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Denisenko E, de Kock L, Tan A, Beasley AB, Beilin M, Jones ME, Hou R, Muirí DÓ, Bilic S, Mohan GRKA, Salfinger S, Fox S, Hmon KPW, Yeow Y, Kim Y, John R, Gilderman TS, Killingbeck E, Gray ES, Cohen PA, Yu Y, Forrest ARR. Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones. Nat Commun 2024; 15:2860. [PMID: 38570491 PMCID: PMC10991508 DOI: 10.1038/s41467-024-47271-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is genetically unstable and characterised by the presence of subclones with distinct genotypes. Intratumoural heterogeneity is linked to recurrence, chemotherapy resistance, and poor prognosis. Here, we use spatial transcriptomics to identify HGSOC subclones and study their association with infiltrating cell populations. Visium spatial transcriptomics reveals multiple tumour subclones with different copy number alterations present within individual tumour sections. These subclones differentially express various ligands and receptors and are predicted to differentially associate with different stromal and immune cell populations. In one sample, CosMx single molecule imaging reveals subclones differentially associating with immune cell populations, fibroblasts, and endothelial cells. Cell-to-cell communication analysis identifies subclone-specific signalling to stromal and immune cells and multiple subclone-specific autocrine loops. Our study highlights the high degree of subclonal heterogeneity in HGSOC and suggests that subclone-specific ligand and receptor expression patterns likely modulate how HGSOC cells interact with their local microenvironment.
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Affiliation(s)
- Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia.
| | - Leanne de Kock
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Adeline Tan
- Anatomical Pathology Department, Clinipath, Sonic Healthcare, Perth, WA, 6017, Australia
| | - Aaron B Beasley
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Maria Beilin
- Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, 12 Salvado Rd, Subiaco, WA, 6008, Australia
| | - Matthew E Jones
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Rui Hou
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Dáithí Ó Muirí
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Sanela Bilic
- Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, 12 Salvado Rd, Subiaco, WA, 6008, Australia
| | - G Raj K A Mohan
- Department of Gynaecological Oncology, Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, 12 Salvado Rd, Subiaco, WA, 6008, Australia
- School of Medicine, University of Notre Dame, Fremantle, WA, 6160, Australia
| | | | - Simon Fox
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Khaing P W Hmon
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | - Yen Yeow
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia
| | | | - Rhea John
- NanoString Technologies, Seattle, WA, USA
| | | | | | - Elin S Gray
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Paul A Cohen
- Division of Obstetrics and Gynaecology, Medical School, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- Institute for Health Research, The University of Notre Dame Australia, 32 Mouat Street Fremantle, Fremantle, WA, 6160, Australia.
| | - Yu Yu
- Division of Obstetrics and Gynaecology, Medical School, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- Curtin Medical School, Curtin University, 410 Koorliny Way, Bentley, WA, 6102, Australia.
- Curtin Health Innovation Research Institute, Curtin University B305, Bentley, WA, 6102, Australia.
| | - Alistair R R Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, 6009, Australia.
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Taton A, Gilderman TS, Ernst DC, Omaga CA, Cohen LA, Rey-Bedon C, Golden JW, Golden SS. Synechococcus elongatus Argonaute reduces natural transformation efficiency and provides immunity against exogenous plasmids. mBio 2023; 14:e0184323. [PMID: 37791787 PMCID: PMC10653904 DOI: 10.1128/mbio.01843-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE S. elongatus is an important cyanobacterial model organism for the study of its prokaryotic circadian clock, photosynthesis, and other biological processes. It is also widely used for genetic engineering to produce renewable biochemicals. Our findings reveal an SeAgo-based defense mechanism in S. elongatus against the horizontal transfer of genetic material. We demonstrate that deletion of the ago gene facilitates genetic studies and genetic engineering of S. elongatus.
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Affiliation(s)
- Arnaud Taton
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Tami S. Gilderman
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Dustin C. Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Carla A. Omaga
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Lucas A. Cohen
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Camilo Rey-Bedon
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - James W. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Susan S. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
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