2018/2.1134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
During phagocytosis, internal membranes are recruited to the site of pathogen binding and fuse with the plasma membrane, providing the membrane needed for pseudopod extension and target uptake. The mechanism by which vesicles destined for the phagosome are generated, targeted, and fuse is unknown. We established that Golgi-associated protein kinase C-epsilon (PKC-ε) is necessary for the addition of membrane during FcyR-mediated phagocytosis. PKC-ε is tethered to the Golgi through interactions between its' regulatory domain and the Golgi lipids PI4P and diacylglycerol; disruption of these interactions prevents PKC-ε concentration at phagosomes and decreases phagocytosis. The accumulated evidence suggests that PKC-ε orchestrates vesicle formation at the Golgi by a mechanism requiring lipid binding but not enzymatic activity. This review discusses how PKC-ε might mediate vesicle formation at the level of budding and fission. Specifically, we discuss PKC-ε binding partners, the formation of lipid subdomains to generate membrane curvature, and PKC-ε mediated links to the actin and microtubule cytoskeleton to provide tension for vesicle fission. Assimilating information from several model systems, we propose a model for PKC-ε mediated vesicle formation for exocytosis during phagocytosis that may be applicable to other processes that require directed membrane delivery and fusion.
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Affiliation(s)
- Anna E. D’Amico
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Avenue Albany, NY 12208, USA
| | - Michelle R. Lennartz
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, 47 New Scotland Avenue Albany, NY 12208, USA
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