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Ma H, Srivastava S, Ho SWT, Xu C, Lian BSX, Ong X, Tay ST, Sheng T, Lum HYJ, Abdul Ghani SAB, Chu Y, Huang KK, Goh YT, Lee M, Hagihara T, Ng CSY, Tan ALK, Zhang Y, Ding Z, Zhu F, Ng MSW, Joseph CRC, Chen H, Li Z, Zhao JJ, Rha SY, Teh M, Yeong J, Yong WP, So JBY, Sundar R, Tan P. Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution. Cancer Discov 2025; 15:767-792. [PMID: 39774838 PMCID: PMC11962405 DOI: 10.1158/2159-8290.cd-24-0605] [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: 05/03/2024] [Revised: 10/17/2024] [Accepted: 01/06/2025] [Indexed: 01/11/2025]
Abstract
SIGNIFICANCE Integration of spatial transcriptomic (GeoMx Digital Spatial Profiler) and single-cell RNA sequencing data from multiple gastric cancers identifies spatially resolved expression-based intratumoral heterogeneity, associated with distinct immune microenvironments. We uncovered two separate evolutionary trajectories associated with specific molecular subtypes, clinical prognoses, stromal neighborhoods, and genetic drivers. Tumor-stroma interfaces emerged as a unique state of tumor ecology.
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Affiliation(s)
- Haoran Ma
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shamaine Wei Ting Ho
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Chang Xu
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | | | - Xuewen Ong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Su Ting Tay
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Taotao Sheng
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | | | - Yunqiang Chu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Kie Kyon Huang
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Yeek Teck Goh
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Minghui Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Takeshi Hagihara
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Clara Shi Ya Ng
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Angie Lay Keng Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Yanrong Zhang
- Department of Information Systems and Analytics, School of Computing, National University of Singapore, Singapore, Singapore
| | - Zichen Ding
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michelle Shu Wen Ng
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Craig Ryan Cecil Joseph
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Hui Chen
- MGI Tech Singapore Pte. Ltd., Singapore, Singapore
| | - Zhen Li
- MGI Tech Singapore Pte. Ltd., Singapore, Singapore
| | - Joseph J. Zhao
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
| | - Sun Young Rha
- Yonsei Cancer Center, Yonsei University Health System, Seoul, Republic of Korea
- Songdang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ming Teh
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joe Yeong
- Department of Pathology, National University Hospital, Singapore, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wei Peng Yong
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore, Singapore
| | - Jimmy Bok-Yan So
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore, Singapore
- Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
- Division of Surgical Oncology, National University Cancer Institute, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Raghav Sundar
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore, Singapore
- The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cellular and Molecular Research, National Cancer Centre, Singapore, Singapore
- Singhealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, Singapore
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Nishio R, Nakanaga K, Yoshinaga R, Kurihara A, Okano F. Development and validation of an antidrug antibody assay for TRK-950 using Melon™ gel and SPEAD pretreatment. Bioanalysis 2025; 17:515-524. [PMID: 40243353 DOI: 10.1080/17576180.2025.2493607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 04/08/2025] [Indexed: 04/18/2025] Open
Abstract
AIM & METHODS TRK-950, a humanized IgG1 monoclonal antibody against CAPRIN-1, which is reported to be expressed on the cell surface of various forms of cancer, is currently being developed for multiple types of solid cancer. We developed an antidrug antibody (ADA) assay that includes two pretreatment processes for use in clinical trials, namely, Melon™ gel treatment and solid-phase extraction with acid dissociation (SPEAD), to reduce baseline variability between individual serum samples and improve drug tolerance. RESULTS Comparing the assay with or without the pretreatment process using commercially available human serum samples, the mean response calculated from 18 individual human samples decreased from 327 to 270, and the coefficient of variation decreased from 41% to 16%. The new assay with the two-step pretreatment met the criteria set by the regulatory agency throughout the validation study. We also confirmed the recovery rates of IgG, IgM, and ADA - drug immune complexes after treatment with Melon™ gel. Clinical trials (NCT05423262) employing this improved analytical method have been conducted, and the results confirm the low immunogenicity of TRK-950. CONCLUSION The combination of pretreatment with Melon™ gel and SPEAD is applicable for clinical ADA assays.
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Affiliation(s)
- Reiji Nishio
- New Projects Development Division, Toray Industries, Inc, Kamakura, Japan
| | - Keita Nakanaga
- New Frontiers Research Laboratories, Toray Industries, Inc, Kamakura, Japan
| | - Ryosuke Yoshinaga
- Biomedical Analysis Laboratories, Toray Research Center, Inc, Kamakura, Japan
| | - Akira Kurihara
- New Projects Development Division, Toray Industries, Inc, Kamakura, Japan
| | - Fumiyoshi Okano
- New Projects Development Division, Toray Industries, Inc, Kamakura, Japan
- New Frontiers Research Laboratories, Toray Industries, Inc, Kamakura, Japan
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Zhang H, Kapitonova E, Orrego A, Spanos C, Strachan J, Bayne EH. Fission yeast Caprin protein is required for efficient heterochromatin establishment. PLoS Genet 2025; 21:e1011620. [PMID: 40063661 PMCID: PMC11918387 DOI: 10.1371/journal.pgen.1011620] [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: 09/19/2024] [Revised: 03/18/2025] [Accepted: 02/12/2025] [Indexed: 03/20/2025] Open
Abstract
Heterochromatin is a key feature of eukaryotic genomes that serves important regulatory and structural roles in regions such as centromeres. In fission yeast, maintenance of existing heterochromatic domains relies on positive feedback loops involving histone methylation and non-coding RNAs. However, requirements for de novo establishment of heterochromatin are less well understood. Here, through a cross-based assay we have identified a novel factor influencing the efficiency of heterochromatin establishment. We determine that the previously uncharacterised protein is an ortholog of human Caprin1, an RNA-binding protein linked to stress granule formation. We confirm that the fission yeast ortholog, here named Cpn1, also associates with stress granules, and we uncover evidence of interplay between heterochromatin integrity and ribonucleoprotein (RNP) granule formation, with heterochromatin mutants showing reduced granule formation in the presence of stress, but increased granule formation in the absence of stress. We link this to regulation of non-coding heterochromatic transcripts, since in heterochromatin-deficient cells, Cpn1 can be seen to colocalise with accumulating pericentromeric transcripts, and absence of Cpn1 leads to hyperaccumulation of these RNAs at centromeres. Together, our findings unveil a novel link between RNP homeostasis and heterochromatin assembly, and implicate Cpn1 and associated factors in facilitating efficient heterochromatin establishment by enabling removal of excess transcripts that would otherwise impair assembly processes.
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Affiliation(s)
- Haidao Zhang
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ekaterina Kapitonova
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Adriana Orrego
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Christos Spanos
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Joanna Strachan
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Elizabeth H. Bayne
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Wofford W, Kim J, Kim D, Janneh AH, Lee HG, Atilgan FC, Oleinik N, Kassir MF, Saatci O, Chakraborty P, Tokat UM, Gencer S, Howley B, Howe P, Mehrotra S, Sahin O, Ogretmen B. Alterations of ceramide synthesis induce PD-L1 internalization and signaling to regulate tumor metastasis and immunotherapy response. Cell Rep 2024; 43:114532. [PMID: 39046874 PMCID: PMC11404065 DOI: 10.1016/j.celrep.2024.114532] [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: 01/09/2024] [Revised: 05/17/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
Programmed death ligand 1, PD-L1 (CD274), facilitates immune evasion and exerts pro-survival functions in cancer cells. Here, we report a mechanism whereby internalization of PD-L1 in response to alterations of bioactive lipid/ceramide metabolism by ceramide synthase 4 (CerS4) induces sonic hedgehog (Shh) and transforming growth factor β receptor signaling to enhance tumor metastasis in triple-negative breast cancers (TNBCs), exhibiting immunotherapy resistance. Mechanistically, data showed that internalized PD-L1 interacts with an RNA-binding protein, caprin-1, to stabilize Shh/TGFBR1/Wnt mRNAs to induce β-catenin signaling and TNBC growth/metastasis, consistent with increased infiltration of FoxP3+ regulatory T cells and resistance to immunotherapy. While mammary tumors developed in MMTV-PyMT/CerS4-/- were highly metastatic, targeting the Shh/PD-L1 axis using sonidegib and anti-PD-L1 antibody vastly decreased tumor growth and metastasis, consistent with the inhibition of PD-L1 internalization and Shh/Wnt signaling, restoring anti-tumor immune response. These data, validated in clinical samples and databases, provide a mechanism-based therapeutic strategy to improve immunotherapy responses in metastatic TNBCs.
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Affiliation(s)
- Wyatt Wofford
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Jisun Kim
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Dosung Kim
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Alhaji H Janneh
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Han Gyul Lee
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - F Cansu Atilgan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Natalia Oleinik
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Mohamed Faisal Kassir
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Ozge Saatci
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Paramita Chakraborty
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Department of Surgery, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Unal Metin Tokat
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Salih Gencer
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Istanbul Medipol University, Health Science and Technologies Research Institute (SABİTA), Cancer Research Center, Istanbul, Turkey
| | - Breege Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Philip Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Shikhar Mehrotra
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Department of Surgery, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Ozgur Sahin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA
| | - Besim Ogretmen
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA.
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Huynh M, Vinck R, Gibert B, Gasser G. Strategies for the Nuclear Delivery of Metal Complexes to Cancer Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311437. [PMID: 38174785 DOI: 10.1002/adma.202311437] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/20/2023] [Indexed: 01/05/2024]
Abstract
The nucleus is an essential organelle for the function of cells. It holds most of the genetic material and plays a crucial role in the regulation of cell growth and proliferation. Since many antitumoral therapies target nucleic acids to induce cell death, tumor-specific nuclear drug delivery could potentiate therapeutic effects and prevent potential off-target side effects on healthy tissue. Due to their great structural variety, good biocompatibility, and unique physico-chemical properties, organometallic complexes and other metal-based compounds have sparked great interest as promising anticancer agents. In this review, strategies for specific nuclear delivery of metal complexes are summarized and discussed to highlight crucial parameters to consider for the design of new metal complexes as anticancer drug candidates. Moreover, the existing opportunities and challenges of tumor-specific, nucleus-targeting metal complexes are emphasized to outline some new perspectives and help in the design of new cancer treatments.
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Affiliation(s)
- Marie Huynh
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Robin Vinck
- Orano, 125 avenue de Paris, Châtillon, 92320, France
| | - Benjamin Gibert
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
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