Core Spotlight – Spatial Technologies Unit

The Harvard Cancer Consortium (HCC) launched its Core Facilities Spotlight Series with the first session featuring the Spatial Technologies Unit (STU), led by Director Ioannis Vlachos, PhD and Scientific Director Shushu Wang, PhD. The workshop showcased how spatial technologies can reveal not only which cells and molecules are present in a tumor, but also where they are located and how they interact within the tissue. The STU provides an integrated workflow spanning tissue processing, spatial assays, sequencing, and data analysis, with platforms including GeoMx, Visium and Visium HD, G4X from Singular Genomics, Xenium, and Illumina’s spatial transcriptomics platform StrataMap. These technologies support applications ranging from targeted protein profiling to whole-transcriptome analysis at near single-cell resolution, including studies of both fresh/frozen and FFPE samples.

The session featured two research presentations demonstrating the biological applications of these technologies. Filipe de Carvalho, MD, PhD, Assistant Professor at Brigham and Women’s Hospital, presented his work in localized muscle-invasive bladder cancer showing how single-cell and spatial profiling identified a relationship between CD44-high cancer cells and SPP1-positive macrophages in tumors resistant to chemotherapy. Spatial mapping helped reveal these interactions as organized cellular niches and contributed to the identification of macrophage reprogramming as a potential therapeutic strategy. Alm Osataphan, MD, MPH, Attending Physician at Dana-Farber Cancer Institute and Beth Israel Deaconess Medical Center and Instructor at Harvard Medical School, presented his research in cholangiocarcinoma using G4X spatial profiling to analyze approximately 2 million cells across different anatomical subtypes. The study identified distinct tumor microenvironments, including differences in fibroblast abundance and immune-infiltrated versus immune-excluded niches, illustrating how spatial organization may help explain biological differences among tumor subtypes and potentially inform treatment response.

A key message of the workshop was that the STU's role extends well beyond generating spatial data. The unit works with investigators from the earliest stages of a project to select appropriate samples and technologies, develop experimental strategies, support grant applications, and provide bioinformatics and data analysis through the final figures. The presentations demonstrated how integrating single-cell and spatial approaches can transform complex tissue data into biological insights, helping HCC investigators investigate tumor heterogeneity, cellular interactions, therapeutic resistance, and the tumor microenvironment. The session also highlighted the STU’s commitment to developing and adopting emerging technologies, including plans to bring the 10x Genomics Xenium platform to HCC and the anticipated introduction of the 10X Genomics Atera platform in Q1 2027.