Author interview: Shruti Ganesh Dhamdhere is a graduate student working in Dr. Sanjeev Shukla’s lab at IISER Bhopal. Her research explores the epigenetic basis of adaptation of breast cancer cells in hypoxic microenvironment.
Lab: Dr. Sanjeev Shukla, Indian Institute of Science Education and Research Bhopal
Research Summary: This research addresses the implications of a stress response gene ATF3 in modulation of collagen deposition by the hypoxic breast cancer cells and the consequent enhancement in their invasive potential.
What was the core problem you aimed to solve with this research?
As oxygen diffusion slows down in solid tumors, a gradient is formed from the closest blood vessels to the core. As a result, hypoxic zones with significantly lower oxygen concentrations are created. It has been shown that cancer cells respond to this stressor by becoming more aggressive and developing an improved invasive capability, which increases metastasis and makes the cells more resistant to treatment. In order to comprehend how these cancer cells intensify these aggressive characteristics numerous investigations have offered a variety of pathways and the underlying molecular mechanisms. However, tumors experience dysregulation of several pathways and genes, therefore, a completely understandable response to this topic has not been discovered yet. Our aim was to understand the role of adaptive stress response genes in hypoxic breast cancer and specifically how these genes bring about alterations in the collagen composition of the tumor microenvironment (TME) to aid in increased invasiveness of the cancer cells.
How did you go about solving this problem?
We started with identifying which adaptive response genes are upregulated under hypoxic conditions in breast cancer. From the transcriptomic analyses we identified Activating Transcription Factor 3 (ATF3) as the one adaptive response gene induced consistently in hypoxic breast cancer cells. Further, we conducted a global RNA sequencing analysis to decipher the ATF3 target genes that are involved in regulation and organization of the extracellular matrix (ECM) within the TME. From this analysis we found Prolyl 4-Hydroxylase Subunit Alpha 1Â (P4HA1), an enzyme that plays a critical role in the hydroxylation and deposition of collagen in the extracellular matrix (ECM) during the evolution of cancer, which is necessary for metastasis. Further, we delineated the molecular mechanisms involved in the ATF3 induction and its impact on metastasis in hypoxic breast cancer.
Dr. Sanjeev Shukla, the corresponding author, states that this research “provides insights into the less explored role of ATF3 and CTCF in regulation of alternative splicing”.
How would you explain your research outcomes (Key findings) to the non-scientific community?
As a solid tumor progresses, the blood vessels within it grow in an unstructured way unlike in a healthy tissue. This leads to generation of areas with decreased supply of oxygen, which are called the hypoxic regions, where the cancer cells are in a state of stress which they try to evade. For doing so they employ several adaptations. One of which is increasing invasion to spread to the nearby tissues. In our study we found that in hypoxic breast cancer cells a gene, ATF3, is induced as a response to the unfavorable stress. ATF3 is a transcription factor that can upregulate various downstream genes in hypoxic breast cancer. From the list of ATF3 target genes we found that P4HA1, which is an enzyme that helps in collagen deposition, is upregulated in hypoxic breast cancer cells by ATF3. Collagens are the structural proteins that form the framework that supports and shapes the three-dimensional structure; and compartmentalizes the growing tumor. There are two isoforms of the P4HA1 gene, of which ATF3 prefers incorporation of the isoform which leads to increased deposition of collagen. The increased collagen in the ECM self-assembles into fibers which acts as highways for the invading cancer cells. Thus, making the ECM invasion conducive within the hypoxic regions of the TME.
What are the potential implications of your findings for the field and society?
Our study is the first one to report induction of ATF3 in hypoxic breast cancer via epigenetic alteration of ATF3 promoter where HIF1É‘ acts as its transcriptional activator. This study also unveils the previously unknown roles of ATF3 in modulation of collagen architecture within the TME via transcriptional upregulation of P4HA1 as well as regulation of its splicing. This research has opened a pristine arena for investigations on adaptive response genes in ECM modulation and invasion in cancers and has provided an attractive target which could be exploited for designing new therapies.
What was the exciting moment during your research?
In any research study each finding is exciting for the researchers. However, looking at the significant effect of our axis on the invasive potential of breast cancer cells was very exciting. Also, when we confirmed expression of ATF3 in tissues sections obtained from breast cancer patients it strengthened our confidence in the study.
Reference: Dhamdhere, S.G., Bansal, A., Singh, P. et al. Hypoxia-induced ATF3 escalates breast cancer invasion by increasing collagen deposition via P4HA1. Cell Death Dis 16, 142 (2025). https://doi.org/10.1038/s41419-025-07461-y
