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Vitale F, Zileri Dal Verme L, Paratore M, Negri M, Nista EC, Ainora ME, Esposto G, Mignini I, Borriello R, Galasso L, Alfieri S, Gasbarrini A, Zocco MA, Nicoletti A. The Past, Present, and Future of Biomarkers for the Early Diagnosis of Pancreatic Cancer. Biomedicines 2024; 12:2840. [PMCID: PMC11673965 DOI: 10.3390/biomedicines12122840] [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: 11/01/2024] [Revised: 11/30/2024] [Accepted: 12/11/2024] [Indexed: 01/04/2025] Open
Abstract
Pancreatic cancer is one of the most aggressive cancers with a very poor 5-year survival rate and reduced therapeutic options when diagnosed in an advanced stage. The dismal prognosis of pancreatic cancer has guided significant efforts to discover novel biomarkers in order to anticipate diagnosis, increasing the population of patients who can benefit from curative surgical treatment. CA 19-9 is the reference biomarker that supports the diagnosis and guides the response to treatments. However, it has significant limitations, a low specificity, and is inefficient as a screening tool. Several potential biomarkers have been discovered in the serum, urine, feces, and pancreatic juice of patients. However, most of this evidence needs further validation in larger cohorts. The advent of advanced omics sciences and liquid biopsy techniques has further enhanced this field of research. The aim of this review is to analyze the historical evolution of the research on novel biomarkers for the early diagnosis of pancreatic cancer, focusing on the current evidence for the most promising biomarkers from different body fluids and the novel trends in research, such as omics sciences and liquid biopsy, in order to favor the application of modern personalized medicine.
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Affiliation(s)
- Federica Vitale
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Lorenzo Zileri Dal Verme
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Mattia Paratore
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Marcantonio Negri
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Enrico Celestino Nista
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Maria Elena Ainora
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Giorgio Esposto
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Irene Mignini
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Raffaele Borriello
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Linda Galasso
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Sergio Alfieri
- Centro Pancreas, Chirurgia Digestiva, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy;
| | - Antonio Gasbarrini
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Maria Assunta Zocco
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
| | - Alberto Nicoletti
- CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.V.); (L.Z.D.V.); (M.P.); (M.N.); (E.C.N.); (M.E.A.); (G.E.); (I.M.); (R.B.); (L.G.); (A.G.); (A.N.)
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Poirah I, Chakraborty D, Dixit P, Samal S, Banerjee S, Mukherjee T, Chattopadhyay S, Nath G, Bhattacharyya A. The influence of hypoxia-mediated CEACAM6 upregulation on epithelial cell and macrophage response in the context of gastric cancer. Eur J Clin Invest 2024; 54 Suppl 2:e14352. [PMID: 39674878 DOI: 10.1111/eci.14352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Accepted: 11/03/2024] [Indexed: 12/17/2024]
Abstract
BACKGROUND The hypoxic microenvironment is a key component of the gastric tumour niche. Carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) is upregulated in gastric cancer and is considered a novel biomarker for the disease. However, no prior studies have elaborated on the status of CEACAM6 and its role in the hypoxic gastric cancer niche. METHODS In this short study, we evaluated the effect of hypoxia in modulating CEACAM6 level in gastric cancer cells (GCCs) through western blotting and determined the effect of CEACAM6 upregulation on gastric cancer progression through clonogenicity, cell proliferation and migration assays. The wound-healing ability of GCCs was downregulated by siRNA-mediated CEACAM6 silencing. Human gastric cancer biopsy samples were examined by immunofluorescence microscopy to assess the level of a hypoxia marker HIF1α and CEACAM6. The effect of empty vector or CEACAM6-expression on peripheral blood-derived mononuclear cell (PBMC)-derived macrophage polarization under normoxia or hypoxia was studied by incubating macrophages in conditioned medium collected from GCC cultures. Macrophage polarization status was observed using flow cytometry and fluorescence microscopy. Reactive oxygen species (ROS) generation by macrophages was evaluated using fluorescence microscopy. RESULTS We identified that hypoxia promoted CEACAM6 in GCCs, and these cells acquired increased proliferative potential and migration ability. Moreover, the cell culture supernatant from hypoxia-exposed CEACAM6-overexpressing cells promoted an M2-like macrophage population and discouraged the M1 phenotype. CONCLUSION This study established that hypoxia increased CEACAM6 which promoted gastric cancer progression by influencing GCC proliferation and motility as well as macrophage polarization.
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Affiliation(s)
- Indrajit Poirah
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
| | - Debashish Chakraborty
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
| | - Pragyesh Dixit
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
| | - Supriya Samal
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
| | - Smaran Banerjee
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
| | - Tathagata Mukherjee
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
| | - Subhasis Chattopadhyay
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
| | - Gautam Nath
- Department of Gastroenterology, Acharya Harihar Post Graduate Institute of Cancer, Cuttack, India
| | - Asima Bhattacharyya
- School of Biological Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
- Centre for Interdisciplinary Sciences (CIS), NISER, An OCC of Homi Bhabha National Institute, Khurda, Odisha, India
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Sugiyanto RN, Metzger C, Inal A, Truckenmueller F, Gür K, Eiteneuer E, Huth T, Fraas A, Heinze I, Kirkpatrick J, Sticht C, Albrecht T, Goeppert B, Poth T, Pusch S, Mehrabi A, Schirmacher P, Ji J, Ori A, Roessler S. Proteomic profiling reveals CEACAM6 function in driving gallbladder cancer aggressiveness through integrin receptor, PRKCD and AKT/ERK signaling. Cell Death Dis 2024; 15:780. [PMID: 39468006 PMCID: PMC11519453 DOI: 10.1038/s41419-024-07171-x] [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: 04/09/2024] [Revised: 10/08/2024] [Accepted: 10/18/2024] [Indexed: 10/30/2024]
Abstract
Gallbladder cancer (GBC) presents as an aggressive malignancy with poor patient outcome. Like other epithelial cancers, the mechanisms of GBC cancer progression remain vague and efforts in finding targeted therapies fall below expectations. This study combined proteomic analysis of formalin-fixed paraffin-embedded (FFPE) GBC samples, functional and molecular characterization of potential oncogenes and identification of potential therapeutic strategies for GBC. We identified Carcinoembryonic Antigen-related Cell Adhesion Molecule 6 (CEACAM6) as one of the significantly most upregulated proteins in GBC. CEACAM6 overexpression has been observed in other cancer entities but the molecular function remains unclear. Our functional analyses in vitro and in vivo mouse models revealed that CEACAM6 supported the initial steps of cancer progression and metastasis by decreasing cell adhesion and promoting migration and invasion of GBC cells. Conversely, CEACAM6 knockdown abolished GBC aggressiveness by increasing cell adhesion while reducing cell migration, cell proliferation, and colony formation. BirA-BioID followed by mass-spectrometry revealed Integrin Beta-1 (ITGB1) and Protein Kinase C Delta (PRKCD) as direct molecular and functional partners of CEACAM6 supporting GBC cell migration. ERK and AKT signaling and their downstream target genes were regulated by CEACAM6 and thus the treatment with AKT inhibitor capivasertib or ERK inhibitor ulixertinib mitigated the CEACAM6-induced migration. These findings demonstrate that CEACAM6 is crucially involved in gallbladder cancer progression by promoting migration and inhibiting cell adhesion through ERK and AKT signaling providing specific options for treatment of CEACAM6-positive cancers.
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Affiliation(s)
- Raisatun Nisa Sugiyanto
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Carmen Metzger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Aslihan Inal
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Felicia Truckenmueller
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Kira Gür
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Eva Eiteneuer
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thorben Huth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Angelika Fraas
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Ivonne Heinze
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Albrecht
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
- Liver Cancer Centre Heidelberg (LCCH), Heidelberg, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology and Neuropathology, RKH Hospital Ludwigsburg, Ludwigsburg, Germany
| | - Tanja Poth
- Center for Model System and Comparative Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Stefan Pusch
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arianeb Mehrabi
- Liver Cancer Centre Heidelberg (LCCH), Heidelberg, Germany
- Department of General Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany
- Liver Cancer Centre Heidelberg (LCCH), Heidelberg, Germany
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg University, Heidelberg, Germany.
- Liver Cancer Centre Heidelberg (LCCH), Heidelberg, Germany.
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Goldstein NB, Berk ZBK, Tomb LC, Hu J, Hoaglin LG, Roop DR, Adiri R, Zhuang Y, Canosa JM, Sanders P, Norris DA, Nocka K, Cha A, Birlea SA. Phosphodiesterase-4 Inhibitors Increase Pigment Cell Proliferation and Melanization in Cultured Melanocytes and within a 3-Dimensional Skin Equivalent Model. J Invest Dermatol 2024:S0022-202X(24)02055-4. [PMID: 39182565 DOI: 10.1016/j.jid.2024.08.005] [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: 01/19/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]
Abstract
Vitiligo is a common chronic autoimmune disease characterized by white macules and patches of the skin, having a negative impact on patients' life and without any definitive cure at present. Identification of new compounds to reverse depigmentation is therefore a pressing need for this disease. The pharmacologic compounds phosphodiesterase-4 inhibitors (PDE4is) are small molecules with immunomodulatory properties used for treatment of inflammatory dermatoses. PDE4is have shown repigmentation effects in patients with vitiligo, in some case reports. We characterized the proliferative and melanogenic potential of 2 known PDE4is-crisaborole and roflumilast-and of a more recently designed compound, PF-07038124. We used 2 in vitro model systems-the primary human melanocyte culture and a 3-dimensional cocultured skin model (MelanoDerm)-with an exploratory testing platform composed of complementary assays (spectrophotometry, melanin and proliferation assays, immunostaining, Fontana-Masson staining, RT-qPCR, western blot, and whole-transcriptome RNA sequencing). We identified that treatment with PDE4is was associated with increased melanocyte proliferation and melanization in both in vitro models and with increase in the melanogenic genes and proteins expression in cultured melanocytes. These effects were found to be enhanced by addition of α-melanocyte-stimulating hormone. Our findings support the further evaluation of PDE4is with or without α-melanocyte-stimulating hormone agonists in vitiligo trials.
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Affiliation(s)
| | - Zachary B K Berk
- Department of Dermatology, University of Colorado, Aurora, Colorado, USA
| | - Landon C Tomb
- Department of Dermatology, University of Colorado, Aurora, Colorado, USA
| | - Junxiao Hu
- Department of Pediatrics Endocrinology, University of Colorado, Aurora, Colorado, USA
| | - Laura G Hoaglin
- Department of Dermatology, University of Colorado, Aurora, Colorado, USA; Gates Center for Regenerative Medicine, University of Colorado, Aurora, Colorado, USA
| | - Dennis R Roop
- Department of Dermatology, University of Colorado, Aurora, Colorado, USA; Gates Center for Regenerative Medicine, University of Colorado, Aurora, Colorado, USA
| | - Roni Adiri
- Pfizer Pharmaceutical, Herzlyia Pituach, Israel
| | - Yonghua Zhuang
- Department of Pediatrics Endocrinology, University of Colorado, Aurora, Colorado, USA
| | | | | | - David A Norris
- Department of Dermatology, University of Colorado, Aurora, Colorado, USA
| | | | - Amy Cha
- Pfizer, New York, New York, USA
| | - Stanca A Birlea
- Department of Dermatology, University of Colorado, Aurora, Colorado, USA; Gates Center for Regenerative Medicine, University of Colorado, Aurora, Colorado, USA.
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Wang C, Huang W, Zhong Y, Zou X, Liu S, Li J, Sun Y, Zhou K, Chen X, Li Z, Wang S, Huang Y, Bai Y, Yin J, Jin X, Liu S, Yuan Y, Deng Q, Jiang M, Liu C, Liu L, Xu X, Wu L. Single-cell multi-modal chromatin profiles revealing epigenetic regulations of cells in hepatocellular carcinoma. Clin Transl Med 2024; 14:e70000. [PMID: 39210544 PMCID: PMC11362026 DOI: 10.1002/ctm2.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/12/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Various epigenetic regulations systematically govern gene expression in cells involving various biological processes. Dysregulation of the epigenome leads to aberrant transcriptional programs and subsequently results in diseases, such as cancer. Therefore, comprehensive profiling epigenomics is essential for exploring the mechanisms underlying gene expression regulation during development and disease. METHODS In this study, we developed single-cell chromatin proteins and accessibility tagmentation (scCPA-Tag), a multi-modal single-cell epigenetic profile capturing technique based on barcoded Tn5 transposases and a droplet microfluidics platform. scCPA-Tag enables the simultaneous capture of DNA profiles of histone modification and chromatin accessibility in the same cell. RESULTS By applying scCPA-Tag to K562 cells and a hepatocellular carcinoma (HCC) sample, we found that the silence of several chromatin-accessible genes can be attributed to lysine-27-trimethylation of the histone H3 tail (H3K27me3) modification. We characterized the epigenetic features of the tumour cells and different immune cell types in the HCC tumour tissue by scCPA-Tag. Besides, a tumour cell subtype (C2) with more aggressive features was identified and characterized by high chromatin accessibility and a lower abundance of H3K27me3 on tumour-promoting genes. CONCLUSIONS Our multi-modal scCPA-Tag provides a comprehensive approach for exploring the epigenetic landscapes of heterogeneous cell types and revealing the mechanisms of gene expression regulation during developmental and pathological processes at the single-cell level. HIGHLIGHTS scCPA-Tag offers a highly efficient and high throughput technique to simultaneously profile histone modification and chromatin accessibility within a single cell. scCPA-Tag enables to uncover multiple epigenetic modification features of cellular compositions within tumor tissues. scCPA-Tag facilitates the exploration of the epigenetic landscapes of heterogeneous cell types and provides the mechanisms governing gene expression regulation.
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Affiliation(s)
- Chunqing Wang
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
- BGI ResearchChongqingChina
- BGI ResearchShenzhenChina
| | - Waidong Huang
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
- BGI ResearchChongqingChina
| | | | - Xuanxuan Zou
- BGI ResearchChongqingChina
- BGI ResearchShenzhenChina
- Department of Medical LaboratoryHubei Provincial Clinical Research Center for Parkinson's DiseaseXiangyang No.1 People's Hospital, Hubei University of MedicineXiangyangChina
| | - Shang Liu
- BGI ResearchChongqingChina
- BGI ResearchShenzhenChina
| | - Jie Li
- BGI ResearchShenzhenChina
| | - Yunfan Sun
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer InvasionMinistry of EducationShanghaiChina
- Zhongshan‐BGI Precision Medical CenterZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Kaiqian Zhou
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer InvasionMinistry of EducationShanghaiChina
- Zhongshan‐BGI Precision Medical CenterZhongshan Hospital, Fudan UniversityShanghaiChina
| | - Xi Chen
- BGI ResearchChongqingChina
- BGI ResearchShenzhenChina
| | - Zihao Li
- BGI ResearchShenzhenChina
- School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouChina
| | | | | | | | | | | | | | - Yue Yuan
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer InvasionMinistry of EducationShanghaiChina
| | - Qiuting Deng
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer InvasionMinistry of EducationShanghaiChina
| | | | - Chuanyu Liu
- BGI ResearchShenzhenChina
- Shanxi Medical University‐BGI Collaborative Center for Future MedicineShanxi Medical UniversityTaiyuanChina
| | - Longqi Liu
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer InvasionMinistry of EducationShanghaiChina
| | - Xun Xu
- BGI ResearchShenzhenChina
| | - Liang Wu
- BGI ResearchChongqingChina
- BGI ResearchShenzhenChina
- Zhongshan‐BGI Precision Medical CenterZhongshan Hospital, Fudan UniversityShanghaiChina
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6
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Rinchai D, Chaussabel D. Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker. F1000Res 2024; 11:1294. [PMID: 39239252 PMCID: PMC11375406 DOI: 10.12688/f1000research.126721.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/11/2024] [Indexed: 09/07/2024] Open
Abstract
Background Changes in blood transcript abundance levels have been associated with pathogenesis in a wide range of diseases. While next generation sequencing technology can measure transcript abundance on a genome-wide scale, downstream clinical applications often require small sets of genes to be selected for inclusion in targeted panels. Here we set out to gather information from the literature and transcriptome datasets that would help researchers determine whether to include the gene CEACAM6 in such panels. Methods We employed a workflow to systematically retrieve, structure, and aggregate information derived from both the literature and public transcriptome datasets. It consisted of profiling the CEACAM6 literature to identify major diseases associated with this candidate gene and establish its relevance as a biomarker. Accessing blood transcriptome datasets identified additional instances where CEACAM6 transcript levels differ in cases vs controls. Finally, the information retrieved throughout this process was captured in a structured format and aggregated in interactive circle packing plots. Results Although it is not routinely used clinically, the relevance of CEACAM6 as a biomarker has already been well established in the cancer field, where it has invariably been found to be associated with poor prognosis. Focusing on the blood transcriptome literature, we found studies reporting elevated levels of CEACAM6 abundance across a wide range of pathologies, especially diseases where inflammation plays a dominant role, such as asthma, psoriasis, or Parkinson's disease. The screening of public blood transcriptome datasets completed this picture, showing higher abundance levels in patients with infectious diseases caused by viral and bacterial pathogens. Conclusions Targeted assays measuring CEACAM6 transcript abundance in blood may be of potential utility for the management of patients with diseases presenting with systemic inflammation and for the management of patients with cancer, where the assay could potentially be run both on blood and tumor tissues.
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Affiliation(s)
- Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, 10065, USA
| | - Damien Chaussabel
- Computer Sciences Department, The Jackson Laboratory, Farmington, CT, 06032, USA
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Michl J, White B, Monterisi S, Bodmer WF, Swietach P. Phenotypic screen of sixty-eight colorectal cancer cell lines identifies CEACAM6 and CEACAM5 as markers of acid resistance. Proc Natl Acad Sci U S A 2024; 121:e2319055121. [PMID: 38502695 PMCID: PMC10990159 DOI: 10.1073/pnas.2319055121] [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: 10/31/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024] Open
Abstract
Elevated cancer metabolism releases lactic acid and CO2 into the under-perfused tumor microenvironment, resulting in extracellular acidosis. The surviving cancer cells must adapt to this selection pressure; thus, targeting tumor acidosis is a rational therapeutic strategy to manage tumor growth. However, none of the major approved treatments are based explicitly on disrupting acid handling, signaling, or adaptations, possibly because the distinction between acid-sensitive and acid-resistant phenotypes is not clear. Here, we report pH-related phenotypes of sixty-eight colorectal cancer (CRC) cell lines by measuring i) extracellular acidification as a readout of acid production by fermentative metabolism and ii) growth of cell biomass over a range of extracellular pH (pHe) levels as a measure of the acid sensitivity of proliferation. Based on these measurements, CRC cell lines were grouped along two dimensions as "acid-sensitive"/"acid-resistant" versus "low metabolic acid production"/"high metabolic acid production." Strikingly, acid resistance was associated with the expression of CEACAM6 and CEACAM5 genes coding for two related cell-adhesion molecules, and among pH-regulating genes, of CA12. CEACAM5/6 protein levels were strongly induced by acidity, with a further induction under hypoxia in a subset of CRC lines. Lack of CEACAM6 (but not of CEACAM5) reduced cell growth and their ability to differentiate. Finally, CEACAM6 levels were strongly increased in human colorectal cancers from stage II and III patients, compared to matched samples from adjacent normal tissues. Thus, CEACAM6 is a marker of acid-resistant clones in colorectal cancer and a potential motif for targeting therapies to acidic regions within the tumors.
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Affiliation(s)
- Johanna Michl
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Bobby White
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Stefania Monterisi
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Walter F. Bodmer
- Department of Oncology, University of Oxford, OxfordOX3 7DQ, United Kingdom
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
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Wu G, Wang D, Xiong F, Wang Q, Liu W, Chen J, Chen Y. The emerging roles of CEACAM6 in human cancer (Review). Int J Oncol 2024; 64:27. [PMID: 38240103 PMCID: PMC10836497 DOI: 10.3892/ijo.2024.5615] [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: 06/14/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Carcinoembryonic antigen (CEA)‑related cell adhesion molecule 6 (CEACAM6) is a cell adhesion protein of the CEA family of glycosyl phosphatidyl inositol anchored cell surface glycoproteins. A wealth of research has demonstrated that CEACAM6 is generally upregulated in pancreatic adenocarcinoma, breast cancer, non‑small cell lung cancer, gastric cancer, colon cancer and other cancers and promotes tumor progression, invasion and metastasis. The transcriptional expression of CEACAM6 is regulated by various factors, including the CD151/TGF‑β1/Smad3 axis, microRNA (miR)‑146, miR‑26a, miR‑29a/b/c, miR‑128, miR‑1256 and DNA methylation. In addition, the N‑glycosylation of CEACAM6 protein at Asn256 is mediated by α‑1,6‑mannosylglycoptotein 6‑β‑N‑acetylglucosaminyltransferase. In terms of downstream signaling pathways, CEACAM6 promotes tumor proliferation by increasing levels of cyclin D1 and cyclin‑dependent kinase 4 proteins. CEACAM6 can activate the ERK1/2/MAPK or SRC/focal adhesion kinase/PI3K/AKT pathways directly or through EGFR, leading to stimulation of tumor proliferation, invasion, migration, resistance to anoikis and chemotherapy, as well as angiogenesis. This article provides a review of the expression pattern, biological function and relationship with prognosis of CEACAM6 in cancer. In summary, CEACAM6 may be a valuable diagnostic biomarker and potential therapeutic target for human cancers exhibiting overexpression of CEACAM6.
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Affiliation(s)
- Guanhua Wu
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Da Wang
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Fei Xiong
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Qi Wang
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Wenzheng Liu
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Junsheng Chen
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Yongjun Chen
- Department of Biliary‑Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
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Lin WR, Liu WQ, Meng XY, Liu XT, Kou ZY, Li WL, Yang J. Identification of driving genes of familial adenomatous polyposis by differential gene expression analysis and weighted gene co-expression network analysis. Technol Health Care 2024; 32:1675-1696. [PMID: 38073344 PMCID: PMC11091565 DOI: 10.3233/thc-230719] [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: 06/01/2023] [Accepted: 10/07/2023] [Indexed: 05/12/2024]
Abstract
BACKGROUND Despite the advancement of new screening strategies and the advances in pharmacological therapies, the cancerization rates of familial adenomatous polyposis (FAP) are stable and even increased in the last years. Therefore, it necessitates additional research to characterize and understand the underlying mechanisms of FAP. OBJECTIVE To determine the genes that drive the pathogenesis of familial adenomatous polyposis (FAP). METHODS We performed on a cohort (GSE111156) gene profile, which consist of four group of gene expressions (the gene expressions of cancer, adenoma and normal tissue of duodenal cancer from patients with FAP were defined as Case N, Case A and Case C respectively, while that of adenoma tissue from patients with FAP who did not have duodenal cancer was Ctrl A). Tracking Tumor Immunophenotype (TIP) website was applied to reveal immune infiltration profile and signature genes of FAP. We merged the genes of key module (pink and midnight module) with signature genes to obtained the biomarkers related with FAP pathogenesis. The expression of these five biomarkers in FAP intratumoral region (IT) and tumor rim (TR) was detected with Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). RESULTS In total, 220, 23 and 63 DEGs were determined in Cases C, A and N, in comparison to Ctrl A. In total, 196 and 10 DEGs were determined in Cases C and A, separately, as compared to Case N. A total of four biomarkers including CCL5, CD3G, CD2 and TLR3 were finally identified associated with pink module, while only one biomarker (KLF2) associated with midnight module was identified. All biomarkers were evidently raised in FAP IT tissues utilizing qRT-PCR. CONCLUSION We identified five potential biomarkers for pathogenesis of FAP to understand the fundamental mechanisms of FAP progression and revealed some probable targets for the diagnosis or treatment of FAP.
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Affiliation(s)
- Wan-Rong Lin
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Wei-Qing Liu
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Department of Internal Medicine-Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xuan-Yu Meng
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xiao-Ting Liu
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Zhi-Yong Kou
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Wen-Liang Li
- Colorectal Cancer Clinical Research Center, Third Affiliated Hospital, Kunming Medical University, Kunming, Yunnan, China
| | - Jun Yang
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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10
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Son SM, Yun J, Kim DW, Jung YS, Han SB, Lee YH, Han HS, Woo CG, Lee HC, Lee OJ. MicroRNA 29a therapy for CEACAM6-expressing lung adenocarcinoma. BMC Cancer 2023; 23:843. [PMID: 37684602 PMCID: PMC10492333 DOI: 10.1186/s12885-023-11352-w] [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: 05/08/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Non-coding microRNAs (miRNAs) play critical roles in tumor progression and hold great promise as therapeutic agents for multiple cancers. MicroRNA 29a (miR-29a) is a tumor suppressor miRNA that inhibits cancer cell growth and tumor progression in non-small cell lung cancer. Carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6), which plays an important role in lung cancer progression, has been identified as a target of miR-29a. Here, we evaluated the therapeutic efficacy of a peptide vector capable of delivering miR-29a intracellularly using the acidic tumor microenvironment in a lung adenocarcinoma xenograft mouse model. METHODS A miRNA delivery vector was constructed by tethering the peptide nucleic acid form of miR-29a to a peptide with a low pH-induced transmembrane structure (pHLIP) to enable transport of the miRNAs across the plasma membrane. Tumor suppressive effects of pHLIP-miR29a on lung adenocarcinoma development in vivo were assessed using a BALB/c xenograft model injected with A549 cells. RESULTS Incubation of A549 cells with pHLIP-miR-29a at an acidic pH downregulated endogenous CEACAM6 expression and reduced cell viability. Intravenous injection of the mice with pHLIP-miR-29a inhibited tumor growth by up to 18.1%. Intraperitoneal injection of cisplatin reduced tumor volume by 29.9%. Combined pHLIP-miR-29a + cisplatin treatment had an additive effect, reducing tumor volume up to 39.7%. CONCLUSIONS Delivery of miR-29a to lung adenocarcinoma cells using a pHLIP-mediated method has therapeutic potential as a unique cancer treatment approach.
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Affiliation(s)
- Seung-Myoung Son
- Department of Pathology, Chungbuk National University Hospital, Cheongju, Republic of Korea
- Department of Pathology, College of Medicine, Chungbuk National University, 1, Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Jieun Yun
- Department of Pharmaceutical Engineering, Cheongju University, Cheongju, Republic of Korea
| | - Dong-Wook Kim
- College of Pharmacy, Wonkwang University, Iksan, Republic of Korea
| | - Young-Suk Jung
- Department of Pharmacy, College of Pharmacy, Research Institute for Drug Development, Pusan National University, Busan, Republic of Korea
| | - Sang-Bae Han
- College of Pharmacy, Chungbuk National University, Cheongju, Republic of Korea
| | - Yong Hee Lee
- Department of Biochemistry, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Hye Sook Han
- Department of Internal Medicine, Chungbuk National University Hospital, Cheongju, Republic of Korea
- Department of Internal Medicine, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Chang Gok Woo
- Department of Pathology, Chungbuk National University Hospital, Cheongju, Republic of Korea
- Department of Pathology, College of Medicine, Chungbuk National University, 1, Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Ho-Chang Lee
- Department of Pathology, Chungbuk National University Hospital, Cheongju, Republic of Korea
- Department of Pathology, College of Medicine, Chungbuk National University, 1, Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Ok-Jun Lee
- Department of Pathology, Chungbuk National University Hospital, Cheongju, Republic of Korea.
- Department of Pathology, College of Medicine, Chungbuk National University, 1, Chungdae-Ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
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11
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Sans M, Makino Y, Min J, Rajapakshe KI, Yip-Schneider M, Schmidt CM, Hurd MW, Burks JK, Gomez JA, Thege FI, Fahrmann JF, Wolff RA, Kim MP, Guerrero PA, Maitra A. Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of the Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential. Cancer Discov 2023; 13:1844-1861. [PMID: 37285225 PMCID: PMC10880589 DOI: 10.1158/2159-8290.cd-22-1200] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/18/2023] [Accepted: 06/05/2023] [Indexed: 06/09/2023]
Abstract
Intraductal papillary mucinous neoplasms (IPMN) of the pancreas are bona fide precursor lesions of pancreatic ductal adenocarcinoma (PDAC). The most common subtype of IPMNs harbors a gastric foveolar-type epithelium, and these low-grade mucinous neoplasms are harbingers of IPMNs with high-grade dysplasia and cancer. The molecular underpinning of gastric differentiation in IPMNs is unknown, although identifying drivers of this indolent phenotype might enable opportunities for intercepting progression to high-grade IPMN and cancer. We conducted spatial transcriptomics on a cohort of IPMNs, followed by orthogonal and cross-species validation studies, which established the transcription factor NKX6-2 as a key determinant of gastric cell identity in low-grade IPMNs. Loss of NKX6-2 expression is a consistent feature of IPMN progression, while reexpression of Nkx6-2 in murine IPMN lines recapitulates the aforementioned gastric transcriptional program and glandular morphology. Our study identifies NKX6-2 as a previously unknown transcription factor driving indolent gastric differentiation in IPMN pathogenesis. SIGNIFICANCE Identification of the molecular features driving IPMN development and differentiation is critical to prevent cancer progression and enhance risk stratification. We used spatial profiling to characterize the epithelium and microenvironment of IPMN, which revealed a previously unknown link between NKX6-2 and gastric differentiation, the latter associated with indolent biological potential. See related commentary by Ben-Shmuel and Scherz-Shouval, p. 1768. This article is highlighted in the In This Issue feature, p. 1749.
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Affiliation(s)
- Marta Sans
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuki Makino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jimin Min
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kimal I. Rajapakshe
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michele Yip-Schneider
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - C Max Schmidt
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mark W. Hurd
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Javier A. Gomez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fredrik I. Thege
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Robert A. Wolff
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michael P. Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paola A. Guerrero
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Anirban Maitra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
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12
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Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Identification and Interaction Analysis of Molecular Markers in Pancreatic Ductal Adenocarcinoma by Bioinformatics and Next-Generation Sequencing Data Analysis. Bioinform Biol Insights 2023; 17:11779322231186719. [PMID: 37529485 PMCID: PMC10387711 DOI: 10.1177/11779322231186719] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/18/2023] [Indexed: 08/03/2023] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is one of the most common cancers worldwide. Intense efforts have been made to elucidate the molecular pathogenesis, but the molecular mechanisms of PDAC are still not well understood. The purpose of this study is to further explore the molecular mechanism of PDAC through integrated bioinformatics analysis. Methods To identify the candidate genes in the carcinogenesis and progression of PDAC, next-generation sequencing (NGS) data set GSE133684 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and Gene Ontology (GO) and pathway enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using Integrated Interactions Database (IID) interactome database and Cytoscape. Subsequently, miRNA-DEG regulatory network and TF-DEG regulatory network were constructed using miRNet database, NetworkAnalyst database, and Cytoscape software. The expression levels of hub genes were validated based on Kaplan-Meier analysis, expression analysis, stage analysis, mutation analysis, protein expression analysis, immune infiltration analysis, and receiver operating characteristic (ROC) curve analysis. Results A total of 463 DEGs were identified, consisting of 232 upregulated genes and 233 downregulated genes. The enriched GO terms and pathways of the DEGs include vesicle organization, secretory vesicle, protein dimerization activity, lymphocyte activation, cell surface, transferase activity, transferring phosphorus-containing groups, hemostasis, and adaptive immune system. Four hub genes (namely, cathepsin B [CCNB1], four-and-a-half LIM domains 2 (FHL2), major histocompatibility complex, class II, DP alpha 1 (HLA-DPA1) and tubulin beta 1 class VI (TUBB1)) were obtained via taking interaction of different analysis results. Conclusions On the whole, the findings of this investigation enhance our understanding of the potential molecular mechanisms of PDAC and provide potential targets for further investigation.
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Affiliation(s)
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Society’s College of Pharmacy, Gadag, India
| | - Rajeshwari Horakeri
- Department of Computer Science, Government First Grade College, Hubballi, India
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Michl J, Monterisi S, White B, Blaszczak W, Hulikova A, Abdullayeva G, Bridges E, Yin Z, Bodmer WF, Swietach P. Acid-adapted cancer cells alkalinize their cytoplasm by degrading the acid-loading membrane transporter anion exchanger 2, SLC4A2. Cell Rep 2023; 42:112601. [PMID: 37270778 DOI: 10.1016/j.celrep.2023.112601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/16/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023] Open
Abstract
Acidic environments reduce the intracellular pH (pHi) of most cells to levels that are sub-optimal for growth and cellular functions. Yet, cancers maintain an alkaline cytoplasm despite low extracellular pH (pHe). Raised pHi is thought to be beneficial for tumor progression and invasiveness. However, the transport mechanisms underpinning this adaptation have not been studied systematically. Here, we characterize the pHe-pHi relationship in 66 colorectal cancer cell lines and identify the acid-loading anion exchanger 2 (AE2, SLC4A2) as a regulator of resting pHi. Cells adapt to chronic extracellular acidosis by degrading AE2 protein, which raises pHi and reduces acid sensitivity of growth. Acidity inhibits mTOR signaling, which stimulates lysosomal function and AE2 degradation, a process reversed by bafilomycin A1. We identify AE2 degradation as a mechanism for maintaining a conducive pHi in tumors. As an adaptive mechanism, inhibiting lysosomal degradation of AE2 is a potential therapeutic target.
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Affiliation(s)
- Johanna Michl
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Stefania Monterisi
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Bobby White
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Wiktoria Blaszczak
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Alzbeta Hulikova
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Gulnar Abdullayeva
- MRC Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Esther Bridges
- Department of NDM Experimental Medicine, MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, JR Hospital, Headington, Oxford OX3 9DS, UK
| | - Zinan Yin
- Department of NDM Experimental Medicine, MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, JR Hospital, Headington, Oxford OX3 9DS, UK
| | - Walter F Bodmer
- MRC Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK.
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14
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Wu CY, Cilic A, Pak O, Dartsch RC, Wilhelm J, Wujak M, Lo K, Brosien M, Zhang R, Alkoudmani I, Witte B, Pedersen F, Watz H, Voswinckel R, Günther A, Ghofrani HA, Brandes RP, Schermuly RT, Grimminger F, Seeger W, Sommer N, Weissmann N, Hadzic S. CEACAM6 as a Novel Therapeutic Target to Boost HO-1-mediated Antioxidant Defense in COPD. Am J Respir Crit Care Med 2023; 207:1576-1590. [PMID: 37219322 DOI: 10.1164/rccm.202208-1603oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 05/23/2023] [Indexed: 05/24/2023] Open
Abstract
Rationale: Tobacco smoking and air pollution are primary causes of chronic obstructive pulmonary disease (COPD). However, only a minority of smokers develop COPD. The mechanisms underlying the defense against nitrosative/oxidative stress in nonsusceptible smokers to COPD remain largely unresolved. Objectives: To investigate the defense mechanisms against nitrosative/oxidative stress that possibly prevent COPD development or progression. Methods: Four cohorts were investigated: 1) sputum samples (healthy, n = 4; COPD, n = 37), 2) lung tissue samples (healthy, n = 13; smokers without COPD, n = 10; smoker+COPD, n = 17), 3) pulmonary lobectomy tissue samples (no/mild emphysema, n = 6), and 4) blood samples (healthy, n = 6; COPD, n = 18). We screened 3-nitrotyrosine (3-NT) levels, as indication of nitrosative/oxidative stress, in human samples. We established a novel in vitro model of a cigarette smoke extract (CSE)-resistant cell line and studied 3-NT formation, antioxidant capacity, and transcriptomic profiles. Results were validated in lung tissue, isolated primary cells, and an ex vivo model using adeno-associated virus-mediated gene transduction and human precision-cut lung slices. Measurements and Main Results: 3-NT levels correlate with COPD severity of patients. In CSE-resistant cells, nitrosative/oxidative stress upon CSE treatment was attenuated, paralleled by profound upregulation of heme oxygenase-1 (HO-1). We identified carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6) as a negative regulator of HO-1-mediated nitrosative/oxidative stress defense in human alveolar type 2 epithelial cells (hAEC2s). Consistently, inhibition of HO-1 activity in hAEC2s increased the susceptibility toward CSE-induced damage. Epithelium-specific CEACAM6 overexpression increased nitrosative/oxidative stress and cell death in human precision-cut lung slices on CSE treatment. Conclusions: CEACAM6 expression determines the hAEC2 sensitivity to nitrosative/oxidative stress triggering emphysema development/progression in susceptible smokers.
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Affiliation(s)
- Cheng-Yu Wu
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Anis Cilic
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Oleg Pak
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Ruth Charlotte Dartsch
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Jochen Wilhelm
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
| | - Magdalena Wujak
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
- Department of Medicinal Chemistry, Collegium Medicum in Bydgoszcz, Faculty of Pharmacy, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Kevin Lo
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Monika Brosien
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Ruoyu Zhang
- Department of General and Thoracic Surgery, University Hospital of Giessen, Giessen, Germany
| | - Ibrahim Alkoudmani
- Department of General and Thoracic Surgery, University Hospital of Giessen, Giessen, Germany
| | - Biruta Witte
- Department of General and Thoracic Surgery, University Hospital of Giessen, Giessen, Germany
| | - Frauke Pedersen
- Pulmonary Research Institute at LungenClinic Grosshansdorf, Airway Research Center North, DZL, Grosshansdorf, Germany
| | - Henrik Watz
- Pulmonary Research Institute at LungenClinic Grosshansdorf, Airway Research Center North, DZL, Grosshansdorf, Germany
| | | | - Andreas Günther
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Hossein A Ghofrani
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany; and
| | - Ralph T Schermuly
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Friedrich Grimminger
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
| | - Werner Seeger
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Natascha Sommer
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Norbert Weissmann
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Stefan Hadzic
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
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15
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Bedard MC, Chihanga T, Carlile A, Jackson R, Brusadelli MG, Lee D, VonHandorf A, Rochman M, Dexheimer PJ, Chalmers J, Nuovo G, Lehn M, Williams DEJ, Kulkarni A, Carey M, Jackson A, Billingsley C, Tang A, Zender C, Patil Y, Wise-Draper TM, Herzog TJ, Ferris RL, Kendler A, Aronow BJ, Kofron M, Rothenberg ME, Weirauch MT, Van Doorslaer K, Wikenheiser-Brokamp KA, Lambert PF, Adam M, Steven Potter S, Wells SI. Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer. Nat Commun 2023; 14:1975. [PMID: 37031202 PMCID: PMC10082832 DOI: 10.1038/s41467-023-37377-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 03/15/2023] [Indexed: 04/10/2023] Open
Abstract
Persistent HPV16 infection is a major cause of the global cancer burden. The viral life cycle is dependent on the differentiation program of stratified squamous epithelium, but the landscape of keratinocyte subpopulations which support distinct phases of the viral life cycle has yet to be elucidated. Here, single cell RNA sequencing of HPV16 infected compared to uninfected organoids identifies twelve distinct keratinocyte populations, with a subset mapped to reconstruct their respective 3D geography in stratified squamous epithelium. Instead of conventional terminally differentiated cells, an HPV-reprogrammed keratinocyte subpopulation (HIDDEN cells) forms the surface compartment and requires overexpression of the ELF3/ESE-1 transcription factor. HIDDEN cells are detected throughout stages of human carcinogenesis including primary human cervical intraepithelial neoplasias and HPV positive head and neck cancers, and a possible role in promoting viral carcinogenesis is supported by TCGA analyses. Single cell transcriptome information on HPV-infected versus uninfected epithelium will enable broader studies of the role of individual keratinocyte subpopulations in tumor virus infection and cancer evolution.
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Affiliation(s)
- Mary C Bedard
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Tafadzwa Chihanga
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Adrean Carlile
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Robert Jackson
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Denis Lee
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Andrew VonHandorf
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mark Rochman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Phillip J Dexheimer
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jeffrey Chalmers
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, 151 W. Woodruff Ave, Columbus, OH, 43210, USA
| | - Gerard Nuovo
- Department of Pathology, Ohio State University Medical Center, Columbus, OH, 43210, USA
| | - Maria Lehn
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - David E J Williams
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721, USA
- Medical Scientist Training M.D.-Ph.D. Program (MSTP), College of Medicine-Tucson, University of Arizona, Tucson, AZ, USA
| | - Aditi Kulkarni
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Molly Carey
- Department of Obstetrics and Gynecology, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA
| | - Amanda Jackson
- Department of Obstetrics and Gynecology, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA
| | - Caroline Billingsley
- Department of Obstetrics and Gynecology, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA
| | - Alice Tang
- Department of Otolaryngology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Chad Zender
- Department of Otolaryngology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Yash Patil
- Department of Otolaryngology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Trisha M Wise-Draper
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Thomas J Herzog
- Department of Obstetrics and Gynecology, University of Cincinnati Medical Center, Cincinnati, OH, 45267, USA
| | - Robert L Ferris
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Ady Kendler
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Matthew Kofron
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Divisions of Human Genetics, Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721, USA
- The BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
- Department of Immunobiology, University of Arizona, Tucson, AZ, 85721, USA
- UA Cancer Center, University of Arizona, Tucson, AZ, 85721, USA
| | - Kathryn A Wikenheiser-Brokamp
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Division of Pathology & Laboratory Medicine and The Perinatal Institute Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| | - Susanne I Wells
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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16
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Werner J, Bernhard P, Cosenza-Contreras M, Pinter N, Fahrner M, Pallavi P, Eberhard J, Bronsert P, Rückert F, Schilling O. Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling. Neoplasia 2023; 36:100871. [PMID: 36610378 PMCID: PMC9841175 DOI: 10.1016/j.neo.2022.100871] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) represents one of the most aggressive and lethal malignancies worldwide with an urgent need for new diagnostic and therapeutic strategies. One major risk factor for PDAC is the pre-indication of chronic pancreatitis (CP), which represents highly inflammatory pancreatic tissue. Kallikreins (KLKs) are secreted serine proteases that play an important role in various cancers as components of the tumor microenvironment. Previous studies of KLKs in solid tumors largely relied on either transcriptomics or immunodetection. We present one of the first targeted mass spectrometry profiling of kallikrein proteases in PDAC, CP, and normal pancreas. We show that KLK6 and KLK10 are significantly upregulated in PDAC (n=14) but not in CP (n=7) when compared to normal pancreas (n=16), highlighting their specific intertwining with malignancy. Additional explorative proteome profiling identified 5936 proteins in our pancreatic cohort and observed disease-specific proteome rearrangements in PDAC and CP. As such, PDAC features an enriched proteome motif for extracellular matrix (ECM) and cell adhesion while there is depletion of mitochondrial energy metabolism proteins, reminiscent of the Warburg effect. Although often regarded as a PDAC hallmark, the ECM fingerprint was also observed in CP, alongside with a prototypical inflammatory proteome motif as well as with an increased wound healing process and proteolytic activity, thereby possibly illustrating tissue autolysis. Proteogenomic analysis based on publicly accessible data sources identified 112 PDAC-specific and 32 CP-specific single amino acid variants, which among others affect KRAS and ANKHD1. Our study emphasizes the diagnostic potential of kallikreins and provides novel insights into proteomic characteristics of PDAC and CP.
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Affiliation(s)
- Janina Werner
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Germany; Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Patrick Bernhard
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Miguel Cosenza-Contreras
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Niko Pinter
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| | - Prama Pallavi
- Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Johannes Eberhard
- Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Felix Rückert
- Department of Surgery, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Surgical Department, Diakonissen-Stiftungs-Krankenhaus Speyer, Paul-Egell-Straße 33, Speyer D-67346, Germany.
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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17
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Elsherbini AM, Alsamman AM, Elsherbiny NM, El-Sherbiny M, Ahmed R, Ebrahim HA, Bakkach J. Decoding Diabetes Biomarkers and Related Molecular Mechanisms by Using Machine Learning, Text Mining, and Gene Expression Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13890. [PMID: 36360783 PMCID: PMC9656783 DOI: 10.3390/ijerph192113890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 05/13/2023]
Abstract
The molecular basis of diabetes mellitus is yet to be fully elucidated. We aimed to identify the most frequently reported and differential expressed genes (DEGs) in diabetes by using bioinformatics approaches. Text mining was used to screen 40,225 article abstracts from diabetes literature. These studies highlighted 5939 diabetes-related genes spread across 22 human chromosomes, with 112 genes mentioned in more than 50 studies. Among these genes, HNF4A, PPARA, VEGFA, TCF7L2, HLA-DRB1, PPARG, NOS3, KCNJ11, PRKAA2, and HNF1A were mentioned in more than 200 articles. These genes are correlated with the regulation of glycogen and polysaccharide, adipogenesis, AGE/RAGE, and macrophage differentiation. Three datasets (44 patients and 57 controls) were subjected to gene expression analysis. The analysis revealed 135 significant DEGs, of which CEACAM6, ENPP4, HDAC5, HPCAL1, PARVG, STYXL1, VPS28, ZBTB33, ZFP37 and CCDC58 were the top 10 DEGs. These genes were enriched in aerobic respiration, T-cell antigen receptor pathway, tricarboxylic acid metabolic process, vitamin D receptor pathway, toll-like receptor signaling, and endoplasmic reticulum (ER) unfolded protein response. The results of text mining and gene expression analyses used as attribute values for machine learning (ML) analysis. The decision tree, extra-tree regressor and random forest algorithms were used in ML analysis to identify unique markers that could be used as diabetes diagnosis tools. These algorithms produced prediction models with accuracy ranges from 0.6364 to 0.88 and overall confidence interval (CI) of 95%. There were 39 biomarkers that could distinguish diabetic and non-diabetic patients, 12 of which were repeated multiple times. The majority of these genes are associated with stress response, signalling regulation, locomotion, cell motility, growth, and muscle adaptation. Machine learning algorithms highlighted the use of the HLA-DQB1 gene as a biomarker for diabetes early detection. Our data mining and gene expression analysis have provided useful information about potential biomarkers in diabetes.
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Affiliation(s)
- Amira M. Elsherbini
- Department of Oral Biology, Faculty of Dentistry, Mansoura University, Mansoura 35116, Egypt
| | - Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Nehal M. Elsherbiny
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35116, Egypt
| | - Mohamed El-Sherbiny
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh 71666, Saudi Arabia
- Department of Anatomy, Mansoura Faculty of Medicine, Mansoura University, Mansoura 35116, Egypt
| | - Rehab Ahmed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan
| | - Hasnaa Ali Ebrahim
- Department of Basic Medical Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Joaira Bakkach
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaâdi University Morocco, Tétouan 93000, Morocco
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18
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Bosi E, Marselli L, Suleiman M, Tesi M, De Luca C, Del Guerra S, Cnop M, Eizirik D, Marchetti P. A single-cell human islet interactome atlas identifies disrupted autocrine and paracrine communications in type 2 diabetes. NAR Genom Bioinform 2022; 4:lqac084. [DOI: 10.1093/nargab/lqac084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 10/04/2022] [Accepted: 10/29/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
A sensible control of hormone secretion from pancreatic islets requires concerted inter-cellular communications, but a comprehensive picture of the whole islet interactome is presently missing. Single-cell transcriptomics allows to overcome this and we used here a single-cell dataset from type 2 diabetic (T2D) and non-diabetic (ND) donors to leverage islet interaction networks. The single-cell dataset contains 3046 cells classified in 7 cell types. The interactions across cell types in T2D and ND were obtained and resulting networks analysed to identify high-centrality genes and altered interactions in T2D. The T2D interactome displayed a higher number of interactions (10 787) than ND (9707); 1289 interactions involved beta cells (1147 in ND). High-centrality genes included EGFR, FGFR1 and FGFR2, important for cell survival and proliferation. In conclusion, this analysis represents the first in silico model of the human islet interactome, enabling the identification of signatures potentially relevant for T2D pathophysiology.
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Affiliation(s)
- Emanuele Bosi
- Department of Experimental and Clinical Medicine, Pancreatic islets laboratory, University of Pisa , Pisa , Italy
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa , Genoa , Italy
| | - Lorella Marselli
- Department of Experimental and Clinical Medicine, Pancreatic islets laboratory, University of Pisa , Pisa , Italy
| | - Mara Suleiman
- Department of Experimental and Clinical Medicine, Pancreatic islets laboratory, University of Pisa , Pisa , Italy
| | - Marta Tesi
- Department of Experimental and Clinical Medicine, Pancreatic islets laboratory, University of Pisa , Pisa , Italy
| | - Carmela De Luca
- Department of Experimental and Clinical Medicine, Pancreatic islets laboratory, University of Pisa , Pisa , Italy
| | - Silvia Del Guerra
- Department of Experimental and Clinical Medicine, Pancreatic islets laboratory, University of Pisa , Pisa , Italy
| | - Miriam Cnop
- ULB Center for Diabetes Research , Université Libre de Bruxelles, Brussels , Belgium
- Division of Endocrinology, Erasmus Hospital , Université Libre de Bruxelles, Brussels , Belgium
| | - Decio L Eizirik
- ULB Center for Diabetes Research , Université Libre de Bruxelles, Brussels , Belgium
| | - Piero Marchetti
- Department of Experimental and Clinical Medicine, Pancreatic islets laboratory, University of Pisa , Pisa , Italy
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19
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Herrera JA, Dingle L, Montero MA, Venkateswaran RV, Blaikley JF, Lawless C, Schwartz MA. The UIP/IPF fibroblastic focus is a collagen biosynthesis factory embedded in a distinct extracellular matrix. JCI Insight 2022; 7:e156115. [PMID: 35852874 PMCID: PMC9462507 DOI: 10.1172/jci.insight.156115] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Usual interstitial pneumonia (UIP) is a histological pattern characteristic of idiopathic pulmonary fibrosis (IPF). The UIP pattern is patchy with histologically normal lung adjacent to dense fibrotic tissue. At this interface, fibroblastic foci (FF) are present and are sites where myofibroblasts and extracellular matrix (ECM) accumulate. Utilizing laser capture microdissection-coupled mass spectrometry, we interrogated the FF, adjacent mature scar, and adjacent alveoli in 6 fibrotic (UIP/IPF) specimens plus 6 nonfibrotic alveolar specimens as controls. The data were subjected to qualitative and quantitative analysis and histologically validated. We found that the fibrotic alveoli protein signature is defined by immune deregulation as the strongest category. The fibrotic mature scar classified as end-stage fibrosis whereas the FF contained an overabundance of a distinctive ECM compared with the nonfibrotic control. Furthermore, FF were positive for both TGFB1 and TGFB3, whereas the aberrant basaloid cell lining of FF was predominantly positive for TGFB2. In conclusion, spatial proteomics demonstrated distinct protein compositions in the histologically defined regions of UIP/IPF tissue. These data revealed that FF are the main site of collagen biosynthesis and that the adjacent alveoli are abnormal. This essential information will inform future mechanistic studies on fibrosis progression.
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Affiliation(s)
| | - Lewis Dingle
- Blond McIndoe Laboratories, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - M. Angeles Montero
- Department of Histopathology, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - Rajamiyer V. Venkateswaran
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Department of Transplant, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - John F. Blaikley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Department of Transplant, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | | | - Martin A. Schwartz
- The Wellcome Centre for Cell-Matrix Research and
- Yale Cardiovascular Research Center and
- Departments of Internal Medicine (Cardiology) and Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut, USA
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20
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Burgos M, Cavero-Redondo I, Álvarez-Bueno C, Galán-Moya EM, Pandiella A, Amir E, Ocaña A. Prognostic value of the immune target CEACAM6 in cancer: a meta-analysis. Ther Adv Med Oncol 2022; 14:17588359211072621. [PMID: 35082925 PMCID: PMC8785271 DOI: 10.1177/17588359211072621] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Identification of membrane proteins differentially expressed on tumor cells is a key step in drug development. The carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) is a cell adhesion protein belonging to the immunoglobulin superfamily. Here, we explore the prognostic role CEACAM6 expression on patient outcome in cancer. METHODS A systematic search for studies evaluating the association between tumor expression of CEACAM6 and overall survival (OS) and disease-free survival (DFS) was performed. Hazard ratios (HR) were pooled in a meta-analysis using generic inverse variance and random effect modeling. Subgroup analyses were conducted based on tumor type and method of HR extraction. RESULTS Sixteen studies met the inclusion criteria. CEACAM6 expression was associated with worse OS [HR = 1.96, 95% confidence interval (CI) = 1.51-2.53], and DFS (HR = 2.49, 95% CI = 2.01-3.07) with subgroup analysis showing no significant differences between disease site subgroups. CONCLUSIONS High expression of CEACAM6 is associated with worse OS and DFS in different malignancies. CEACAM6 is a target for the future development of novel therapeutics.
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Affiliation(s)
- Miguel Burgos
- Translational Research Unit, Translational Oncology Laboratory, Albacete University Hospital, Albacete, SpainCentro Regional de Investigaciones Biomédicas, Castilla-La Mancha University (CRIB-UCLM), Albacete, SpainDepartment of Nutrition, Food Science and Physiology, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Iván Cavero-Redondo
- Health and Social Care Research Center, Universidad de Castilla-La Mancha, Cuenca, SpainRehabilitation in Health Research Center (CIRES), Universidad de las Américas, Santiago, Chile
| | - Celia Álvarez-Bueno
- Health and Social Care Research Center, Universidad de Castilla-La Mancha, Cuenca, Spain
| | - Eva María Galán-Moya
- Centro Regional de Investigaciones Biomédicas, Castilla-La Mancha University (CRIB-UCLM), Albacete, SpainFaculty of Nursing, Castilla-La Mancha University (UCLM), Albacete, Spain
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Salamanca, SpainInstituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, SpainCIBERONC, Salamanca, SpainConsejo Superior de Investigaciones Científicas (CSIC), Salamanca, Spain
| | - Eitan Amir
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, and Department of Medicine, University of Toronto, 610 University Avue, 700U, 7-721, Toronto, ON, M5G 2M9, Canada
| | - Alberto Ocaña
- Hospital Clínico San Carlos and CIBERONC, 28040 Madrid, SpainCentro Regional de Investigaciones Biomédicas, Castilla-La Mancha University (CRIB-UCLM), Albacete, Spain
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21
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Surucu Yilmaz N, Bilgic Eltan S, Kayaoglu B, Geckin B, Heredia RJ, Sefer AP, Kiykim A, Nain E, Kasap N, Dogru O, Yucelten AD, Cinel L, Karasu G, Yesilipek A, Sozeri B, Kaya GG, Yilmaz IC, Baydemir I, Aydin Y, Cansen Kahraman D, Haimel M, Boztug K, Karakoc-Aydiner E, Gursel I, Ozen A, Baris S, Gursel M. Low Density Granulocytes and Dysregulated Neutrophils Driving Autoinflammatory Manifestations in NEMO Deficiency. J Clin Immunol 2022; 42:582-596. [PMID: 35028801 DOI: 10.1007/s10875-021-01176-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
NF-κB essential modulator (NEMO, IKK-γ) deficiency is a rare combined immunodeficiency caused by mutations in the IKBKG gene. Conventionally, patients are afflicted with life threatening recurrent microbial infections. Paradoxically, the spectrum of clinical manifestations includes severe inflammatory disorders. The mechanisms leading to autoinflammation in NEMO deficiency are currently unknown. Herein, we sought to investigate the underlying mechanisms of clinical autoinflammatory manifestations in a 12-years old male NEMO deficiency (EDA-ID, OMIM #300,291) patient by comparing the immune profile of the patient before and after hematopoietic stem cell transplantation (HSCT). Response to NF-kB activators were measured by cytokine ELISA. Neutrophil and low-density granulocyte (LDG) populations were analyzed by flow cytometry. Peripheral blood mononuclear cells (PBMC) transcriptome before and after HSCT and transcriptome of sorted normal-density neutrophils and LDGs were determined using the NanoString nCounter gene expression panels. ISG15 expression and protein ISGylation was based on Immunoblotting. Consistent with the immune deficiency, PBMCs of the patient were unresponsive to toll-like and T cell receptor-activators. Paradoxically, LDGs comprised 35% of patient PBMCs and elevated expression of genes such as MMP9, LTF, and LCN2 in the granulocytic lineage, high levels of IP-10 in the patient's plasma, spontaneous ISG15 expression and protein ISGylation indicative of a spontaneous type I interferon (IFN) signature were observed, all of which normalized after HSCT. Collectively, our results suggest that type I IFN signature observed in the patient, dysregulated LDGs and spontaneously activated neutrophils, potentially contribute to tissue damage in NEMO deficiency.
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Affiliation(s)
- Naz Surucu Yilmaz
- Department of Biological Sciences, Middle East Technical University, B-58, Üniversiteler Mah. Dumlupınar Bulvarı No:1, Ankara, Turkey
| | - Sevgi Bilgic Eltan
- Division of Pediatric Allergy and Immunology, Marmara University, Fevzi Çakmak Mah. No: 41, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Basak Kayaoglu
- Department of Biological Sciences, Middle East Technical University, B-58, Üniversiteler Mah. Dumlupınar Bulvarı No:1, Ankara, Turkey
| | - Busranur Geckin
- Department of Biological Sciences, Middle East Technical University, B-58, Üniversiteler Mah. Dumlupınar Bulvarı No:1, Ankara, Turkey
| | - Raul Jimenez Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Asena Pinar Sefer
- Division of Pediatric Allergy and Immunology, Marmara University, Fevzi Çakmak Mah. No: 41, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ayca Kiykim
- Faculty of Medicine, Pediatric Allergy and Immunology, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ercan Nain
- Division of Pediatric Allergy and Immunology, Marmara University, Fevzi Çakmak Mah. No: 41, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Nurhan Kasap
- Division of Pediatric Allergy and Immunology, Marmara University, Fevzi Çakmak Mah. No: 41, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Omer Dogru
- Division of Pediatric Hematology-Oncology, Marmara University, Istanbul, Turkey
| | | | - Leyla Cinel
- Division of Pathology, Marmara University, Istanbul, Turkey
| | - Gulsun Karasu
- Goztepe Medicalpark Hospital, Pediatric Stem Cell Transplantation Unit, İstanbul, Turkey
| | - Akif Yesilipek
- Goztepe Medicalpark Hospital, Pediatric Stem Cell Transplantation Unit, İstanbul, Turkey
| | - Betul Sozeri
- Division of Pediatric Rheumatology, University of Health Sciences, Umraniye Research and Training Hospital, Istanbul, Turkey
| | - Goksu Gokberk Kaya
- Therapeutic ODN Research Lab, Department of Molecular Biology and Genetics, Bilkent University, Bilkent, 06800, Ankara, Turkey
| | - Ismail Cem Yilmaz
- Department of Biological Sciences, Middle East Technical University, B-58, Üniversiteler Mah. Dumlupınar Bulvarı No:1, Ankara, Turkey
| | - Ilayda Baydemir
- Department of Biological Sciences, Middle East Technical University, B-58, Üniversiteler Mah. Dumlupınar Bulvarı No:1, Ankara, Turkey
| | - Yagmur Aydin
- Department of Biological Sciences, Middle East Technical University, B-58, Üniversiteler Mah. Dumlupınar Bulvarı No:1, Ankara, Turkey
| | - Deniz Cansen Kahraman
- KanSiL, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Matthias Haimel
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, Marmara University, Fevzi Çakmak Mah. No: 41, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ihsan Gursel
- Therapeutic ODN Research Lab, Department of Molecular Biology and Genetics, Bilkent University, Bilkent, 06800, Ankara, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, Marmara University, Fevzi Çakmak Mah. No: 41, Istanbul, Turkey.,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, Marmara University, Fevzi Çakmak Mah. No: 41, Istanbul, Turkey. .,Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey. .,The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey.
| | - Mayda Gursel
- Department of Biological Sciences, Middle East Technical University, B-58, Üniversiteler Mah. Dumlupınar Bulvarı No:1, Ankara, Turkey.
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22
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Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJH, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell 2021; 184:5031-5052.e26. [PMID: 34534465 PMCID: PMC8654574 DOI: 10.1016/j.cell.2021.08.023] [Citation(s) in RCA: 273] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/19/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues. Proteomic, phosphoproteomic, and glycoproteomic analyses were used to characterize proteins and their modifications. In addition, whole-genome sequencing, whole-exome sequencing, methylation, RNA sequencing (RNA-seq), and microRNA sequencing (miRNA-seq) were performed on the same tissues to facilitate an integrated proteogenomic analysis and determine the impact of genomic alterations on protein expression, signaling pathways, and post-translational modifications. To ensure robust downstream analyses, tumor neoplastic cellularity was assessed via multiple orthogonal strategies using molecular features and verified via pathological estimation of tumor cellularity based on histological review. This integrated proteogenomic characterization of PDAC will serve as a valuable resource for the community, paving the way for early detection and identification of novel therapeutic targets.
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Affiliation(s)
- Liwei Cao
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - T Mamie Lih
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David J Clark
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | | | | | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Jianbo Pan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wen Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rita Jui-Hsien Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ruiyang Liu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Houxiang Zhu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Peter Ronning
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Hariharan Easwaran
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Ludmila Danilova
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Arvind Singh Mer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Seungyeul Yoo
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Joshua M Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | | | - Qing Kay Li
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Michael H Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Pei Wang
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | | | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Oliver F Bathe
- Departments of Surgery and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.
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23
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O'Neill RS, Stoita A. Biomarkers in the diagnosis of pancreatic cancer: Are we closer to finding the golden ticket? World J Gastroenterol 2021; 27:4045-4087. [PMID: 34326612 PMCID: PMC8311531 DOI: 10.3748/wjg.v27.i26.4045] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/24/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PC) is a leading cause of cancer related mortality on a global scale. The disease itself is associated with a dismal prognosis, partly due to its silent nature resulting in patients presenting with advanced disease at the time of diagnosis. To combat this, there has been an explosion in the last decade of potential candidate biomarkers in the research setting in the hope that a diagnostic biomarker may provide a glimmer of hope in what is otherwise quite a substantial clinical dilemma. Currently, serum carbohydrate antigen 19-9 is utilized in the diagnostic work-up of patients diagnosed with PC however this biomarker lacks the sensitivity and specificity associated with a gold-standard marker. In the search for a biomarker that is both sensitive and specific for the diagnosis of PC, there has been a paradigm shift towards a focus on liquid biopsy and the use of diagnostic panels which has subsequently proved to have efficacy in the diagnosis of PC. Currently, promising developments in the field of early detection on PC using diagnostic biomarkers include the detection of microRNA (miRNA) in serum and circulating tumour cells. Both these modalities, although in their infancy and yet to be widely accepted into routine clinical practice, possess merit in the early detection of PC. We reviewed over 300 biomarkers with the aim to provide an in-depth summary of the current state-of-play regarding diagnostic biomarkers in PC (serum, urinary, salivary, faecal, pancreatic juice and biliary fluid).
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Affiliation(s)
- Robert S O'Neill
- Department of Gastroenterology, St Vincent's Hospital Sydney, Sydney 2010, Australia
- St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales, Sydney 2010, Australia
| | - Alina Stoita
- Department of Gastroenterology, St Vincent's Hospital Sydney, Sydney 2010, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney 2010, Australia
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24
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An F, Zheng C, Zhang G, Zhou L, Wu Y, Hou Z, Zhou Z, Chen K, Zhan Q. Carcinoembryonic Antigen Related Cell Adhesion Molecule 6 Promotes Carcinogenesis of Gastric Cancer and Anti-CEACAM6 Fluorescent Probe Can Diagnose the Precancerous Lesions. Front Oncol 2021; 11:643669. [PMID: 34221964 PMCID: PMC8248535 DOI: 10.3389/fonc.2021.643669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/20/2021] [Indexed: 12/16/2022] Open
Abstract
The diagnosis of precancerous lesions or early gastric cancer (EGC) is very important for patient survival. Molecular imaging is a visualized method that can easily and precisely diagnose tumors. However, there are currently few studies about molecular imaging diagnosis of EGC. Here, we studied the expression of carcinoembryonic antigen related cell adhesion molecule 6 (CEACAM6) in the progression of GC. Then, the regulatory roles of CEACAM6 in GC cells were investigated. Furthermore, both the fluorescent-labeled and near infrared molecular-labeled probes were synthesized, and the diagnostic value of anti-CEACAM6 probes in GC was evaluated in vivo using a GC mice model as well as in vitro using fresh dysplastic gastric mucosa obtained from endoscopic submucosal dissection (ESD) operations. Our study showed that CEACAM6 was over expressed in GC tissues compared to adjacent tissues, and the patients with higher CEACAM6 expression had lower survival time. Moreover, the CEACAM6 expression was higher in the dysplastic gastric mucosa than in the adjacent normal mucosa. CEACAM6 accelerated the growth, proliferation, and invasion of GC cells in the in vitro and in vivo studies. Moreover, up regulated CEACAM6 can induce the expression of proteins related to GC progression. Furthermore, the anti-CEACAM6 probes exhibited good affinity with GC cell lines. The probes can track tumors as well as metastases in the mice model in vivo, and can precisely identify the area of dysplastic gastric mucosa using specimens obtained from ESD operations by wide field fluorescent endoscopy. The surface micro features of the mucosa can also be observed using fluorescent micro endoscopy, and the degree of atypia can be distinguished by both the signal intensity and surface micro morphology. CEACAM6 is a key molecular marker in GC progression, and the anti-CEACAM6 probe-assisted fluorescent endoscopy may be a potential option for the diagnosis of precancerous lesions.
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Affiliation(s)
- Fangmei An
- Department of Gastroenterology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Chuwei Zheng
- Department of Gastroenterology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Guoqiang Zhang
- Department of Gastroenterology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Liangyun Zhou
- Department of Gastroenterology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Yuqing Wu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zheng Hou
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhiyi Zhou
- Department of Pathology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Ke Chen
- Department of Gastroenterology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Qiang Zhan
- Department of Gastroenterology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
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25
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Kurlinkus B, Ger M, Kaupinis A, Jasiunas E, Valius M, Sileikis A. CEACAM6's Role as a Chemoresistance and Prognostic Biomarker for Pancreatic Cancer: A Comparison of CEACAM6's Diagnostic and Prognostic Capabilities with Those of CA19-9 and CEA. Life (Basel) 2021; 11:life11060542. [PMID: 34207784 PMCID: PMC8226832 DOI: 10.3390/life11060542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Survival rates from pancreatic cancer have remained stagnant for decades due to the heterogenic nature of the disease. This study aimed to find a new advanced biomarker and evaluate its clinical capabilities, thus enabling more individualised pancreatic cancer management. Between 2013 and 2020, 267 patients were included in the study. Surgically collected pancreatic tissue samples were analysed via high-definition mass spectrometry. Carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) was discovered as a possible promising pancreatic cancer biomarker. The predominance of CEACAM6 to pancreatic cancer was validated using antibodies in tissue samples. CEACAM6, carbohydrate antigen 19-9 (CA19-9), and carcinoembryonic antigen (CEA) blood serum concentrations were evaluated for clinical evaluation and comparison. Kaplan-Meier survival analyses were used to evaluate disease-free survival (DFS) and overall survival (OS). Poorer overall survival was significantly dependent on increased CEACAM6 blood serum concentrations (17.0 vs. 12.6 months, p = 0.017) in pancreatic cancer patients after radical treatment and adjuvant chemotherapy. Increased CEA and CA19-9 concentrations showed no significant dependencies with survival. Thus, CEACAM6 is a promising new biomarker with significant prognostic value and prediction of chemoresistance properties, enabling the improvement of individualised approaches to patients with pancreatic cancer.
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Affiliation(s)
- Benediktas Kurlinkus
- Clinic of Gastroenterology, Nephrourology and Surgery, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, LT-03101 Vilnius, Lithuania;
- Correspondence: ; Tel.: +370-67437295
| | - Marija Ger
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, LT-10257 Vilnius, Lithuania; (M.G.); (A.K.); (M.V.)
| | - Algirdas Kaupinis
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, LT-10257 Vilnius, Lithuania; (M.G.); (A.K.); (M.V.)
| | - Eugenijus Jasiunas
- Centre of Informatics and Development, Vilnius University Hospital Santaros Klinikos, LT-08661 Vilnius, Lithuania;
| | - Mindaugas Valius
- Proteomics Center, Institute of Biochemistry, Vilnius University Life Sciences Center, LT-10257 Vilnius, Lithuania; (M.G.); (A.K.); (M.V.)
| | - Audrius Sileikis
- Clinic of Gastroenterology, Nephrourology and Surgery, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, LT-03101 Vilnius, Lithuania;
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26
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Chong ZX, Ho WY, Yeap SK, Wang ML, Chien Y, Verusingam ND, Ong HK. Single-cell RNA sequencing in human lung cancer: Applications, challenges, and pathway towards personalized therapy. J Chin Med Assoc 2021; 84:563-576. [PMID: 33883467 DOI: 10.1097/jcma.0000000000000535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Lung cancer is one of the most prevalent human cancers, and single-cell RNA sequencing (scRNA-seq) has been widely used to study human lung cancer at the cellular, genetic, and molecular level. Even though there are published reviews, which summarized the applications of scRNA-seq in human cancers like breast cancer, there is lack of a comprehensive review, which could effectively highlight the broad use of scRNA-seq in studying lung cancer. This review, therefore, was aimed to summarize the various applications of scRNA-seq in human lung cancer research based on the findings from different published in vitro, in vivo, and clinical studies. The review would first briefly outline the concept and principle of scRNA-seq, followed by the discussion on the applications of scRNA-seq in studying human lung cancer. Finally, the challenges faced when using scRNA-seq to study human lung cancer would be discussed, and the potential applications and challenges of scRNA-seq to facilitate the development of personalized cancer therapy in the future would be explored.
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Affiliation(s)
- Zhi-Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Wan-Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Swee-Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Mong-Lien Wang
- Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Food Safety and Health Risk Assessment, School of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Yueh Chien
- Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Nalini Devi Verusingam
- Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Centre for Stem Cell Research, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia
- National Cancer Council (MAKNA), Kuala Lumpur, Malaysia
| | - Han-Kiat Ong
- Centre for Stem Cell Research, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia
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27
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Beata S, Michał T, Mateusz O, Urszula W, Choroszy M, Andrzej T, Piotr D. Norepinephrine affects the interaction of adherent-invasive Escherichia coli with intestinal epithelial cells. Virulence 2021; 12:630-637. [PMID: 33538227 PMCID: PMC7872043 DOI: 10.1080/21505594.2021.1882780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Norepinephrine (NE), the stress hormone, stimulates many bacterial species’ growth and virulence, including Escherichia coli. However, the hormone’s impact on the adherent-invasive E. coli (AIEC) implicated in Crohn’s disease is poorly understood. In the study, we have investigated the effect of NE on the interaction of six AIEC strains isolated from an intestinal biopsy from 6 children with Crohn’s disease with Caco-2 cells. Our study focused on type 1 fimbria and CEACAM6 molecules serving as docking sites for these adhesins. The study results demonstrated that the hormone significantly increased the adherence and invasion of AIEC to Caco-2 cells in vitro. However, the effect was not associated with the impact of NE on the increased proliferation rate of AIEC or the fimA gene expression vital for their interaction with intestinal epithelial cells. Instead, the carcinoembryonic antigen-related cell-adhesion-molecule-6 (CEACAM6) level was increased significantly in NE-treated Caco-2 cells infected with AIEC in contrast to control uninfected NE-treated cells. These results indicated that NE influenced the interaction of AIEC with intestinal epithelium by increasing the level of CEACAM6 in epithelial cells, strengthening their adherence and invasion.
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Affiliation(s)
| | - Turniak Michał
- Department of Microbiology, Wroclaw Medical University , Wroclaw, Poland
| | - Olbromski Mateusz
- Department of Histology and Embryology, Wroclaw Medical University , Wroclaw, Poland
| | - Walczuk Urszula
- Department of Microbiology, Wroclaw Medical University , Wroclaw, Poland
| | - Marcin Choroszy
- Department of Microbiology, Wroclaw Medical University , Wroclaw, Poland
| | - Tukiendorf Andrzej
- Department of Public Health, Wroclaw Medical University , Wroclaw, Poland
| | - Dzięgiel Piotr
- Department of Histology and Embryology, Wroclaw Medical University , Wroclaw, Poland
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28
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Lambert A, Conroy T, Ducreux M. Future directions in drug development in pancreatic cancer. Semin Oncol 2021; 48:47-56. [PMID: 33674067 DOI: 10.1053/j.seminoncol.2021.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 12/24/2022]
Abstract
Pancreatic cancer is still one of the most lethal cancers with a reported 5-year relative survival rate of approximatively 9% and medical treatment remains a major challenge. Systemic treatment is recommended in every setting: resectable, borderline resectable, locally advanced and metastatic. Yet, few groundbreaking changes in practice have occurred in the last 30 years compared to other cancers and new treatments options are highly desirable. Most treatment approaches using chemotherapy have failed to improve patients' life expectancy and the few therapies finally found to have statistically significant benefit actually have modest clinical impact. It is becoming imperative to find new paths for improvement, such as encapsulated agents, new generation targeted therapies and treatments directed against the tumor microenvironment. We report here the new drugs of interest in pancreatic cancer and analyze the most recent failures.
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Affiliation(s)
- Aurélien Lambert
- Medical Oncology Department, Institut de Cancérologie de Lorraine, Vandœuvre-lès-Nancy, France; Université de Lorraine, Nancy, France.
| | - Thierry Conroy
- Medical Oncology Department, Institut de Cancérologie de Lorraine, Vandœuvre-lès-Nancy, France; Université de Lorraine, Nancy, France
| | - Michel Ducreux
- Gastrointestinal Oncology Department, Gustave Roussy, Villejuif, France; Université Paris-Saclay, Saint-Aubin, France
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29
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Naruse M, Ochiai M, Sekine S, Taniguchi H, Yoshida T, Ichikawa H, Sakamoto H, Kubo T, Matsumoto K, Ochiai A, Imai T. Re-expression of REG family and DUOXs genes in CRC organoids by co-culturing with CAFs. Sci Rep 2021; 11:2077. [PMID: 33483567 PMCID: PMC7822883 DOI: 10.1038/s41598-021-81475-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
Organoids derived from epithelial tumors have recently been utilized as a preclinical model in basic and translational studies. This model is considered to represent the original tumor in terms of 3D structure, genetic and cellular heterogeneity, but not tumor microenvironment. In this study, we established organoids and paired cancer-associated fibroblasts (CAFs) from surgical specimens of colorectal carcinomas (CRCs), and evaluated gene expression profiles in organoids with and without co-culture with CAFs to assess interactions between tumor cells and CAFs in tumor tissues. We found that the expression levels of several genes, which are highly expressed in original CRC tissues, were downregulated in organoids but re-expressed in organoids by co-culturing with CAFs. They comprised immune response- and external stimulus-related genes, e.g., REG family and dual oxidases (DUOXs), which are known to have malignant functions, leading tumor cells to proliferative and/or anti-apoptotic states and drug resistant phenotypes. In addition, the degree of differential induction of REG1 and DUOX2 in the co-culture system varied depending on CAFs from each CRC case. In conclusion, the co-culture system of CRC organoids with paired CAFs was able to partially reproduce the tumor microenvironment.
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Affiliation(s)
- Mie Naruse
- Central Animal Division, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Masako Ochiai
- Central Animal Division, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shigeki Sekine
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hirokazu Taniguchi
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Teruhiko Yoshida
- Department of Clinical Genomics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hitoshi Ichikawa
- Department of Clinical Genomics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hiromi Sakamoto
- Department of Clinical Genomics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takashi Kubo
- Department of Clinical Genomics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Atsushi Ochiai
- Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Toshio Imai
- Central Animal Division, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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30
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Huang C, Chen J. Laminin‑332 mediates proliferation, apoptosis, invasion, migration and epithelial‑to‑mesenchymal transition in pancreatic ductal adenocarcinoma. Mol Med Rep 2021; 23:11. [PMID: 33179081 PMCID: PMC7673329 DOI: 10.3892/mmr.2020.11649] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022] Open
Abstract
The poor prognosis of patients with pancreatic ductal adenocarcinoma (PDAC) is primarily due to the invasive and metastatic behaviors of this disease. Laminin‑332 (LM‑332) is a key component of the basement membrane barrier, and is associated with tumor metastasis. The present study provides evidence towards the potential function of LM‑332 in carcinoma, indicating the distinct roles of the three LM‑332 subunits (α3, β3 and γ2) in cell proliferation, migration, invasion, apoptosis and the epithelial‑to‑mesenchymal transition (EMT) in cancer. The roles of the α3, β3 and γ2 subunits in the malignant biological behavior of PDAC were investigated in the present study. It was revealed that the α3, β3 and γ2 subunits were upregulated in PDAC. Inhibition of all LM‑332 subunits abrogated the tumorigenic outcomes, which included cell proliferation, apoptosis, invasion, migration and EMT in vitro. However, the three LM‑332 subunits had different degrees of effects on biological behavior. It was observed that LAMA3 (α3) had a stronger effect on cell proliferation, migration and invasion. In addition, LAMB3 (β3) knockdown significantly increased E‑cadherin levels and decreased vimentin levels, indicating that LAMB3 was associated with EMT. Likewise, LAMC2 (γ2) mediated proliferation, apoptosis, invasion and migration. However, small interfering (si)‑LAMC2 promoted the progression of EMT, which was the opposite effect to that of si‑LAMB3. The LM‑332 subunits (α3, β3 and γ2) may be novel therapeutic targets of PDAC in the future.
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Affiliation(s)
- Caiqun Huang
- Department of Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 321000, P.R. China
| | - Jun Chen
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 321000, P.R. China
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31
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Mucciolo G, Roux C, Scagliotti A, Brugiapaglia S, Novelli F, Cappello P. The dark side of immunotherapy: pancreatic cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:491-520. [PMID: 35582441 PMCID: PMC8992483 DOI: 10.20517/cdr.2020.13] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/23/2020] [Accepted: 04/07/2020] [Indexed: 12/13/2022]
Abstract
Since the journal Science deemed cancer immunotherapy as the "breakthrough of the year" in 2014, there has been an explosion of clinical trials involving immunotherapeutic approaches that, in the last decade - thanks also to the renaissance of the immunosurveillance theory (renamed the three Es theory) - have been continuously and successfully developed. In the latest update of the development of the immuno-oncology drug pipeline, published last November by Nature Review Drug Discovery, it was clearly reported that the immunoactive drugs under study almost doubled in just two years. Of the different classes of passive and active immunotherapies, "cell therapy" is the fastest growing. The aim of this review is to discuss the preclinical and clinical studies that have focused on different immuno-oncology approaches applied to pancreatic cancer, which we assign to the "dark side" of immunotherapy, in the sense that it represents one of the solid tumors showing less response to this type of therapeutic strategy.
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Affiliation(s)
- Gianluca Mucciolo
- Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza di Torino, Turin 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
- The two authors contributed equally
| | - Cecilia Roux
- Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza di Torino, Turin 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
- The two authors contributed equally
| | - Alessandro Scagliotti
- Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza di Torino, Turin 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
| | - Silvia Brugiapaglia
- Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza di Torino, Turin 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
| | - Francesco Novelli
- Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza di Torino, Turin 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
- Molecular Biotechnology Center, University of Turin, Turin 10126, Italy
| | - Paola Cappello
- Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza di Torino, Turin 10126, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
- Molecular Biotechnology Center, University of Turin, Turin 10126, Italy
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