Alan Mcintyre - Investigating spatially resolved metabolic and RNA-SEQ profiles of triplenegative breast cancer brain metastases
Lay summary
Background: Triple negative breast cancer (TNBC) represents the most difficult to treatform of breast cancer. TNBC accounts for approximately 10-15% of breastcancer cases. Nearly half of advanced TNBC patients develop brainmetastasis with dismal mortality rates of 80% within the first year ofdiagnosis. Environmental variations in oxygen levels and acidityfrequently identified in TNBC are known to increase therapy resistance.This highlights an urgent need for innovative treatment strategies and adeeper molecular understanding of TNBC-brain metastases.
Aims: Our project aims to leverage recent advancements in diagnostic imaging,ultrahigh magnetic field (UHF) 7-Tesla MRI. This technology has thepotential to revolutionize the detection and characterization of TNBCbrain metastases, providing imaging of the tumour’s molecularproperties. Our research will characterise the environmental variationsin tumour oxygen and acidity and the impact of these on tumour genetic and metabolic profiles. This will characterise these tumours at a higherresolution than previously and support developing novel precisiontherapy approaches linked to clinical imaging.
Techniques: We will investigate ultrahigh magnetic field (UHF) MRI analysed patienttumours. We will compare the UHF MRI information with spatiallyresolved RNA sequencing and metabolic analyses alongside analysis ofbiomarkers of tumour variations in oxygen levels and acidity. This willenable us to correlate the properties that we identify using UHF MRI withhigh resolution molecular data in the same tumours.
Impact: Our analyses will validate the novel UHF MRI approach helping makeMRI scans more useful for doctors treating TNBC brain metastases. Thewealth of data about the characteristics of TNBC-brain metastases willsupport development of better ways to treat breast cancer patients thathave the lowest chance of survival. This approach aims to target thecancer more precisely and potentially transform the clinicalmanagement of TNBC.
Scientific summary
Background: Triple negative breast cancer (TNBC) has the lowest patient survival withhighest metastatic potential of breast cancer subtypes. The incidence ofbrain metastasis is as high as 46% among advanced TNBC patients. Themortality rate of brain metastasis can be as high as 80% within the firstyear. Treating TNBC brain metastasis remains a significant clinicalchallenge. Therapeutic options are limited to surgical resection and/or radiotherapy and palliative care. Inter- and intra- heterogeneity of TNBCnegatively impacts therapeutic response. Hence, to enhance treatmentstrategies for TNBC-brain metastasis there is urgent need for bettermolecular characterisation.Clinical magnetic resonance imaging (MRI) is utilised to identify regionsof brain metastasis. Ultrahigh magnetic field (UHF) 7T MRI, offers thepotential to enhance diagnostic imaging characterising molecularproperties of the tumour. This includes characterisation of tumourmicroenvironment (TME) properties including hypoxia (>1% O2) andextracellular acidic pH (pHe), which contribute to therapy resistance.Hypoxia is prevalent in 50% of primary TNBC and hypoxic markers aremore prevalent in brain metastases than primary tumours.
Aims:The focus of this research will be to validate in vivo UHF MRI of TNBCbrain metastases with ex vivo analyses. This data will also provide novelspatial molecular characterisation of tumours from a group of patientsof significant clinical need.
1. Use spatially resolved transcriptomics (GeoMx, Nanostring) toinvestigate the transcriptional heterogeneity in TNBC brainmetastasis.
2. Identify the impact of physiological features and gene expressionprofiles on spatially resolved metabolomics (3D OrbiSIMs).
3. Correlate the biomarkers for hypoxia (CA9) and acidosis (LAMP2)with UHF MRI analyses.
4. Identify therapeutic targets from molecular characteristics foranalyses in follow-on investigations.
Techniques and Methodology: Patients with TNBC brain metastases will undergo advanced UHF 7T MRIimaging and the tumour will be surgically resected. The tumour tissuewill then be sectioned and characterised using three approaches.Immunohistochemistry for hypoxia and acidosis biomarkers CA9 andLAMP2 (Figure1A-D) and spatial transcriptomics (GeoMx, Nanostring)and spatial metabolomics (3D OrbiSIMs)(Figure1F-I) providingcomprehensive mapping of TME characteristics, gene expression andmetabolic patterns. GeoMx sequencing has successfully worked ontissue ranging from 10 years old FFPE to current (MP). Michael Portelli(CoI) is also applying for Wellcome Trust funding to try to amalgamateOrbiSIMs and GeoMx data together using mathematical modelling.
Impact on breast cancer research: The lack of therapeutic options for TNBC brain metastases present animportant avenue of research to address. Validation of clinical imagingwith molecular characterizations will support novel diagnosticdevelopment. Furthermore, spatially resolved transcriptomics andmetabolomics analyses will provide a more comprehensive view of TNBC brain metastases TME, and provide novel therapeutic opportunity discoveries.