Single‐Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma

Abstract

The effective treatment of advanced cervical cancer remains challenging. Herein, single-nucleus RNA sequencing (snRNA-seq) and SpaTial enhanced resolution omics-sequencing (Stereo-seq) are used to investigate the immunological microenvironment of cervical squamous cell carcinoma (CSCC). The expression levels of most immune suppressive genes in the tumor and inflammation areas of CSCC are not significantly higher than those in the non-cancer samples, except for LGALS9 and IDO1. Stronger signals of CD56 + NK cells and immature dendritic cells are found in the hypermetabolic tumor areas, whereas more eosinophils, immature B cells, and Treg cells are found in the hypometabolic tumor areas. Moreover, a cluster of pro-tumorigenic cancer-associated myofibroblasts (myCAFs) are identified. The myCAFs may support the growth and metastasis of tumors by inhibiting lymphocyte infiltration and remodeling of the tumor extracellular matrix. Furthermore, these myCAFs are associated with poorer survival probability in patients with CSCC, predict resistance to immunotherapy, and might be present in a small fraction (< 30%) of patients with advanced cancer. Immunohistochemistry and multiplex immunofluorescence staining are conducted to validate the spatial distribution and potential function of myCAFs. Collectively, these findings enhance the understanding of the immunological microenvironment of CSCC and shed light on the treatment of advanced CSCC.

Improved Protocol for Single-Nucleus RNA-sequencing of Frozen Human Bladder Tumor Biopsies

“…However, in another study, Gouin et al performed snRNA-seq on fresh frozen bladder tumor samples and identified a fraction of immune cells (5%) comprising T-cells, dendritic cells, macrophages, and B-cells defined by classic immune marker genes 4 . A third study on human cervical squamous cell carcinoma also performing snRNA-seq identified a diverse population of immune cells as well 20 . Although they identify immune cells, these studies may underestimate the true fraction of immune cells present in their natural conditions after all.…”

Spatial transcriptomics technology in cancer research

“…In HCC, Wu et al proposed high TLS-50 signature score was associated with good prognosis (16). Unsurprisingly, higher CAF signature predicted unfavourable PFS and OS in cervical SCC (93) and GC (126).…”

“…Interestingly, in cervical SCC, CAFs were enriched around certain tumor areas. Compared with tumors without surrounded by CAFs, CAF-surrounded tumors were more active in metabolism and cell growth and downregulated cellular adhesion, apoptosis, and immune response, suggesting a supportive TME for tumor progression and metastasis ( 93 ). On the other hand, fibroblast subpopulations may have mutually exclusive locations.…”

Re‐exploring tissue regeneration by novel spatial transcriptomics technologies

“…Ou et al. found unique immune cell types enriched in tumour areas with different metabolic activity 9 . By analyzing neighboring cell composition from spatial transcriptomics data, Cong et al.…”

“…8 Ou et al found unique immune cell types enriched in tumour areas with different metabolic activity. 9 By analyzing neighboring cell composition from spatial transcriptomics data, Cong et al identified a specific macrophage subgroup for SARS-CoV-2 clearance and inflammation resolution 10 (Figure 1).…”