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Zhang R, Chen Y, Feng Z, Cai B, Cheng Y, Du Y, Ou S, Chen H, Pan M, Liu H, Pei D, Cao S. Reprogramming human urine cells into intestinal organoids with long-term expansion ability and barrier function. Heliyon 2024; 10:e33736. [PMID: 39040281 PMCID: PMC11261862 DOI: 10.1016/j.heliyon.2024.e33736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Generation of intestinal organoids from human somatic cells by reprogramming would enable intestinal regeneration, disease modeling, and drug screening in a personalized pattern. Here, we report a direct reprogramming protocol for the generation of human urine cells induced intestinal organoids (U-iIOs) under a defined medium. U-iIOs expressed multiple intestinal specific genes and showed resembling gene expression profiles to primary small intestines. U-iIOs can be stably long-term expanded and further differentiated into more mature intestinal lineage cells with high expression of metallothionein and cytochrome P450 (CYP450) genes. These specific molecular features of U-iIOs differ from human pluripotent stem cells derived intestinal organoids (P-iIOs) and intestinal immortalized cell lines. Furthermore, U-iIOs exhibit intestinal barriers indicated by blocking FITC-dextran permeation and uptaking of the specific substrate rhodamine 123. Our study provides a novel platform for patient-specific intestinal organoid generation, which may lead to precision treatment of intestinal diseases and facilitate drug discovery.
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Affiliation(s)
- Ruifang Zhang
- Key Laboratory of Biological Targeting Diagnosis, Therapy, and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Yating Chen
- Key Laboratory of Biological Targeting Diagnosis, Therapy, and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Ziyu Feng
- Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Baomei Cai
- Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Yiyi Cheng
- Key Laboratory of Biological Targeting Diagnosis, Therapy, and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yunjing Du
- School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Sihua Ou
- Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Huan Chen
- Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Mengjie Pan
- Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - He Liu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shangtao Cao
- Key Laboratory of Biological Targeting Diagnosis, Therapy, and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou, Guangdong, China
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2
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Vilarinho T, Pádua D, Pereira B, Mesquita P, Almeida R. MISP Is Overexpressed in Intestinal Metaplasia and Gastric Cancer. Curr Oncol 2024; 31:2769-2779. [PMID: 38785491 PMCID: PMC11120023 DOI: 10.3390/curroncol31050210] [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: 04/03/2024] [Revised: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Gastric cancer is the fifth most common cancer and the fourth cause of global cancer mortality. The identification of new biomarkers and drug targets is crucial to allow the better prognosis and treatment of patients. The mitotic spindle positioning (MISP) protein has the function of correcting mitotic spindle positioning and centrosome clustering and has been implicated in the cytokinesis and migration of cancer cells. The goal of this work was to evaluate the expression and clinical relevance of MISP in gastric cancer. MISP expression was evaluated by immunohistochemistry in a single hospital series (n = 286) of gastric adenocarcinomas and compared with normal gastric mucosa and intestinal metaplasia, a preneoplastic lesion. MISP was detected on the membrane in 83% of the cases, being overexpressed in gastric cancer compared to normal gastric mucosa (n = 10). Its expression was negatively associated with diffuse and poorly cohesive types. On the other hand, it was strongly expressed in intestinal metaplasia where it was associated with MUC2 and CDX2 expression. Furthermore, when we silenced MISP in vitro, a significant decrease in the viability of gastric carcinoma cells was observed. In conclusion, MISP is overexpressed in gastric cancer, being associated with an intestinal phenotype in gastric carcinogenesis and having a role in cellular proliferation.
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Affiliation(s)
- Tomás Vilarinho
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (T.V.); (D.P.); (B.P.); (P.M.)
| | - Diana Pádua
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (T.V.); (D.P.); (B.P.); (P.M.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
| | - Bruno Pereira
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (T.V.); (D.P.); (B.P.); (P.M.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
| | - Patrícia Mesquita
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (T.V.); (D.P.); (B.P.); (P.M.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
| | - Raquel Almeida
- i3S—Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (T.V.); (D.P.); (B.P.); (P.M.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-465 Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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3
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Lorzadeh A, Ye G, Sharma S, Jadhav U. DNA methylation-dependent and -independent binding of CDX2 directs activation of distinct developmental and homeostatic genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579850. [PMID: 38405700 PMCID: PMC10888781 DOI: 10.1101/2024.02.11.579850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of TFs. However, how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci is still not well understood. Here we show that Cdx2 - a pioneer TF that binds distinct targets in developing versus adult intestinal epithelial cells - has a preferential affinity for a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at embryonic and fetal Cdx2 target loci and the specifically methylated state of the CpG during development allows selective Cdx2 binding and activation of developmental enhancers and linked genes. Conversely, demethylation at these enhancers prohibits ectopic Cdx2 binding in adult cells, where Cdx2 binds its canonical motif without a CpG. This differential Cdx2 binding allows for corecruitment of Ctcf and Hnf4, facilitating the establishment of intestinal superenhancers during development and enhancers mediating adult homeostatic functions, respectively. Induced gain of DNA methylation in the adult mouse epithelium or cultured cells causes ectopic recruitment of Cdx2 to the developmental target loci and facilitates cobinding of the partner TFs. Together, our results demonstrate that the differential CpG motif requirements for Cdx2 binding to developmental versus adult target sites allow it to navigate different DNA methylation profiles and activate cell type-specific genes at appropriate times.
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Affiliation(s)
- Alireza Lorzadeh
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - George Ye
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - Sweta Sharma
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - Unmesh Jadhav
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
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4
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Yang L, Tu L, Bisht S, Mao Y, Petkovich D, Thursby SJ, Liang J, Patel N, Yen RWC, Largent T, Zahnow C, Brock M, Gabrielson K, Salimian KJ, Baylin SB, Easwaran H. Tissue-location-specific transcription programs drive tumor dependencies in colon cancer. Nat Commun 2024; 15:1384. [PMID: 38360902 PMCID: PMC10869357 DOI: 10.1038/s41467-024-45605-4] [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: 05/16/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Cancers of the same tissue-type but in anatomically distinct locations exhibit different molecular dependencies for tumorigenesis. Proximal and distal colon cancers exemplify such characteristics, with BRAFV600E predominantly occurring in proximal colon cancers along with increased DNA methylation phenotype. Using mouse colon organoids, here we show that proximal and distal colon stem cells have distinct transcriptional programs that regulate stemness and differentiation. We identify that the homeobox transcription factor, CDX2, which is silenced by DNA methylation in proximal colon cancers, is a key mediator of the differential transcriptional programs. Cdx2-mediated proximal colon-specific transcriptional program concurrently is tumor suppressive, and Cdx2 loss sufficiently creates permissive state for BRAFV600E-driven transformation. Human proximal colon cancers with CDX2 downregulation showed similar transcriptional program as in mouse proximal organoids with Cdx2 loss. Developmental transcription factors, such as CDX2, are thus critical in maintaining tissue-location specific transcriptional programs that create tissue-type origin specific dependencies for tumor development.
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Affiliation(s)
- Lijing Yang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Lei Tu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shilpa Bisht
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Yiqing Mao
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Daniel Petkovich
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Sara-Jayne Thursby
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Jinxiao Liang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Nibedita Patel
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Ray-Whay Chiu Yen
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Tina Largent
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Cynthia Zahnow
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Malcolm Brock
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Kathy Gabrielson
- Department of Comparative Medicine, Johns Hopkins Medical Institutions, 863 Broadway Research Building, 733 N. Broadway, Baltimore, MD, 21205-2196, USA
| | - Kevan J Salimian
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Stephen B Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA.
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5
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Nakamura T, Fujikura J, Ito R, Keidai Y, Inagaki N. Human RFX6 regulates endoderm patterning at the primitive gut tube stage. PNAS NEXUS 2024; 3:pgae001. [PMID: 38239755 PMCID: PMC10794167 DOI: 10.1093/pnasnexus/pgae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/26/2023] [Indexed: 01/22/2024]
Abstract
Transcriptional factor RFX6 is known to be a causal gene of Mitchell-Riley syndrome (MRS), an autosomal recessive neonatal diabetes associated with pancreatic hypoplasia and intestinal atresia/malformation. The morphological defects are limited to posterior foregut and mid-hindgut endodermal lineages and do not occur in the anterior foregut lineage; the mechanism remains to be fully elucidated. In this study, we generated RFX6+/eGFP heterozygous knockin and RFX6eGFP/eGFP homozygous knockin/knockout human-induced pluripotent stem cell (hiPSC) lines and performed in vitro endoderm differentiation to clarify the role of RFX6 in early endoderm development. RFX6 expression was found to surge at the primitive gut tube (PGT) stage in comparison with that in the undifferentiated or definitive endoderm stage. At the PGT stage, the expression of PDX1 and CDX2, posterior foregut and mid-hindgut master regulators, respectively, was decreased by the RFX6 deficit. PDX1+ and CDX2+ cells were mostly green fluorescent protein (GFP)+ in RFX6+/eGFP hiPSCs, but their cell number was markedly decreased in RFX6eGFP/eGFP hiPSCs. The expression of SOX2, an anterior foregut marker, was not affected by the RFX6 deficit. In addition, we found a putative RFX6-binding X-box motif using cap analysis of gene expression-seq and the motif-containing sequences in the enhancer regions of PDX1 and CDX2 bound to RFX6 in vitro. Thus, RFX6 regulates the ParaHox genes PDX1 and CDX2 but does not affect SOX2 in early endodermal differentiation, suggesting that defects in early stage endoderm patterning account for the morphological pathology of MRS.
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Affiliation(s)
- Toshihiro Nakamura
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Junji Fujikura
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ryo Ito
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yamato Keidai
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Medical Research Institute, Kitano Hospital, PIIF Tazuke-kofukai, Osaka 530-8480, Japan
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6
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Feng Y, Zhang Z, Hong Y, Ding Y, Liu L, Gao S, Fang H, Shi J. A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns. Genome Res 2023; 33:2041-2052. [PMID: 37940553 PMCID: PMC10760529 DOI: 10.1101/gr.278146.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
DNA methylation and associated regulatory elements play a crucial role in gene expression regulation. Previous studies have focused primarily on the distribution of mean methylation levels. Advances in whole-genome bisulfite sequencing (WGBS) have enabled the characterization of DNA methylation haplotypes (MHAPs), representing CpG sites from the same read fragment on a single chromosome, and the subsequent identification of methylation haplotype blocks (MHBs), in which adjacent CpGs on the same fragment are comethylated. Using our expert-curated WGBS data sets, we report comprehensive landscapes of MHBs in 17 representative normal somatic human tissues and during early human embryonic development. Integrative analysis reveals MHBs as a distinctive type of regulatory element characterized by comethylation patterns rather than mean methylation levels. We show the enrichment of MHBs in open chromatin regions, tissue-specific histone marks, and enhancers, including super-enhancers. Moreover, we find that MHBs tend to localize near tissue-specific genes and show an association with differential gene expression that is independent of mean methylation. Similar findings are observed in the context of human embryonic development, highlighting the dynamic nature of MHBs during early development. Collectively, our comprehensive MHB landscapes provide valuable insights into the tissue specificity and developmental dynamics of DNA methylation.
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Affiliation(s)
- Yan Feng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yuyang Hong
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Ding
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Leiqin Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Siqi Gao
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiantao Shi
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China;
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7
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Badia-Ramentol J, Gimeno-Valiente F, Duréndez E, Martínez-Ciarpaglini C, Linares J, Iglesias M, Cervantes A, Calon A, Tarazona N. The prognostic potential of CDX2 in colorectal cancer: Harmonizing biology and clinical practice. Cancer Treat Rev 2023; 121:102643. [PMID: 37871463 DOI: 10.1016/j.ctrv.2023.102643] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Adjuvant chemotherapy following surgical intervention remains the primary treatment option for patients with localized colorectal cancer (CRC). However, a significant proportion of patients will have an unfavorable outcome after current forms of chemotherapy. While reflecting the increasing complexity of CRC, the clinical application of molecular biomarkers provides information that can be utilized to guide therapeutic strategies. Among these, caudal-related homeobox transcription factor 2 (CDX2) emerges as a biomarker of both prognosis and relapse after therapy. CDX2 is a key transcription factor that controls intestinal fate. Although rarely mutated in CRC, loss of CDX2 expression has been reported mostly in right-sided, microsatellite-unstable tumors and is associated with aggressive carcinomas. The pathological assessment of CDX2 by immunohistochemistry can thus identify patients with high-risk CRC, but the evaluation of CDX2 expression remains challenging in a substantial proportion of patients. In this review, we discuss the roles of CDX2 in homeostasis and CRC and the alterations that lead to protein expression loss. Furthermore, we review the clinical significance of CDX2 assessment, with a particular focus on its current use as a biomarker for pathological evaluation and clinical decision-making. Finally, we attempt to clarify the molecular implications of CDX2 deficiency, ultimately providing insights for a more precise evaluation of CDX2 protein expression.
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Affiliation(s)
- Jordi Badia-Ramentol
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - Elena Duréndez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain
| | | | - Jenniffer Linares
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mar Iglesias
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain; Department of Pathology, Hospital del Mar, Barcelona, CIBERONC, Spain
| | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain
| | - Alexandre Calon
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain.
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8
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Múnera JO, Kechele DO, Bouffi C, Qu N, Jing R, Maity P, Enriquez JR, Han L, Campbell I, Mahe MM, McCauley HA, Zhang X, Sundaram N, Hudson JR, Zarsozo-Lacoste A, Pradhan S, Tominaga K, Sanchez JG, Weiss AA, Chatuvedi P, Spence JR, Hachimi M, North T, Daley GQ, Mayhew CN, Hu YC, Takebe T, Helmrath MA, Wells JM. Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon. Cell Stem Cell 2023; 30:1434-1451.e9. [PMID: 37922878 PMCID: PMC10913028 DOI: 10.1016/j.stem.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/31/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
Most organs have tissue-resident immune cells. Human organoids lack these immune cells, which limits their utility in modeling many normal and disease processes. Here, we describe that pluripotent stem cell-derived human colonic organoids (HCOs) co-develop a diverse population of immune cells, including hemogenic endothelium (HE)-like cells and erythromyeloid progenitors that undergo stereotypical steps in differentiation, resulting in the generation of functional macrophages. HCO macrophages acquired a transcriptional signature resembling human fetal small and large intestine tissue-resident macrophages. HCO macrophages modulate cytokine secretion in response to pro- and anti-inflammatory signals and were able to phagocytose and mount a robust response to pathogenic bacteria. When transplanted into mice, HCO macrophages were maintained within the colonic organoid tissue, established a close association with the colonic epithelium, and were not displaced by the host bone-marrow-derived macrophages. These studies suggest that HE in HCOs gives rise to multipotent hematopoietic progenitors and functional tissue-resident macrophages.
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Affiliation(s)
- Jorge O Múnera
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Daniel O Kechele
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Carine Bouffi
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Na Qu
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ran Jing
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Pritiprasanna Maity
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Jacob R Enriquez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Lu Han
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Ian Campbell
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Maxime M Mahe
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Heather A McCauley
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Xinghao Zhang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jonathan R Hudson
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Adrian Zarsozo-Lacoste
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Suman Pradhan
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Kentaro Tominaga
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - J Guillermo Sanchez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Alison A Weiss
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Praneet Chatuvedi
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA
| | - Jason R Spence
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mariam Hachimi
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Trista North
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christopher N Mayhew
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Pluripotent Stem Cell Facility, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Pluripotent Stem Cell Facility, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Takanori Takebe
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Helmrath
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229-3039, USA; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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9
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Saadeldin IM, Bang S, Maigoro AY, Yun SH, Kim SI, Lee S, Cho J. Proteomic Analysis and Reprogramming Potential of the Porcine Intra-Ooplasmic Nanovesicles. Cell Reprogram 2023; 25:238-250. [PMID: 37725012 DOI: 10.1089/cell.2023.0050] [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] [Indexed: 09/21/2023] Open
Abstract
Oocytes contain reprogramming machinery that can transform somatic cells into totipotent cells. In this study, we aimed to isolate and characterize nanovesicles from mature porcine oocytes and described them for the first time as "intra-ooplasmic vesicles (IOVs)". Isolated IOVs had an average diameter of 186.3 ± 10.8 nm. Proteomic analysis revealed 467 peptide reads, with the top 20 proteins related to reprogramming, antioxidative defense, cytoskeleton, heat shock proteins, and metabolism. Protein-protein interaction and gene ontology analysis indicated that these proteins were involved in various biological pathways, including protein folding, metabolism, and cellular responses to stress. Supplementing cultured fibroblasts with IOVs resulted in the expression of the pluripotency marker OCT4 and the early trophoblastic marker CDX2 and increased expression of the corresponding mRNAs together with increasing KLF4 and SALL4 expression. IOV treatment of fibroblasts for 14 consecutive days resulted in changes in cell morphology, with increased expression of ZEB2 and YBX3 as markers for epithelial-to-mesenchymal transition (EMT). These results provide a rationale for further characterization of IOVs, investigation of potential reprogramming capabilities for EMT, and the generation of induced pluripotent or oligopotent stem cells.
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Affiliation(s)
- Islam M Saadeldin
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
- Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Seonggyu Bang
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Abdulkadir Y Maigoro
- Department of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Sung Ho Yun
- Korea Basic Science Institute (KBSI), Ochang, Republic of Korea
| | - Seung Ii Kim
- Korea Basic Science Institute (KBSI), Ochang, Republic of Korea
| | - Sanghoon Lee
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Jongki Cho
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
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10
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Maharati A, Moghbeli M. PI3K/AKT signaling pathway as a critical regulator of epithelial-mesenchymal transition in colorectal tumor cells. Cell Commun Signal 2023; 21:201. [PMID: 37580737 PMCID: PMC10424373 DOI: 10.1186/s12964-023-01225-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 08/16/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most frequent gastrointestinal malignancies that are considered as a global health challenge. Despite many progresses in therapeutic methods, there is still a high rate of mortality rate among CRC patients that is associated with poor prognosis and distant metastasis. Therefore, investigating the molecular mechanisms involved in CRC metastasis can improve the prognosis. Epithelial-mesenchymal transition (EMT) process is considered as one of the main molecular mechanisms involved in CRC metastasis, which can be regulated by various signaling pathways. PI3K/AKT signaling pathway has a key role in CRC cell proliferation and migration. In the present review, we discussed the role of PI3K/AKT pathway CRC metastasis through the regulation of the EMT process. It has been shown that PI3K/AKT pathway can induce the EMT process by down regulation of epithelial markers, while up regulation of mesenchymal markers and EMT-specific transcription factors that promote CRC metastasis. This review can be an effective step toward introducing the PI3K/AKT/EMT axis to predict prognosis as well as a therapeutic target among CRC patients. Video Abstract.
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Affiliation(s)
- Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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11
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Jiménez S, Schreiber V, Mercier R, Gradwohl G, Molina N. Characterization of cell-fate decision landscapes by estimating transcription factor dynamics. CELL REPORTS METHODS 2023; 3:100512. [PMID: 37533652 PMCID: PMC10391345 DOI: 10.1016/j.crmeth.2023.100512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/23/2023] [Accepted: 06/01/2023] [Indexed: 08/04/2023]
Abstract
Time-specific modulation of gene expression during differentiation by transcription factors promotes cell diversity. However, estimating their dynamic regulatory activity at the single-cell level and in a high-throughput manner remains challenging. We present FateCompass, an integrative approach that utilizes single-cell transcriptomics data to identify lineage-specific transcription factors throughout differentiation. By combining a probabilistic framework with RNA velocities or differentiation potential, we estimate transition probabilities, while a linear model of gene regulation is employed to compute transcription factor activities. Considering dynamic changes and correlations of expression and activities, FateCompass identifies lineage-specific regulators. Our validation using in silico data and application to pancreatic endocrine cell differentiation datasets highlight both known and potentially novel lineage-specific regulators. Notably, we uncovered undescribed transcription factors of an enterochromaffin-like population during in vitro differentiation toward ß-like cells. FateCompass provides a valuable framework for hypothesis generation, advancing our understanding of the gene regulatory networks driving cell-fate decisions.
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Affiliation(s)
- Sara Jiménez
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Valérie Schreiber
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Reuben Mercier
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Gérard Gradwohl
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Nacho Molina
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
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12
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Yu D, Lu Z, Wang R, Xiang Y, Li H, Lu J, Zhang L, Chen H, Li W, Luan X, Chen L. FXR agonists for colorectal and liver cancers, as a stand-alone or in combination therapy. Biochem Pharmacol 2023; 212:115570. [PMID: 37119860 DOI: 10.1016/j.bcp.2023.115570] [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: 02/21/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
Farnesoid X receptor (FXR, NR1H4) is generally considered as a tumor suppressor of colorectal and liver cancers. The interaction between FXR, bile acids (BAs) and gut microbiota is closely associated with an increased risk of colorectal and liver cancers. Increasing evidence shows that FXR agonists may be potential therapeutic agents for colorectal and liver cancers. However, FXR agonists alone do not produce the desired results due to the complicated pathogenesis and single therapeutic mechanism, which suggests that effective treatments will require a multimodal approach. Based on the principle of improvingefficacy andreducingside effects, combination therapy is currently receiving considerable attention. In this review, colorectal and liver cancers are grouped together to discuss the effects of FXR agonists alone or in combination for combating the two cancers. We hope that this review will provide a theoretical basis for the clinical application of novel FXR agonists or combination with FXR agonists against colorectal and liver cancers.
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Affiliation(s)
- Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhou Lu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Ruyu Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yusen Xiang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Lijun Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xin Luan
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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13
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Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O’Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535726. [PMID: 37066300 PMCID: PMC10104014 DOI: 10.1101/2023.04.05.535726] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Riza M. Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Truc-Mai Le
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eva K. Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Megan L. Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Olivia Fulton
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diana R. O’Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Saskia Ilcisin
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christine M. Disteche
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Kimelman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-cell genomics and Population dynamics, The Rockefeller University, New York, NY, USA
| | - Alexander F. Schier
- Biozentrum, University of Basel, Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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14
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Asahina Y, Hashimoto H, Aihara M, Noie T, Morikawa T. Impact of Neoadjuvant Chemotherapy on SATB2 Expression in Colorectal Carcinomas: SATB2 Positivity is Preserved in Most Cases, but Down-Expressed in Effective Cases of Chemotherapy. Int J Surg Pathol 2023; 31:46-55. [PMID: 35343276 DOI: 10.1177/10668969221088881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Special AT-rich sequence-binding protein 2 (SATB2) is a novel, diagnostically useful, and highly sensitive immunohistochemical marker for both primary and metastatic colorectal or appendiceal tumors. In the present study, we aimed to assess the impact of neoadjuvant chemotherapy on SATB2 expression in primary colorectal carcinomas and their corresponding liver metastases. Forty-four patients with colorectal carcinomas who received neoadjuvant chemotherapy were included. SATB2 expression in specimens of biopsy, resected primary colorectal carcinomas, and resected metastatic foci were examined by immunohistochemistry and compared to caudal-type homeobox transcription factor 2 (CDX2). Using a modified H-score, expressions were scored semiquantitatively for both staining intensity and tumor cell proportion with nuclear staining. SATB2 was positive in 43/44 cases (98%) in biopsy specimens, 42/44 cases (96%) in resected colorectal carcinomas with neoadjuvant chemotherapy, and 9/9 cases (100%) with liver metastases. However, these expressions were variably decreased, and the H-score was lower in resected colorectal carcinomas (158 ± 69) than in biopsy specimens (174 ± 60) (p < 0.01). The proportion of SATB2-positive area of colorectal carcinoma was 93% in metastatic foci, while the CDX2-positive area was 78%. When categorized by histopathological tumor regression, the most effective tumors of chemotherapy showed the lowest H-score in resected colorectal carcinomas among the three groups (p < 0.01). SATB2 is a useful marker for both primary colorectal carcinoma and corresponding liver metastases, even with neoadjuvant chemotherapy. However, caution should be exercised when performing needle biopsy for metastatic foci with neoadjuvant therapy because expressions could be decreased, especially in chemotherapy-effective cases, and show immunohistochemically negative results.
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Affiliation(s)
- Yuichi Asahina
- Department of Ophthalmology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan.,Department of Diagnostic Pathology, 13635NTT Medical Center Tokyo, 5-9-22 Higashi-Gotanda, Shinagawa-ku, Tokyo 141-8625, Japan
| | - Hirotsugu Hashimoto
- Department of Diagnostic Pathology, 13635NTT Medical Center Tokyo, 5-9-22 Higashi-Gotanda, Shinagawa-ku, Tokyo 141-8625, Japan.,Faculty of Healthcare, Tokyo Healthcare University, 4-1-17, Higashi-Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Makoto Aihara
- Department of Ophthalmology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Tamaki Noie
- Department of Surgery, 13635NTT Medical Center Tokyo, 5-9-22 Higashi-Gotanda, Shinagawa-ku, Tokyo 141-8625, Japan
| | - Teppei Morikawa
- Department of Diagnostic Pathology, 13635NTT Medical Center Tokyo, 5-9-22 Higashi-Gotanda, Shinagawa-ku, Tokyo 141-8625, Japan.,Faculty of Healthcare, Tokyo Healthcare University, 4-1-17, Higashi-Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
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15
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Li J, Tan R, Wu J, Guo W, Wang Y, You G, Zhang Y, Yu Z, Geng Y, Zan J, Su J. A cellular senescence-related genes model allows for prognosis and treatment stratification of hepatocellular carcinoma: A bioinformatics analysis and experimental verification. Front Genet 2023; 13:1099148. [PMID: 36712870 PMCID: PMC9877353 DOI: 10.3389/fgene.2022.1099148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction: Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer with low 5-year survival rate. Cellular senescence, characterized by permanent and irreversible cell proliferation arrest, plays an important role in tumorigenesis and development. This study aims to develop a cellular senescence-based stratified model, and a multivariable-based nomogram for guiding clinical therapy for HCC. Materials and methods: The mRNAs expression data of HCC patients and cellular senescence-related genes were obtained from TCGA and CellAge database, respectively. Through multiple analysis, a four cellular senescence-related genes-based prognostic stratified model was constructed and its predictive performance was validated through various methods. Then, a nomogram based on the model was constructed and HCC patients stratified by the model were analyzed for tumor mutation burden, tumor microenvironment, immune infiltration, drug sensitivity and immune checkpoint. Functional enrichment analysis was performed to explore potential biological pathways. Finally, we verified this model by siRNA transfection, scratch assay and Transwell Assay. Results: We established an cellular senescence-related genes-based stratified model, and a multivariable-based nomogram, which could accurately predict the prognosis of HCC patients in the ICGC database. The low and high risk score HCC patients stratified by the model showed different tumor mutation burden, tumor microenvironment, immune infiltration, drug sensitivity and immune checkpoint expressions. Functional enrichment analysis suggested several biological pathways related to the process and prognosis of HCC. Scratch assay and transwell assay indicated the promotion effects of the four cellular senescence-related genes (EZH2, G6PD, CBX8, and NDRG1) on the migraiton and invasion of HCC. Conclusion: We established a cellular senescence-based stratified model, and a multivariable-based nomogram, which could predict the survival of HCC patients and guide clinical treatment.
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Affiliation(s)
- Jiaming Li
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China,Department of Pharmacy, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Rongzhi Tan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Jie Wu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Wenjie Guo
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Yupeng Wang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Guoxing You
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Yuting Zhang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Zhiyong Yu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Yan Geng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Jie Zan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China,*Correspondence: Jianfen Su, ; Jie Zan,
| | - Jianfen Su
- Department of Pharmacy, Guangzhou Panyu Central Hospital, Guangzhou, China,*Correspondence: Jianfen Su, ; Jie Zan,
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16
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Sabbatini S, Ganji N, Chusilp S, Balsamo F, Li B, Pierro A. Intestinal atresia and necrotizing enterocolitis: Embryology and anatomy. Semin Pediatr Surg 2022; 31:151234. [PMID: 36417784 DOI: 10.1016/j.sempedsurg.2022.151234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The primitive gut originates at week 3 of gestation from the endoderm, with posterior incorporation of the remaining embryo layers. Wnt, Notch and TLR4 pathways have been shown to play central roles in the correct development of the intestine. The classical hypothesis for intestinal atresia development consists of failure in bowel recanalization or a vascular accident with secondary bowel reabsorption. These have been challenged due to the high frequency of associated malformations, and furthermore, with the discovery of molecular pathways and genes involved in bowel formation and correlated defects producing atresia. Necrotizing enterocolitis (NEC) has a multifactorial pathogenesis with prematurity being the most important risk factor; therefore, bowel immaturity plays a central role in NEC. Some of the same molecular pathways involved in gut maturation have been found to correlate with the predisposition of the immature bowel to develop the pathological findings seen in NEC.
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Affiliation(s)
- S Sabbatini
- Translational Medicine Program, The Hospital for Sick Children, Toronto
| | - N Ganji
- Translational Medicine Program, The Hospital for Sick Children, Toronto
| | - S Chusilp
- Translational Medicine Program, The Hospital for Sick Children, Toronto
| | - F Balsamo
- Translational Medicine Program, The Hospital for Sick Children, Toronto
| | - B Li
- Translational Medicine Program, The Hospital for Sick Children, Toronto
| | - A Pierro
- Translational Medicine Program, The Hospital for Sick Children, Toronto; Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto.
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17
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Mochizuki K, Kudo SE, Kato K, Kudo K, Ogawa Y, Kouyama Y, Takashina Y, Ichimasa K, Tobo T, Toshima T, Hisamatsu Y, Yonemura Y, Masuda T, Miyachi H, Ishida F, Nemoto T, Mimori K. Molecular and clinicopathological differences between depressed and protruded T2 colorectal cancer. PLoS One 2022; 17:e0273566. [PMID: 36264865 PMCID: PMC9584453 DOI: 10.1371/journal.pone.0273566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/11/2022] [Indexed: 11/05/2022] Open
Abstract
Background Colorectal cancer (CRC) can be classified into four consensus molecular subtypes (CMS) according to genomic aberrations and gene expression profiles. CMS is expected to be useful in predicting prognosis and selecting chemotherapy regimens. However, there are still no reports on the relationship between the morphology and CMS. Methods This retrospective study included 55 subjects with T2 CRC undergoing surgical resection, of whom 30 had the depressed type and 25 the protruded type. In the classification of the CMS, we first defined cases with deficient mismatch repair as CMS1. And then, CMS2/3 and CMS4 were classified using an online classifier developed by Trinh et al. The staining intensity of CDX2, HTR2B, FRMD6, ZEB1, and KER and the percentage contents of CDX2, FRMD6, and KER are input into the classifier to obtain automatic output classifying the specimen as CMS2/3 or CMS4. Results According to the results yielded by the online classifier, of the 30 depressed-type cases, 15 (50%) were classified as CMS2/3 and 15 (50%) as CMS4. Of the 25 protruded-type cases, 3 (12%) were classified as CMS1 and 22 (88%) as CMS2/3. All of the T2 CRCs classified as CMS4 were depressed CRCs. More malignant pathological findings such as lymphatic invasion were associated with the depressed rather than protruded T2 CRC cases. Conclusions Depressed-type T2 CRC had a significant association with CMS4, showing more malignant pathological findings such as lymphatic invasion than the protruded-type, which could explain the reported association between CMS4 CRC and poor prognosis.
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Affiliation(s)
- Kenichi Mochizuki
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Shin-ei Kudo
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Kazuki Kato
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Koki Kudo
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Yushi Ogawa
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Yuta Kouyama
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Yuki Takashina
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Katsuro Ichimasa
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
- Department of Gastroenterology and Hepatology, National University Hospital, Singapore, Singapore
| | - Taro Tobo
- Department of Clinical Laboratory, Kyushu University Beppu Hospital, Beppu, Japan
| | - Takeo Toshima
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yuichi Hisamatsu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Yusuke Yonemura
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - Hideyuki Miyachi
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Fumio Ishida
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Tetsuo Nemoto
- Department of Diagnostic Pathology, School of Medicine, Showa University, Yokohama Northern Hospital, Kanagawa, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
- * E-mail:
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18
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CDX2 as a Predictive Biomarker Involved in Immunotherapy Response Suppresses Metastasis through EMT in Colorectal Cancer. DISEASE MARKERS 2022; 2022:9025668. [PMID: 36277982 PMCID: PMC9582897 DOI: 10.1155/2022/9025668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/12/2022] [Accepted: 09/30/2022] [Indexed: 11/18/2022]
Abstract
Background Studies have confirmed that Caudal Type Homeobox 2 (CDX2) plays a tumor suppressor role in colorectal cancer (CRC) and as a prognostic and predictive marker for colorectal cancer. The epithelial to mesenchymal transition (EMT) is a transdifferentiation process, providing migratory and invasive properties to cancer cells during tumor progression. However, the role of CDX2 during the activation of EMT in CRC maintains controversial. Aim To investigate whether CDX2 is associated with EMT in CRC. Methods Forty-six CRC patients were included in the study. Expressions of CDX2, E-cadherin, and N-cadherin in all CRC patients were detected by IHC. ROC assays were applied to detect cut-off points for IHC scores to distinguish high and low expressions of CDX2 in 46 CRC samples. The prognostic value of CDX2 was statistically analyzed. MTT, Western blot, invasion, and migration assays in vitro were employed to explore the function of CDX2. Results We observed that high expressions of CDX2 and E-cadherin as well as low expressions of N-cadherin were significantly correlated with favorable prognosis. The levels of CDX2 protein exhibited a positive associated with E-cadherin while negative correlation with N-cadherin. Then, the low expression of CDX2 and high expression of CA199 in combination are positively related with poor prognosis. Overexpression of CDX2 reduced expression of MMP-2 and diminished cell proliferation, invasion, and migration, while knockdown CDX2 enhanced MMP-2 expression and increased cell proliferation, invasion, and migration in HCT-116 cells. CDX2 was correlated with expression of EMT markers. Overexpression of CDX2 suppressed the EMT markers indicating that CDX2 suppresses CRC cell viability, invasion, and metastasis through inhibiting EMT. Finally, we found that the expression of CDX2 was negatively associated with Th1 cells, macrophages, Th2 cells, cytotoxic cells, T cells, and T helper cells. Conclusions These results indicated CDX2 as prognostic biomarkers involved in immunotherapy response for CRC. CDX2 loss promotes metastasis in CRC through a CDX2-dependent mechanism.
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19
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Felsenthal N, Vignjevic DM. Stand by me: Fibroblasts regulation of the intestinal epithelium during development and homeostasis. Curr Opin Cell Biol 2022; 78:102116. [PMID: 35914344 DOI: 10.1016/j.ceb.2022.102116] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 01/31/2023]
Abstract
The epithelium of the small intestine is composed of a single layer of cells that line two functionally distinct compartments, the villi that project into the lumen of the gut and the crypts that descend into the underlying connective tissue. Stem cells are located in crypts, where they divide and give rise to transit-amplifying cells that differentiate into secretory and absorptive epithelial cells. Most differentiated cells travel upwards from the crypt towards the villus tip, where they shed into the lumen. While some of these cell behaviors are an intrinsic property of the epithelium, it is becoming evident that tight coordination between the epithelium and the underlying fibroblasts plays a critical role in tissue morphogenesis, stem-cell niche maintenance and regionalized gene expression along the crypt-villus axis. Here, we will review the current literature describing the interaction between epithelium and fibroblasts during crypt-villus axis development and intestinal epithelium renewal during homeostasis.
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Affiliation(s)
- Neta Felsenthal
- Institut Curie, PSL Research University, CNRS UMR 144, F-75005 Paris, France.
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20
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Chen L, Yang F, Qi Z, Tai J. Predicting lymph node metastasis and recurrence in patients with early stage colorectal cancer. Front Med (Lausanne) 2022; 9:991785. [PMID: 36186777 PMCID: PMC9520336 DOI: 10.3389/fmed.2022.991785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Tumor budding (TB), a powerful, independent predictor of colorectal cancer (CRC), is important for making appropriate treatment decisions. Currently, TB is assessed only using the tumor bud count (TBC). In this study, we aimed to develop a novel prediction model, which includes different TB features, for lymph node metastasis (LNM) and local recurrence in patients with pT1 CRC. Enrolled patients (n = 354) were stratified into training and validation cohorts. Independent predictors of LNM and recurrence were identified to generate predictive nomograms that were assessed using the area under the receiver operating characteristic (AUROC) and decision curve analysis (DCA). Seven LNM predictors [gross type, histological grade, lymphovascular invasion (LVI), stroma type, TBC, TB mitosis, and TB CDX2 expression] were identified in the training cohort. LNM, histology grade, LVI, TBC, stroma type, and TB mitosis were independent predictors of recurrence. We constructed an LNM predictive nomogram with a high clinical application value using the DCA. Additionally, a nomogram predicting recurrence-free survival (RFS) was constructed. It presented an AUROC value of 0.944 for the training cohort. These models may assist surgeons in making treatment decisions. In the high-risk group, radical surgery with a postoperative adjuvant chemotherapy was associated with RFS. Postoperative chemotherapy can be better for high-risk patients with pT1 CRC. We showed that TB features besides TBC play important roles in CRC pathogenesis, and our study provides prognostic information to guide the clinical management of patients with early stage CRC.
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Affiliation(s)
- Lei Chen
- Colorectal and Anal Surgery, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Funing Yang
- Pediatric Outpatient Clinic, First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhaoyan Qi
- Colorectal and Anal Surgery, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiandong Tai
- Colorectal and Anal Surgery, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Jiandong Tai,
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21
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Jahan S, Awaja N, Hess B, Hajjar S, Sad S, Lohnes D. The transcription factor Cdx2 regulates inflammasome activity through expression of the NLRP3 suppressor TRIM31 to maintain intestinal homeostasis. J Biol Chem 2022; 298:102386. [PMID: 35985421 PMCID: PMC9508567 DOI: 10.1016/j.jbc.2022.102386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 11/03/2022] Open
Abstract
The intestine-specific transcription factor Cdx2 is essential for intestinal homeostasis and has been implicated in the pathogenesis of disorders including inflammatory bowel disease. However, the mechanism by which Cdx2 influences intestinal disease is not clear. Here, we present evidence supporting a novel Cdx2–TRIM31–NLRP3 (NLR family, pyrin domain containing 3) signaling pathway, which may represent a mechanistic means by which Cdx2 impacts intestinal inflammation. We found that conditional loss of Cdx function resulted in an increase in proinflammatory cytokines, including tumor necrosis factor alpha, interleukin (IL)-1β, and IL-6, in the mouse colon. We further show that TRIM31, which encodes a suppressor of NLRP3 (a central component of the NLRP3 inflammasome complex) is a novel Cdx2 target gene and is attenuated in the colon of Cdx conditional mutants. Consistent with this, we found that attenuation of TRIM31 in Cdx mutant intestine occurs concomitant with elevated levels of NLRP3 and an increase in inflammasome products. We demonstrate that specific inhibition of NLRP3 activity significantly reduced IL-1β and IL-6 levels and extended the life span of Cdx conditional mutants, reflecting the therapeutic potential of targeting NLRP3. Tumor necrosis factor-alpha levels were also induced independent of NLRP3, potentially via elevated activity of the proinflammatory NF-κB signaling pathway in Cdx mutants. Finally, in silico analysis of ulcerative colitis patients revealed attenuation of CDX2 and TRIM31 expression coincident with enhanced expression of proinflammatory cytokines. We conclude that the novel Cdx2–TRIM31–NLRP3 signaling pathway promotes proinflammatory cytokine expression, and its inhibition may have therapeutic potential in human intestinal diseases.
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Affiliation(s)
- Sanzida Jahan
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Nidaa Awaja
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Bradley Hess
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Stephanie Hajjar
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Subash Sad
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - David Lohnes
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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22
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Smith RJ, Zhang H, Hu SS, Yung T, Francis R, Lee L, Onaitis MW, Dirks PB, Zang C, Kim TH. Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions. Nat Commun 2022; 13:2965. [PMID: 35618699 PMCID: PMC9135761 DOI: 10.1038/s41467-022-30624-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/06/2022] [Indexed: 01/07/2023] Open
Abstract
Development of the gastrointestinal system occurs after gut tube closure, guided by spatial and temporal control of gene expression. However, it remains unclear what forces regulate these spatiotemporal gene expression patterns. Here we perform single-cell chromatin profiling of the primitive gut tube to reveal organ-specific chromatin patterns that reflect the anatomical patterns of distinct organs. We generate a comprehensive map of epigenomic changes throughout gut development, demonstrating that dynamic chromatin accessibility patterns associate with lineage-specific transcription factor binding events to regulate organ-specific gene expression. Additionally, we show that loss of Sox2 and Cdx2, foregut and hindgut lineage-specific transcription factors, respectively, leads to fate shifts in epigenomic patterns, linking transcription factor binding, chromatin accessibility, and lineage fate decisions in gut development. Notably, abnormal expression of Sox2 in the pancreas and intestine impairs lineage fate decisions in both development and adult homeostasis. Together, our findings define the chromatin and transcriptional mechanisms of organ identity and lineage plasticity in development and adult homeostasis. The primitive gut tube gives rise to all major internal organs, while underlying regulatory mechanisms are unclear. Here, the authors analyze its chromatin landscape at the single-cell level and define the epigenetic regulation of lineage fate decisions and plasticity in organ development and homeostasis.
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Affiliation(s)
- Ryan J Smith
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Hongpan Zhang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Shengen Shawn Hu
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Theodora Yung
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Roshane Francis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Lilian Lee
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Mark W Onaitis
- Division of Cardiovascular and Thoracic Surgery, University of California San Diego Medical Center, San Diego, CA, USA
| | - Peter B Dirks
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| | - Tae-Hee Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
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23
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Yu J, Yang K, Zheng J, Zhao P, Xia J, Sun X, Zhao W. Activation of FXR and inhibition of EZH2 synergistically inhibit colorectal cancer through cooperatively accelerating FXR nuclear location and upregulating CDX2 expression. Cell Death Dis 2022; 13:388. [PMID: 35449124 PMCID: PMC9023572 DOI: 10.1038/s41419-022-04745-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/09/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022]
Abstract
Our previous study indicated that colon cancer cells varied in sensitivity to pharmacological farnesoid X receptor (FXR) activation. Herein, we explore the regulatory mechanism of FXR in colorectal cancer (CRC) development and aim to design effective strategies of combined treatment based on the regulatory axis. We found that the expression of FXR was negatively correlated with enhancer of zeste homolog 2 (EZH2) in colon cancer tissues. EZH2 transcriptionally suppressed FXR via H3K27me3. The combination of FXR agonist OCA plus EZH2 inhibitor GSK126 acted in a synergistic manner across four colon cancer cells, efficiently inhibiting clonogenic growth and invasion in vitro, retarding tumor growth in vivo, preventing the G0/G1 to S phase transition, and inducing caspase-dependent apoptosis. Benign control cells FHC were growth-arrested without apoptosis induction, but retained long-term proliferation and invasion capacity. Mechanistically, the drug combination dramatically accelerated FXR nuclear location and cooperatively upregulated caudal-related homeobox transcription factor 2 (CDX2) expression. The depletion of CDX2 antagonized the synergistic effects of the drug combination on tumor inhibition. In conclusion, our study demonstrated histone modification-mediated FXR silencing by EZH2 in colorectal tumorigenesis, which offers useful evidence for the clinical use of FXR agonists combined with EZH2 inhibitors in combating CRC.
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Affiliation(s)
- Junhui Yu
- grid.452438.c0000 0004 1760 8119Department of General Surgery, First Affiliated Hospital of Xi’an Jiaotong University, 710061 Xi’an, PR China
| | - Kui Yang
- grid.452438.c0000 0004 1760 8119Department of General Surgery, First Affiliated Hospital of Xi’an Jiaotong University, 710061 Xi’an, PR China
| | - Jianbao Zheng
- grid.452438.c0000 0004 1760 8119Department of General Surgery, First Affiliated Hospital of Xi’an Jiaotong University, 710061 Xi’an, PR China
| | - Pengwei Zhao
- grid.452438.c0000 0004 1760 8119Department of General Surgery, First Affiliated Hospital of Xi’an Jiaotong University, 710061 Xi’an, PR China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 100050, Beijing, PR China.
| | - Xuejun Sun
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, PR China.
| | - Wei Zhao
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiaotong University, 710061, Xi'an, PR China.
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24
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Lee JA, Seo MK, Yoo SY, Cho NY, Kwak Y, Lee K, Kim JH, Kang GH. Comprehensive clinicopathologic, molecular, and immunologic characterization of colorectal carcinomas with loss of three intestinal markers, CDX2, SATB2, and KRT20. Virchows Arch 2022; 480:543-555. [PMID: 35029777 DOI: 10.1007/s00428-021-03260-w] [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: 08/22/2021] [Revised: 12/04/2021] [Accepted: 12/22/2021] [Indexed: 11/24/2022]
Abstract
Caudal-type homeobox 2 (CDX2), special AT-rich sequence-binding protein 2 (SATB2), and keratin 20 (KRT20) are frequently used as intestinal epithelium-specific markers in immunohistochemical studies. However, subsets of colorectal carcinomas (CRCs) show loss of these markers. We analyzed The Cancer Genome Atlas data to explore molecular correlates of CDX2, SATB2, and KRT20 genes in 390 CRCs. The decreased mRNA expression of each of the three genes commonly correlated with microsatellite instability-high (MSI-H), CpG island methylator phenotype-high (CIMP-H), BRAF/RNF43 mutations, consensus molecular subtype 1, and high tumor mutational burden. The downregulation of CDX2 or SATB2 was dependent on both MSI-H and CIMP-H, whereas that of KRT20 was more dependent on MSI-H than on CIMP-H. Next, we evaluated the immunohistochemical expression of CDX2, SATB2, and KRT20 in 436 primary CRCs. In contrast to RNA-level expression, decreased expression of CDX2 and SATB2 was more dependent on CIMP-H than on MSI-H. However, consistent with RNA-level expression, decreased expression of KRT20 was more dependent on MSI-H than on CIMP-H. CIMP-H and lymphatic invasion were consistently associated with both CDX2 loss and SATB2 loss in CRCs, regardless of MSI status. In microsatellite stable CRCs, CDX2 loss correlated with BRAF mutation, whereas SATB2 loss was associated with KRAS mutations and decreased T-cell infiltration. Cases with concurrent loss of all three markers were found exclusively in MLH1-methylated MSI-H/CIMP-H CRCs. In conclusion, MSI-H and/or CIMP-H are major common correlates of decreased CDX2/SATB2/KRT20 expression in CRCs, but the specific features associated with the loss of each marker are different in CRCs.
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Affiliation(s)
- Ji Ae Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Mi-Kyoung Seo
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, South Korea.,Department of Nuclear Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Seung-Yeon Yoo
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Nam-Yun Cho
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Yoonjin Kwak
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Kyoungbun Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jung Ho Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea. .,Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
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25
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Ericsson AC, Bains M, McAdams Z, Daniels J, Busi SB, Waschek JA, Dorsam GP. The G Protein-Coupled Receptor, VPAC1, Mediates Vasoactive Intestinal Peptide-Dependent Functional Homeostasis of the Gut Microbiota. GASTRO HEP ADVANCES 2022; 1:253-264. [PMID: 36910129 PMCID: PMC9997614 DOI: 10.1016/j.gastha.2021.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND AIMS Vasoactive intestinal peptide (VIP) is a neuropeptide involved in the regulation of feeding behavior and circadian rhythms, metabolism, and immunity. Previous studies revealed the homeostatic effects of VIP signaling on the gut microbiota. VIP-deficient mice demonstrate a gut microbiota dysbiosis characterized by reduced α-diversity and decreased relative abundance (RA) of Gram-positive Firmicutes. However, the mechanism by which VIP signaling affects changes in the microbiota is unknown. METHODS To investigate the role of the 2 cognate G protein-coupled receptors for VIP (VPAC1 and VPAC2) in VIP-mediated homeostasis of the microbiota, fecal samples from VPAC1- and VPAC2-deficient, heterozygous, and wild-type littermate mice were assessed via targeted amplicon sequencing. Their microbiota profiles were additionally compared with microbiota from VIP-deficient, heterozygous, and wild-type littermates, where genotype-dependent changes in the composition and predicted function of each cohort were compared. RESULTS While wild-type mice in each line differed in α-diversity and β-diversity, consistent changes in both metrics were observed in VIP-deficient and VPAC1-deficient mice. This includes a dramatic reduction in α-diversity, increased RA of Proteobacteria and Bacteroidetes, and decreased RA of Lachnospiraceae, Ruminococcaceae, Muribaculaceae, and Rikenellaceae. Specific amplicon sequence variants and predicted functions found to differ significantly based on VIP or VPAC1 genotype were concordant in their directions of change. Multiplatform predicted functional profiling suggested a defective VIP-VPAC1 axis was associated with reduced amino acid degradation along with reduced quinol and quinone biosynthesis. Furthermore, alterations in predicted functions include increased sugar degradation, nitrate reduction, and fatty acid biosynthetic pathways, among other changes. CONCLUSION We conclude that VIP signaling through VPAC1 is critical for the maintenance of normal function of the gut microbiota.
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Affiliation(s)
- Aaron C. Ericsson
- Department of Veterinary Pathobiology, University of Missouri Metagenomics Center, College of Veterinary Medicine, University of Missouri, Columbia, Missouri
| | - Manpreet Bains
- Department of Microbiological Sciences, College of Agriculture, Food Systems and Natural Resources, North Dakota State University, Fargo, North Dakota
| | - Zachary McAdams
- Department of Veterinary Pathobiology, University of Missouri Metagenomics Center, College of Veterinary Medicine, University of Missouri, Columbia, Missouri
| | - Justin Daniels
- Department of Microbiological Sciences, College of Agriculture, Food Systems and Natural Resources, North Dakota State University, Fargo, North Dakota
| | - Susheel B. Busi
- Department of Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - James A. Waschek
- Department of Psychiatry and Biobehavioral Sciences, Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior/Neuropsychiatric Institute, University of California, Los Angeles, Los Angeles, California
| | - Glenn P. Dorsam
- Department of Microbiological Sciences, College of Agriculture, Food Systems and Natural Resources, North Dakota State University, Fargo, North Dakota
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26
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Saberi S, Esmaeili M, Tashakoripour M, Eshagh Hosseini M, Baharvand H, Mohammadi M. Infection with a hypervirulent strain of Helicobacter pylori primes gastric cells toward intestinal transdifferentiation. Microb Pathog 2021; 162:105353. [PMID: 34896202 DOI: 10.1016/j.micpath.2021.105353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/05/2021] [Accepted: 12/05/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND Intestinal metaplasia, gastric-to-intestinal transdifferentiation, occurs as a result of the misexpression of certain regulatory factors, leading to genetic reprogramming. Here, we have evaluated the H. pylori-induced expression patterns of these candidate genes. METHODS The expression levels of 1) tissue-specific transcription factors (RUNX3, KLF5, SOX2, SALL4, CDX1 and CDX2), 2) stemness factors (TNFRSF19, LGR5, VIL1) and 3) tissue-specific mucins (MUC5AC, MUC2) were evaluated by quantitative real-time PCR in gastric primary cells (GPCs), in parallel with two gastric cancer (MKN45 and AGS) cell lines, up to 96h following H. pylori infection. RESULTS Following H. pylori infection of GPCs, RUNX3 declined at 24h post infection (-6.2 ± 0.3) and remained downregulated for up to 96h. Subsequently, overexpression of self-renewal and pluripotency transcription factors, KLF5 (3.6 ± 0.2), SOX2 (7.6 ± 0.5) and SALL4 (4.3 ± 0.2) occurred. The expression of TNFRSF19 and LGR5, demonstrated opposing trends, with an early rise of the former (4.5 ± 0.3) at 8h, and a simultaneous fall of the latter (-1.8 ± 0.5). This trend was reversed at 96h, with the decline in TNFRSF19 (-5.5 ± 0.2), and escalation of LGR5 (2.6 ± 0.2) and VIL1 (1.8 ± 0.3). Ultimately, CDX1 and CDX2 were upregulated by 1.9 and 4.7-fold, respectively. The above scenario was, variably observed in MKN45 and AGS cells. CONCLUSION Our data suggests an interdependent gene regulatory network, induced by H. pylori infection. This interaction begins with the downregulation of RUNX3, upregulation of self-renewal and pluripotency transcription factors, KLF5, SOX2 and SALL4, leading to the downregulation of TNFRSF19, upregulation of LGR5 and aberrant expression of intestine-specific transcription factors, potentially facilitating the process of gastric-to-intestinal transdifferentiation.
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Affiliation(s)
- Samaneh Saberi
- HPGC Research Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Esmaeili
- HPGC Research Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Tashakoripour
- Gastroenterology Department, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Eshagh Hosseini
- Gastroenterology Department, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Marjan Mohammadi
- HPGC Research Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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27
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Azcue P, Guerrero Setas D, Encío I, Ibáñez-Beroiz B, Mercado M, Vera R, Gómez-Dorronsoro ML. A Novel Prognostic Biomarker Panel for Early-Stage Colon Carcinoma. Cancers (Basel) 2021; 13:5909. [PMID: 34885019 PMCID: PMC8656725 DOI: 10.3390/cancers13235909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/09/2022] Open
Abstract
Molecular characterization of colorectal cancer has helped us understand better the biology of the disease. However, previous efforts have yet to provide significant clinical value in order to be integrated into clinical practice for patients with early-stage colon cancer (CC). The purpose of this study was to assess PD-L1, GLUT-1, e-cadherin, MUC2, CDX2, and microsatellite instability (dMMR) and to propose a risk-panel with prognostic capabilities. Biomarkers were immunohistochemically assessed through tissue microarrays in a cohort of 144 patients with stage II/III colon cancer. A biomarker panel consisting of PD-L1, GLUT-1, dMMR, and potentially CDX2 was constructed that divided patients into low, medium, and high risk of overall survival or disease-free survival (DFS) in equally sized groups. Compared with low-risk patients, medium-risk patients have almost twice the risk of death (HR = 2.10 (0.99-4.46), p = 0.054), while high-risk patients have almost four times the risk (HR = 3.79 (1.77-8.11), p = 0.001). The multivariate goodness of fit was 0.756 and was correlated with Kaplan-Meier curves (p = 0.002). Consistent results were found for DFS. This study provides a critical basis for the future development of an immunohistochemical assessment capable of discerning early-stage CC patients as a function of their prognosis. This tool may aid with treatment personalization in daily clinical practice and improve survival outcomes.
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Affiliation(s)
- Pablo Azcue
- Department of Health Science, Public University of Navarra, 31008 Pamplona, Spain; (I.E.); (B.I.-B.)
| | - David Guerrero Setas
- Department of Pathology, University Hospital of Navarra, 31008 Pamplona, Spain; (D.G.S.); (M.M.)
- Campus Arrosadia, Public University of Navarra, 31006 Pamplona, Spain
- Molecular Pathology of Cancer Group–Navarrabiomed, 31008 Pamplona, Spain
- Department of Medical Oncology, University Hospital of Navarra, 31008 Pamplona, Spain;
| | - Ignacio Encío
- Department of Health Science, Public University of Navarra, 31008 Pamplona, Spain; (I.E.); (B.I.-B.)
- Institute for Health Research Navarra (IdISNA), 31008 Pamplona, Spain
| | - Berta Ibáñez-Beroiz
- Department of Health Science, Public University of Navarra, 31008 Pamplona, Spain; (I.E.); (B.I.-B.)
- Institute for Health Research Navarra (IdISNA), 31008 Pamplona, Spain
- Unit of Methodology-Navarrabiomed-University Hospital of Navarra, 31008 Pamplona, Spain
- Research Network on Health Services Research and Chronic Diseases (REDISSEC), 31008 Pamplona, Spain
| | - María Mercado
- Department of Pathology, University Hospital of Navarra, 31008 Pamplona, Spain; (D.G.S.); (M.M.)
| | - Ruth Vera
- Department of Medical Oncology, University Hospital of Navarra, 31008 Pamplona, Spain;
- Institute for Health Research Navarra (IdISNA), 31008 Pamplona, Spain
| | - María Luisa Gómez-Dorronsoro
- Department of Pathology, University Hospital of Navarra, 31008 Pamplona, Spain; (D.G.S.); (M.M.)
- Institute for Health Research Navarra (IdISNA), 31008 Pamplona, Spain
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Abstract
The intestinal epithelium is a unique tissue, serving both as a barrier against pathogens and to conduct the end digestion and adsorption of nutrients. As regards the former, the intestinal epithelium contains a diverse repertoire of immune cells, including a variety of resident lymphocytes, macrophages and dendritic cells. These cells serve a number of roles including mitigation of infection and to stimulate regeneration in response to damage. The transcription factor Cdx2, and to a lesser extent Cdx1, plays essential roles in intestinal homeostasis, and acts as a context-dependent tumour suppressor in colorectal cancer. Deletion of Cdx2 from the murine intestinal epithelium leads to macrophage infiltration resulting in a chronic inflammatory response. However the mechanisms by which Cdx2 loss evokes this response are poorly understood. To better understand this relationship, we used a conditional mouse model lacking all intestinal Cdx function to identify potential target genes which may contribute to this inflammatory phenotype. One such candidate encodes the histocompatability complex protein H2-T3, which functions to regulate intestinal iCD8α lymphocyte activity. We found that Cdx2 occupies the H3-T3 promoter in vivo and directly regulates its expression via a Cdx response element. Loss of Cdx function leads to a rapid and pronounced attenuation of H2-T3, followed by a decrease in iCD8α cell number, an increase in macrophage infiltration and activation of pro-inflammatory cascades. These findings suggest a previously unrecognized role for Cdx in intestinal homeostasis through H2-T3-dependent regulation of iCD8α cells.
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The Interplay between Nutrition, Innate Immunity, and the Commensal Microbiota in Adaptive Intestinal Morphogenesis. Nutrients 2021; 13:nu13072198. [PMID: 34206809 PMCID: PMC8308283 DOI: 10.3390/nu13072198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022] Open
Abstract
The gastrointestinal tract is a functionally and anatomically segmented organ that is colonized by microbial communities from birth. While the genetics of mouse gut development is increasingly understood, how nutritional factors and the commensal gut microbiota act in concert to shape tissue organization and morphology of this rapidly renewing organ remains enigmatic. Here, we provide an overview of embryonic mouse gut development, with a focus on the intestinal vasculature and the enteric nervous system. We review how nutrition and the gut microbiota affect the adaptation of cellular and morphologic properties of the intestine, and how these processes are interconnected with innate immunity. Furthermore, we discuss how nutritional and microbial factors impact the renewal and differentiation of the epithelial lineage, influence the adaptation of capillary networks organized in villus structures, and shape the enteric nervous system and the intestinal smooth muscle layers. Intriguingly, the anatomy of the gut shows remarkable flexibility to nutritional and microbial challenges in the adult organism.
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Yu Q, Kilik U, Holloway EM, Tsai YH, Harmel C, Wu A, Wu JH, Czerwinski M, Childs CJ, He Z, Capeling MM, Huang S, Glass IA, Higgins PDR, Treutlein B, Spence JR, Camp JG. Charting human development using a multi-endodermal organ atlas and organoid models. Cell 2021; 184:3281-3298.e22. [PMID: 34019796 PMCID: PMC8208823 DOI: 10.1016/j.cell.2021.04.028] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 12/11/2022]
Abstract
Organs are composed of diverse cell types that traverse transient states during organogenesis. To interrogate this diversity during human development, we generate a single-cell transcriptome atlas from multiple developing endodermal organs of the respiratory and gastrointestinal tract. We illuminate cell states, transcription factors, and organ-specific epithelial stem cell and mesenchyme interactions across lineages. We implement the atlas as a high-dimensional search space to benchmark human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) under multiple culture conditions. We show that HIOs recapitulate reference cell states and use HIOs to reconstruct the molecular dynamics of intestinal epithelium and mesenchyme emergence. We show that the mesenchyme-derived niche cue NRG1 enhances intestinal stem cell maturation in vitro and that the homeobox transcription factor CDX2 is required for regionalization of intestinal epithelium and mesenchyme in humans. This work combines cell atlases and organoid technologies to understand how human organ development is orchestrated.
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Affiliation(s)
- Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Umut Kilik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christoph Harmel
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ian A Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Peter D R Higgins
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland.
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Devall MA, Casey G. Controlling for cellular heterogeneity using single-cell deconvolution of gene expression reveals novel markers of colorectal tumors exhibiting microsatellite instability. Oncotarget 2021; 12:767-782. [PMID: 33889300 PMCID: PMC8057268 DOI: 10.18632/oncotarget.27935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
Approximately 15% of colorectal cancer (CRC) cases present with high levels of microsatellite instability (MSI-H). Bulk RNA-sequencing approaches have been employed to elucidate transcriptional differences between MSI-H and microsatellite stable (MSS) CRC tumors. These approaches are frequently confounded by the complex cellular heterogeneity of tumors. We performed single-cell deconvolution of bulk RNA-sequencing on The Cancer Genome Atlas colon adenocarcinoma (TCGA-COAD) dataset. Cell composition within each dataset was estimated using CIBERSORTx. Cell composition differences were analyzed using linear regression. Significant differences in abundance were observed for 13 of 19 cell types between MSI-H and MSS/MSI-L tumors in TCGA-COAD. This included a novel finding of increased enteroendocrine (q = 3.71E-06) and reduced colonocyte populations (q = 2.21E-03) in MSI-H versus MSS/MSI-L tumors. We were able to validate some of these differences in an independent biopsy dataset. By incorporating cell composition into our regression model, we identified 3,193 differentially expressed genes (q = 0.05), of which 556 were deemed novel. We subsequently validated many of these genes in an independent dataset of colon cancer cell lines. In summary, we show that some of the challenges associated with cellular heterogeneity can be overcome using single-cell deconvolution, and through our analysis we highlight several novel gene targets for further investigation.
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Affiliation(s)
- Matthew A.M. Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
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32
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Zhu Y, Hryniuk A, Foley T, Hess B, Lohnes D. Cdx2 Regulates Intestinal EphrinB1 through the Notch Pathway. Genes (Basel) 2021; 12:genes12020188. [PMID: 33525395 PMCID: PMC7911442 DOI: 10.3390/genes12020188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 01/23/2021] [Indexed: 01/07/2023] Open
Abstract
The majority of colorectal cancers harbor loss-of-function mutations in APC, a negative regulator of canonical Wnt signaling, leading to intestinal polyps that are predisposed to malignant progression. Comparable murine APC alleles also evoke intestinal polyps, which are typically confined to the small intestine and proximal colon, but do not progress to carcinoma in the absence of additional mutations. The Cdx transcription factors Cdx1 and Cdx2 are essential for homeostasis of the intestinal epithelium, and loss of Cdx2 has been associated with more aggressive subtypes of colorectal cancer in the human population. Consistent with this, concomitant loss of Cdx1 and Cdx2 in a murine APC mutant background leads to an increase in polyps throughout the intestinal tract. These polyps also exhibit a villous phenotype associated with the loss of EphrinB1. However, the basis for these outcomes is poorly understood. To further explore this, we modeled Cdx2 loss in SW480 colorectal cancer cells. We found that Cdx2 impacted Notch signaling in SW480 cells, and that EphrinB1 is a Notch target gene. As EphrinB1 loss also leads to a villus tumor phenotype, these findings evoke a mechanism by which Cdx2 impacts colorectal cancer via Notch-dependent EphrinB1 signaling.
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Affiliation(s)
- Yalun Zhu
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (Y.Z.); (A.H.); (T.F.); (B.H.)
| | - Alexa Hryniuk
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (Y.Z.); (A.H.); (T.F.); (B.H.)
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
| | - Tanya Foley
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (Y.Z.); (A.H.); (T.F.); (B.H.)
| | - Bradley Hess
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (Y.Z.); (A.H.); (T.F.); (B.H.)
| | - David Lohnes
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; (Y.Z.); (A.H.); (T.F.); (B.H.)
- Correspondence: ; Tel.: +1-613-562-5800 (ext. 8684)
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Sprangers J, Zaalberg IC, Maurice MM. Organoid-based modeling of intestinal development, regeneration, and repair. Cell Death Differ 2021; 28:95-107. [PMID: 33208888 PMCID: PMC7852609 DOI: 10.1038/s41418-020-00665-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
The intestinal epithelium harbors a remarkable adaptability to undergo injury-induced repair. A key part of the regenerative response is the transient reprogramming of epithelial cells into a fetal-like state, which drives uniform proliferation, tissue remodeling, and subsequent restoration of the homeostatic state. In this review, we discuss how Wnt and YAP signaling pathways control the intestinal repair response and the transitioning of cell states, in comparison with the process of intestinal development. Furthermore, we highlight how organoid-based applications have contributed to the characterization of the mechanistic principles and key players that guide these developmental and regenerative events.
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Affiliation(s)
- Joep Sprangers
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Irene C Zaalberg
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Madelon M Maurice
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium. Nat Rev Gastroenterol Hepatol 2021; 18:7-23. [PMID: 33024279 PMCID: PMC7997278 DOI: 10.1038/s41575-020-00357-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2020] [Indexed: 12/19/2022]
Abstract
The intestinal epithelium serves the unique and critical function of harvesting dietary nutrients, while simultaneously acting as a cellular barrier separating tissues from the luminal environment and gut microbial ecosystem. Two salient features of the intestinal epithelium enable it to perform these complex functions. First, cells within the intestinal epithelium achieve a wide range of specialized identities, including different cell types and distinct anterior-posterior patterning along the intestine. Second, intestinal epithelial cells are sensitive and responsive to the dynamic milieu of dietary nutrients, xenobiotics and microorganisms encountered in the intestinal luminal environment. These diverse identities and responsiveness of intestinal epithelial cells are achieved in part through the differential transcription of genes encoded in their shared genome. Here, we review insights from mice and other vertebrate models into the transcriptional regulatory mechanisms underlying intestinal epithelial identity and microbial responsiveness, including DNA methylation, chromatin accessibility, histone modifications and transcription factors. These studies are revealing that most transcription factors involved in intestinal epithelial identity also respond to changes in the microbiota, raising both opportunities and challenges to discern the underlying integrative transcriptional regulatory networks.
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CDX2 inhibits epithelial-mesenchymal transition in colorectal cancer by modulation of Snail expression and β-catenin stabilisation via transactivation of PTEN expression. Br J Cancer 2020; 124:270-280. [PMID: 33239678 PMCID: PMC7782852 DOI: 10.1038/s41416-020-01148-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/21/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
Background Emerging evidence suggests the involvement of caudal-related homoeobox transcription factor 2 (CDX2) in tumorigenesis of various cancers. Although CDX2 functions in cancer invasion and metastasis, fewer studies focus on the role of CDX2 during the induction of epithelial–mesenchymal transition (EMT) in colorectal cancer (CRC). Methods Immunohistochemical analysis of CDX2 was performed. A series of in vitro and in vivo experiments were conducted to reveal the role of CDX2 in the invasion and metastasis of CRC. Results CDX2 was downregulated in CRC tissues and reduced CDX2 correlated with poor prognosis. Knockdown of CDX2 promoted colon cancer cell invasion in vitro and facilitated liver metastasis in vivo with inducing EMT phenotypes. Further investigation indicated that CDX2 retarded Akt and GSK-3β phosphorylation, and thereby diminished Snail expression, β-catenin stabilisation and nuclear translocation. The depletion of β-catenin neutralised the regulation of Slug and ZEB1 by CDX2 knockdown. Mechanistically, CDX2 antagonised PI3K/Akt activity in CRC by modulating PTEN expression. CDX2 directly bound to the promoter of PTEN and transactivated its expression. Conclusions Our study first uncovered that CDX2 inhibits EMT and metastasis of CRC by regulation of Snail expression and β-catenin stabilisation via transactivation of PTEN expression. ![]()
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Naumovska E, Aalderink G, Wong Valencia C, Kosim K, Nicolas A, Brown S, Vulto P, Erdmann KS, Kurek D. Direct On-Chip Differentiation of Intestinal Tubules from Induced Pluripotent Stem Cells. Int J Mol Sci 2020; 21:ijms21144964. [PMID: 32674311 PMCID: PMC7404294 DOI: 10.3390/ijms21144964] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/03/2020] [Accepted: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
Intestinal organoids have emerged as the new paradigm for modelling the healthy and diseased intestine with patient-relevant properties. In this study, we show directed differentiation of induced pluripotent stem cells towards intestinal-like phenotype within a microfluidic device. iPSCs are cultured against a gel in microfluidic chips of the OrganoPlate, in which they undergo stepwise differentiation. Cells form a tubular structure, lose their stem cell markers and start expressing mature intestinal markers, including markers for Paneth cells, enterocytes and neuroendocrine cells. Tubes develop barrier properties as confirmed by transepithelial electrical resistance (TEER). Lastly, we show that tubules respond to pro-inflammatory cytokine triggers. The whole procedure for differentiation lasts 14 days, making it an efficient process to make patient-specific organoid tubules. We anticipate the usage of the platform for disease modelling and drug candidate screening.
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Affiliation(s)
- Elena Naumovska
- Mimetas BV, Model Development, J.H. Oortweg 16, 2333 CH Leiden, The Netherlands; (E.N.); (G.A.); (K.K.); (A.N.); (P.V.)
- Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; (C.W.V.); (S.B.)
| | - Germaine Aalderink
- Mimetas BV, Model Development, J.H. Oortweg 16, 2333 CH Leiden, The Netherlands; (E.N.); (G.A.); (K.K.); (A.N.); (P.V.)
| | - Christian Wong Valencia
- Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; (C.W.V.); (S.B.)
| | - Kinga Kosim
- Mimetas BV, Model Development, J.H. Oortweg 16, 2333 CH Leiden, The Netherlands; (E.N.); (G.A.); (K.K.); (A.N.); (P.V.)
- Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; (C.W.V.); (S.B.)
| | - Arnaud Nicolas
- Mimetas BV, Model Development, J.H. Oortweg 16, 2333 CH Leiden, The Netherlands; (E.N.); (G.A.); (K.K.); (A.N.); (P.V.)
| | - Stephen Brown
- Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; (C.W.V.); (S.B.)
| | - Paul Vulto
- Mimetas BV, Model Development, J.H. Oortweg 16, 2333 CH Leiden, The Netherlands; (E.N.); (G.A.); (K.K.); (A.N.); (P.V.)
| | - Kai S. Erdmann
- Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; (C.W.V.); (S.B.)
- Correspondence: (K.S.E.); (D.K.)
| | - Dorota Kurek
- Mimetas BV, Model Development, J.H. Oortweg 16, 2333 CH Leiden, The Netherlands; (E.N.); (G.A.); (K.K.); (A.N.); (P.V.)
- Correspondence: (K.S.E.); (D.K.)
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Kostouros A, Koliarakis I, Natsis K, Spandidos DA, Tsatsakis A, Tsiaoussis J. Large intestine embryogenesis: Molecular pathways and related disorders (Review). Int J Mol Med 2020; 46:27-57. [PMID: 32319546 PMCID: PMC7255481 DOI: 10.3892/ijmm.2020.4583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
The large intestine, part of the gastrointestinal tract (GI), is composed of all three germ layers, namely the endoderm, the mesoderm and the ectoderm, forming the epithelium, the smooth muscle layers and the enteric nervous system, respectively. Since gastrulation, these layers develop simultaneously during embryogenesis, signaling to each other continuously until adult age. Two invaginations, the anterior intestinal portal (AIP) and the caudal/posterior intestinal portal (CIP), elongate and fuse, creating the primitive gut tube, which is then patterned along the antero‑posterior (AP) axis and the radial (RAD) axis in the context of left‑right (LR) asymmetry. These events lead to the formation of three distinct regions, the foregut, midgut and hindgut. All the above‑mentioned phenomena are under strict control from various molecular pathways, which are critical for the normal intestinal development and function. Specifically, the intestinal epithelium constitutes a constantly developing tissue, deriving from the progenitor stem cells at the bottom of the intestinal crypt. Epithelial differentiation strongly depends on the crosstalk with the adjacent mesoderm. Major molecular pathways that are implicated in the embryogenesis of the large intestine include the canonical and non‑canonical wingless‑related integration site (Wnt), bone morphogenetic protein (BMP), Notch and hedgehog systems. The aberrant regulation of these pathways inevitably leads to several intestinal malformation syndromes, such as atresia, stenosis, or agangliosis. Novel theories, involving the regulation and homeostasis of intestinal stem cells, suggest an embryological basis for the pathogenesis of colorectal cancer (CRC). Thus, the present review article summarizes the diverse roles of these molecular factors in intestinal embryogenesis and related disorders.
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Affiliation(s)
- Antonios Kostouros
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion
| | - Ioannis Koliarakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion
| | - Konstantinos Natsis
- Department of Anatomy and Surgical Anatomy, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki
| | | | - Aristidis Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, 71409 Heraklion, Greece
| | - John Tsiaoussis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion
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Wesolowska-Andersen A, Jensen RR, Alcántara MP, Beer NL, Duff C, Nylander V, Gosden M, Witty L, Bowden R, McCarthy MI, Hansson M, Gloyn AL, Honore C. Analysis of Differentiation Protocols Defines a Common Pancreatic Progenitor Molecular Signature and Guides Refinement of Endocrine Differentiation. Stem Cell Reports 2019; 14:138-153. [PMID: 31883919 PMCID: PMC6962645 DOI: 10.1016/j.stemcr.2019.11.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 11/29/2019] [Accepted: 11/29/2019] [Indexed: 12/30/2022] Open
Abstract
Several distinct differentiation protocols for deriving pancreatic progenitors (PPs) from human pluripotent stem cells have been described, but it remains to be shown how similar the PPs are across protocols and how well they resemble their in vivo counterparts. Here, we evaluated three differentiation protocols, performed RNA and assay for transposase-accessible chromatin using sequencing on isolated PPs derived with these, and compared them with fetal human pancreas populations. This enabled us to define a shared transcriptional and epigenomic signature of the PPs, including several genes not previously implicated in pancreas development. Furthermore, we identified a significant and previously unappreciated cross-protocol variation of the PPs through multi-omics analysis and demonstrate how such information can be applied to refine differentiation protocols for derivation of insulin-producing beta-like cells. Together, our study highlights the importance of a detailed characterization of defined cell populations derived from distinct differentiation protocols and provides a valuable resource for exploring human pancreatic development.
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Affiliation(s)
| | | | | | - Nicola L. Beer
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, OX3 7LE Oxford, UK
| | - Claire Duff
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, OX3 7LE Oxford, UK
| | - Vibe Nylander
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, OX3 7LE Oxford, UK
| | - Matthew Gosden
- The MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Lorna Witty
- Wellcome Centre Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Rory Bowden
- Wellcome Centre Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Mark I. McCarthy
- Wellcome Centre Human Genetics, University of Oxford, OX3 7BN Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, OX3 7LE Oxford, UK,NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | | | - Anna L. Gloyn
- Wellcome Centre Human Genetics, University of Oxford, OX3 7BN Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, OX3 7LE Oxford, UK,NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | - Christian Honore
- Stem Cell R&D, Novo Nordisk A/S, 2760 Måløv, Denmark,Corresponding author
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Chen L, Toke NH, Luo S, Vasoya RP, Aita R, Parthasarathy A, Tsai YH, Spence JR, Verzi MP. HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine. Development 2019; 146:dev.179432. [PMID: 31345929 DOI: 10.1242/dev.179432] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022]
Abstract
As embryos mature, cells undergo remarkable transitions that are accompanied by shifts in transcription factor regulatory networks. Mechanisms driving developmental transitions are incompletely understood. The embryonic intestine transitions from a rapidly proliferating tube with pseudostratified epithelium prior to murine embryonic day (E) 14.5 to an exquisitely folded columnar epithelium in fetal stages. We sought to identify factors driving mouse fetal intestinal maturation by mining chromatin accessibility data for transcription factor motifs. ATAC-seq accessible regions shift during tissue maturation, with CDX2 transcription factor motifs abundant at chromatin-accessible regions of the embryo. Hepatocyte nuclear factor 4 (HNF4) transcription factor motifs are the most abundant in the fetal stages (>E16.5). Genetic inactivation of Hnf4a and its paralog Hnf4g revealed that HNF4 factors are redundantly required for fetal maturation. CDX2 binds to and activates Hnf4 gene loci to elevate HNF4 expression at fetal stages. HNF4 and CDX2 transcription factors then occupy shared genomic regulatory sites to promote chromatin accessibility and gene expression in the maturing intestine. Thus, HNF4 paralogs are key components of an intestinal transcription factor network shift during the embryonic to fetal transition.
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Affiliation(s)
- Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Natalie H Toke
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Shirley Luo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Roshan P Vasoya
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Rohit Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Aditya Parthasarathy
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA.,Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
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Foley TE, Hess B, Savory JGA, Ringuette R, Lohnes D. Role of Cdx factors in early mesodermal fate decisions. Development 2019; 146:146/7/dev170498. [PMID: 30936115 DOI: 10.1242/dev.170498] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 03/01/2019] [Indexed: 12/30/2022]
Abstract
Murine cardiac and hematopoietic progenitors are derived from Mesp1+ mesoderm. Cdx function impacts both yolk sac hematopoiesis and cardiogenesis in zebrafish, suggesting that Cdx family members regulate early mesoderm cell fate decisions. We found that Cdx2 occupies a number of transcription factor loci during embryogenesis, including key regulators of both cardiac and blood development, and that Cdx function is required for normal expression of the cardiogenic transcription factors Nkx2-5 and Tbx5 Furthermore, Cdx and Brg1, an ATPase subunit of the SWI/SNF chromatin remodeling complex, co-occupy a number of loci, suggesting that Cdx family members regulate target gene expression through alterations in chromatin architecture. Consistent with this, we demonstrate loss of Brg1 occupancy and altered chromatin structure at several cardiogenic genes in Cdx-null mutants. Finally, we provide evidence for an onset of Cdx2 expression at E6.5 coinciding with egression of cardiac progenitors from the primitive streak. Together, these findings suggest that Cdx functions in multi-potential mesoderm to direct early cell fate decisions through transcriptional regulation of several novel target genes, and provide further insight into a potential epigenetic mechanism by which Cdx influences target gene expression.
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Affiliation(s)
- Tanya E Foley
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Bradley Hess
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Joanne G A Savory
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Randy Ringuette
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - David Lohnes
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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Kumar N, Tsai YH, Chen L, Zhou A, Banerjee KK, Saxena M, Huang S, Toke NH, Xing J, Shivdasani RA, Spence JR, Verzi MP. The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development. Development 2019; 146:dev172189. [PMID: 30745430 PMCID: PMC6432663 DOI: 10.1242/dev.172189] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/30/2019] [Indexed: 12/11/2022]
Abstract
Lineage-restricted transcription factors, such as the intestine-specifying factor CDX2, often have dual requirements across developmental time. Embryonic loss of CDX2 triggers homeotic transformation of intestinal fate, whereas adult-onset loss compromises crucial physiological functions but preserves intestinal identity. It is unclear how such diverse requirements are executed across the developmental continuum. Using primary and engineered human tissues, mouse genetics, and a multi-omics approach, we demonstrate that divergent CDX2 loss-of-function phenotypes in embryonic versus adult intestines correspond to divergent CDX2 chromatin-binding profiles in embryonic versus adult stages. CDX2 binds and activates distinct target genes in developing versus adult mouse and human intestinal cells. We find that temporal shifts in chromatin accessibility correspond to these context-specific CDX2 activities. Thus, CDX2 is not sufficient to activate a mature intestinal program; rather, CDX2 responds to its environment, targeting stage-specific genes to contribute to either intestinal patterning or mature intestinal function. This study provides insights into the mechanisms through which lineage-specific regulatory factors achieve divergent functions over developmental time.
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Affiliation(s)
- Namit Kumar
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lei Chen
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Anbo Zhou
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Kushal K Banerjee
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Madhurima Saxena
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Sha Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natalie H Toke
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Jinchuan Xing
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Jason R Spence
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Rutgers, the State University of New Jersey, Department of Genetics, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, and Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
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Li X, Zhang C, Gong T, Ni X, Li J, Zhan D, Liu M, Song L, Ding C, Xu J, Zhen B, Wang Y, Qin J. A time-resolved multi-omic atlas of the developing mouse stomach. Nat Commun 2018; 9:4910. [PMID: 30464175 PMCID: PMC6249217 DOI: 10.1038/s41467-018-07463-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023] Open
Abstract
The mammalian stomach is structurally highly diverse and its organ functionality critically depends on a normal embryonic development. Although there have been several studies on the morphological changes during stomach development, a system-wide analysis of the underlying molecular changes is lacking. Here, we present a comprehensive, temporal proteome and transcriptome atlas of the mouse stomach at multiple developmental stages. Quantitative analysis of 12,108 gene products allows identifying three distinct phases based on changes in proteins and RNAs and the gain of stomach functions on a longitudinal time scale. The transcriptome indicates functionally important isoforms relevant to development and identifies several functionally unannotated novel splicing junction transcripts that we validate at the peptide level. Importantly, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer. Overall, our study provides a resource to understand stomach development and its connection to gastric cancer tumorigenesis.
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Affiliation(s)
- Xianju Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Chunchao Zhang
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tongqing Gong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Xiaotian Ni
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.,Department of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jin'e Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China.,Department of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Jianming Xu
- Department of Gastrointestinal Oncology, Affiliated Hospital Cancer Center, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Bei Zhen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, China. .,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.
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43
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Role of AMP activated protein kinase signaling pathway in intestinal development of mammals. Ann Anat 2018; 220:51-54. [DOI: 10.1016/j.aanat.2018.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 12/31/2022]
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Banerjee KK, Saxena M, Kumar N, Chen L, Cavazza A, Toke NH, O'Neill NK, Madha S, Jadhav U, Verzi MP, Shivdasani RA. Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development. Genes Dev 2018; 32:1430-1442. [PMID: 30366903 PMCID: PMC6217732 DOI: 10.1101/gad.318832.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
After acquiring competence for selected cell fates, embryonic primordia may remain plastic for variable periods before tissue identity is irrevocably determined. Banerjee et al. show that the midgut endoderm is primed for heterologous cell fates and that transcription factors act on a background of shifting chromatin access to determine intestinal at the expense of foregut identity. After acquiring competence for selected cell fates, embryonic primordia may remain plastic for variable periods before tissue identity is irrevocably determined (commitment). We investigated the chromatin basis for these developmental milestones in mouse endoderm, a tissue with recognizable rostro–caudal patterning and transcription factor (TF)-dependent interim plasticity. Foregut-specific enhancers are as accessible and active in early midgut as in foregut endoderm, and intestinal enhancers and identity are established only after ectopic cis-regulatory elements are decommissioned. Depletion of the intestinal TF CDX2 before this cis element transition stabilizes foregut enhancers, reinforces ectopic transcriptional programs, and hence imposes foregut identities on the midgut. Later in development, as the window of chromatin plasticity elapses, CDX2 depletion weakens intestinal, without strengthening foregut, enhancers. Thus, midgut endoderm is primed for heterologous cell fates, and TFs act on a background of shifting chromatin access to determine intestinal at the expense of foregut identity. Similar principles likely govern other fate commitments.
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Affiliation(s)
- Kushal K Banerjee
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Madhurima Saxena
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Namit Kumar
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Lei Chen
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Alessia Cavazza
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Natalie H Toke
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Nicholas K O'Neill
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Shariq Madha
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Unmesh Jadhav
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA.,Cancer Institute of New Jersey, Piscataway, New Jersey 08854, USA.,Human Genetics Institute of New Jersey, Piscataway, New Jersey 08854, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02139, USA
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Shigematsu Y, Inamura K, Yamamoto N, Mise Y, Saiura A, Ishikawa Y, Takahashi S, Kanda H. Impact of CDX2 expression status on the survival of patients after curative resection for colorectal cancer liver metastasis. BMC Cancer 2018; 18:980. [PMID: 30326864 PMCID: PMC6192098 DOI: 10.1186/s12885-018-4902-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The prognostic biomarker for patients undergoing curative liver metastasectomy for colorectal cancer (CRC) is lacking. The purpose was to investigate the prognostic role of a lack of CDX2 expression, which has been proposed as a potential biomarker for high-risk relapse in early-stage CRC, in patients undergoing curative liver metastasectomy. METHODS A total of 396 consecutive patients with CRC liver metastasis who underwent potentially curative liver metastasectomy at a single center in Japan between 2005 and 2015 were included. For the immunohistochemical analysis of nuclear CDX2 expression, we adopted the tissue microarray approach using the resected metastatic liver CRCs. Patient subgroups were compared with respect to disease-free survival (DFS) and overall survival (OS) by applying the Kaplan-Meier curve, log-rank tests, and multivariate analyses based on the Cox proportional hazards method. OS is defined as the period from the date of curative liver resection for metastatic CRC until death. DFS is defined as the length of time from curative liver resection to either the first recurrence or death. In patients without recurrence, the latest imaging inspection date was used as the censored date. RESULTS Thirty-six of the 396 CRCs (9.1%) reduced CDX2 expression. The reduced expression of CDX2 was associated with poor differentiation (P = 0.02). DFS in days was lower in the patients with CDX2-low CRC than in the patients with CDX2-high CRC (median DFS: 245 days versus 420 days; hazard ratio for disease recurrence: 1.64; 95% confidence interval: 1.08-2.38; P = 0.02). OS in days was lower in the patients with CDX2-low CRC than in the patients with CDX2-high CRC (median OS: 1024 days versus 3145 days; hazard ratio: 2.41; 95% confidence interval: 1.52-3.85; P < 0.001). In patients with CDX2-low CRC, both DFS and OS were similar between the with and without pre- or post-operative chemotherapy groups (median DFS: 243 versus 247 days; P = 0.73, median OS: 1016 versus 1363 days; P = 0.69). CONCLUSIONS Reduced expression of CDX2 indicates poor DFS and OS, however, it might not represent chemosensitivity in patients undergoing curative liver metastasectomy. (339/350).
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Affiliation(s)
- Yasuyuki Shigematsu
- Department of Pathology, The Cancer Institute of Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan.
| | - Kentaro Inamura
- Department of Pathology, The Cancer Institute of Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
| | - Noriko Yamamoto
- Department of Pathology, The Cancer Institute of Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
| | - Yoshihiro Mise
- Division of Gastroenterology Center, The Cancer Institute Hospital, JFCR, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
| | - Akio Saiura
- Division of Gastroenterology Center, The Cancer Institute Hospital, JFCR, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
| | - Yuichi Ishikawa
- Department of Pathology, The Cancer Institute of Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
| | - Shunji Takahashi
- Division of General Oncology, The Cancer Institute Hospital, JFCR, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
| | - Hiroaki Kanda
- Department of Pathology, The Cancer Institute of Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan.,Department of Pathology, Saitama Cancer Center, 780 Komuro, Ina, Kita-adachi-gun, Saitama, 362-0806, Japan
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Abstract
Chronic injury and inflammation in the esophagus can cause a change in cellular differentiation known as metaplasia. Most commonly, the differentiation changes manifest as Barrett's esophagus (BE), characterized by the normal stratified squamous epithelium converting into a cuboidal-columnar, glandular morphology. BE cells can phenotypically resemble specific normal cell types of the stomach or intestine, or they can have overlapping phenotypes in disorganized admixtures. The stomach can also undergo metaplasia characterized by aberrant gastric or intestinal differentiation patterns. In both organs, it has been argued that metaplasia may represent a recapitulation of the embryonic or juvenile gastrointestinal tract, as cells access a developmental progenitor genetic program that can help repair damaged tissue. Here, we review the normal development of esophagus and stomach, and describe how BE represents an intermixing of cells resembling gastric pseudopyloric (SPEM) and intestinal metaplasia. We discuss a cellular process recently termed "paligenosis" that governs how mature, differentiated cells can revert to a proliferating progenitor state in metaplasia. We discuss the "Cyclical Hit" theory in which paligenosis might be involved in the increased risk of metaplasia for progression to cancer. However, somatic mutations might occur in proliferative phases and then be warehoused upon redifferentiation. Through years of chronic injury and many rounds of paligenosis and dedifferentiation, eventually a cell with a mutation that prevents dedifferentiation may arise and clonally expand fueling stable metaplasia and potentially thereafter acquiring additional mutations and progressing to dysplasia and cancer.
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Affiliation(s)
- Ramon U Jin
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason C Mills
- Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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Id2 Determines Intestinal Identity through Repression of the Foregut Transcription Factor Irx5. Mol Cell Biol 2018; 38:MCB.00250-17. [PMID: 29463648 PMCID: PMC5902590 DOI: 10.1128/mcb.00250-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 02/13/2018] [Indexed: 12/12/2022] Open
Abstract
The cellular components and function of the gastrointestinal epithelium exhibit distinct characteristics depending on the region, e.g., stomach or intestine. How these region-specific epithelial characteristics are generated during development remains poorly understood. Here, we report on the involvement of the helix-loop-helix inhibitor Id2 in establishing the specific characteristics of the intestinal epithelium. Id2−/− mice developed tumors in the small intestine. Histological analysis indicated that the intestinal tumors were derived from gastric metaplasia formed in the small intestine during development. Heterotopic Id2 expression in developing gastric epithelium induced a fate change to intestinal epithelium. Gene expression analysis revealed that foregut-enriched genes encoding Irx3 and Irx5 were highly induced in the midgut of Id2−/− embryos, and transgenic mice expressing Irx5 in the midgut endoderm developed tumors recapitulating the characteristics of Id2−/− mice. Altogether, our results demonstrate that Id2 plays a crucial role in the development of regional specificity in the gastrointestinal epithelium.
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48
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CDX2 expression is concordant between primary colorectal cancer lesions and corresponding liver metastases independent of chemotherapy: a single-center retrospective study in Japan. Oncotarget 2018; 9:17056-17065. [PMID: 29682204 PMCID: PMC5908305 DOI: 10.18632/oncotarget.24842] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 02/28/2018] [Indexed: 01/17/2023] Open
Abstract
Objective Loss of caudal-type homeobox transcription factor 2 (CDX2) expression in colorectal cancers (CRCs) has recently been proposed as a promising predictive biomarker for not only prognosis but also response to chemotherapy. However, the relationship between alterations in CDX2 expression during cancer progression and response to chemotherapy remains unclear. We herein aimed to determine the concordance of CDX2 expression between primary CRCs and corresponding liver metastases, in association with chemotherapy. Results Primary CRCs exhibited heterogeneous CDX2 expression. Seven of the 144 CRCs in the cohort (4.9%, 95% confidential interval, 2.0%–9.8%) were CDX2-negative. The concordance rate of the CDX2 expression status in patients who did not receive chemotherapy was 100% (P = 0.041), whereas the concordance rate among patients who received chemotherapy only after primary resection was 96.3% (P = 0.005). Moreover, the concordance rate in patients who received chemotherapy before both primary resection and liver metastasectomy was 100% (P < 0.001). Conclusion CDX2 expression status was highly concordant between primary CRCs and corresponding liver metastases, independent of chemotherapy, suggesting that the CDX2 expression status in CRCs was not affected by metastasis or chemotherapy. Methods A total of 144 consecutive patients with CRC who were treated at a single center in Japan between 2006 and 2014 were included. Formalin-fixed paraffin-embedded whole sections of surgically resected primary CRCs and corresponding liver metastases were assessed for CDX2 expression by immunohistochemistry.
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Thompson CA, DeLaForest A, Battle MA. Patterning the gastrointestinal epithelium to confer regional-specific functions. Dev Biol 2018; 435:97-108. [PMID: 29339095 PMCID: PMC6615902 DOI: 10.1016/j.ydbio.2018.01.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/01/2018] [Accepted: 01/10/2018] [Indexed: 12/12/2022]
Abstract
The gastrointestinal (GI) tract, in simplest terms, can be described as an epithelial-lined muscular tube extending along the cephalocaudal axis from the oral cavity to the anus. Although the general architecture of the GI tract organs is conserved from end to end, the presence of different epithelial tissue structures and unique epithelial cell types within each organ enables each to perform the distinct digestive functions required for efficient nutrient assimilation. Spatiotemporal regulation of signaling pathways and downstream transcription factors controls GI epithelial morphogenesis during development to confer essential regional-specific epithelial structures and functions. Here, we discuss the fundamental functions of each GI tract organ and summarize the diversity of epithelial structures present along the cephalocaudal axis of the GI tract. Next, we discuss findings, primarily from genetic mouse models, that have defined the roles of key transcription factors during epithelial morphogenesis, including p63, SOX2, SOX15, GATA4, GATA6, HNF4A, and HNF4G. Additionally, we examine how the Hedgehog, WNT, and BMP signaling pathways contribute to defining unique epithelial features along the cephalocaudal axis of the GI tract. Lastly, we examine the molecular mechanisms controlling regionalized cytodifferentiation of organ-specific epithelial cell types within the GI tract, concentrating on the stomach and small intestine. The delineation of GI epithelial patterning mechanisms in mice has provided fundamental knowledge to guide the development and refinement of three-dimensional GI organotypic culture models such as those derived from directed differentiation of human pluripotent stem cells and those derived directly from human tissue samples. Continued examination of these pathways will undoubtedly provide vital insights into the mechanisms of GI development and disease and may afford new avenues for innovative tissue engineering and personalized medicine approaches to treating GI diseases.
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Affiliation(s)
- Cayla A Thompson
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Ann DeLaForest
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Michele A Battle
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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Delker DA, Wood AC, Snow AK, Samadder NJ, Samowitz WS, Affolter KE, Boucher KM, Pappas LM, Stijleman IJ, Kanth P, Byrne KR, Burt RW, Bernard PS, Neklason DW. Chemoprevention with Cyclooxygenase and Epidermal Growth Factor Receptor Inhibitors in Familial Adenomatous Polyposis Patients: mRNA Signatures of Duodenal Neoplasia. Cancer Prev Res (Phila) 2018; 11:4-15. [PMID: 29109117 PMCID: PMC5754246 DOI: 10.1158/1940-6207.capr-17-0130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/31/2017] [Accepted: 10/02/2017] [Indexed: 12/20/2022]
Abstract
To identify gene expression biomarkers and pathways targeted by sulindac and erlotinib given in a chemoprevention trial with a significant decrease in duodenal polyp burden at 6 months (P < 0.001) in familial adenomatous polyposis (FAP) patients, we biopsied normal and polyp duodenal tissues from patients on drug versus placebo and analyzed the RNA expression. RNA sequencing was performed on biopsies from the duodenum of FAP patients obtained at baseline and 6-month endpoint endoscopy. Ten FAP patients on placebo and 10 on sulindac and erlotinib were selected for analysis. Purity of biopsied polyp tissue was calculated from RNA expression data. RNAs differentially expressed between endpoint polyp and paired baseline normal were determined for each group and mapped to biological pathways. Key genes in candidate pathways were further validated by quantitative RT-PCR. RNA expression analyses of endpoint polyp compared with paired baseline normal for patients on placebo and drug show that pathways activated in polyp growth and proliferation are blocked by this drug combination. Directly comparing polyp gene expression between patients on drug and placebo also identified innate immune response genes (IL12 and IFNγ) preferentially expressed in patients on drug. Gene expression analyses from tissue obtained at endpoint of the trial demonstrated inhibition of the cancer pathways COX2/PGE2, EGFR, and WNT. These findings provide molecular evidence that the drug combination of sulindac and erlotinib reached the intended tissue and was on target for the predicted pathways. Furthermore, activation of innate immune pathways from patients on drug may have contributed to polyp regression. Cancer Prev Res; 11(1); 4-15. ©2017 AACRSee related editorial by Shureiqi, p. 1.
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Affiliation(s)
- Don A Delker
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Austin C Wood
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Angela K Snow
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - N Jewel Samadder
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Wade S Samowitz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Kajsa E Affolter
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Kenneth M Boucher
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Lisa M Pappas
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Inge J Stijleman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Priyanka Kanth
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Kathryn R Byrne
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Randall W Burt
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Philip S Bernard
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Deborah W Neklason
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
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