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Supplementary Figure 3 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment

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posted on 2024-06-04, 07:42 authored by Rohan Chaubal, Nilesh Gardi, Shalaka Joshi, Gouri Pantvaidya, Rasika Kadam, Vaibhav Vanmali, Rohini Hawaldar, Elizabeth Talker, Jaya Chitra, Poonam Gera, Dimple Bhatia, Prajakta Kalkar, Mamta Gurav, Omshree Shetty, Sangeeta Desai, Neeraja M. Krishnan, Nita Nair, Vani Parmar, Amit Dutt, Binay Panda, Sudeep Gupta, Rajendra Badwe

Supplementary Figure 3 summarises differential genes identified via class comparisons AvB, BvC and AvC in replicate analysis of breast cancer RNA-Seq data.

Funding

Department of Atomic Energy, Government of India (DAE)

Department of Biotechnology, Ministry of Science and Technology, India (DBT)

Sunil Gupta

Akhil Gupta

Womens Cancer Initiative

Mizuho Bank Limited

History

ARTICLE ABSTRACT

Surgery exposes tumor tissue to severe hypoxia and mechanical stress leading to rapid gene expression changes in the tumor and its microenvironment, which remain poorly characterized. We biopsied tumor and adjacent normal tissues from patients with breast (n = 81) and head/neck squamous cancers (HNSC; n = 10) at the beginning (A), during (B), and end of surgery (C). Tumor/normal RNA from 46/81 patients with breast cancer was subjected to mRNA-Seq using Illumina short-read technology, and from nine patients with HNSC to whole-transcriptome microarray with Illumina BeadArray. Pathways and genes involved in 7 of 10 known cancer hallmarks, namely, tumor-promoting inflammation (TNF-A, NFK-B, IL18 pathways), activation of invasion and migration (various extracellular matrix–related pathways, cell migration), sustained proliferative signaling (K-Ras Signaling), evasion of growth suppressors (P53 signaling, regulation of cell death), deregulating cellular energetics (response to lipid, secreted factors, and adipogenesis), inducing angiogenesis (hypoxia signaling, myogenesis), and avoiding immune destruction (CTLA4 and PDL1) were significantly deregulated during surgical resection (time points A vs. B vs. C). These findings were validated using NanoString assays in independent pre/intra/post-operative breast cancer samples from 48 patients. In a comparison of gene expression data from biopsy (analogous to time point A) with surgical resection samples (analogous to time point C) from The Cancer Genome Atlas study, the top deregulated genes were the same as identified in our analysis, in five of the seven studied cancer types. This study suggests that surgical extirpation deregulates the hallmarks of cancer in primary tumors and adjacent normal tissue across different cancers. Surgery deregulates hallmarks of cancer in human tissue.