Work done in the lab of Prof. Pradip Sinha and Prof. Bushra Ateeq at BSBE department, IIT Kanpur.
Mahima Bharti is a doctoral student at the Department of Biological Sciences and Bioengineering (BSBE), IIT Kanpur, under the mentorship of Professors Pradip Sinha and Bushra Ateeq. She earned her master’s degree in science from Banaras Hindu University, Varanasi. She believes we could better understand new facets of science if we adopted a more multidisciplinary mindset.
Cancer development may result from the aberrant activation of master transcription factors at the top of a given cell type’s regulatory hierarchy. One such example is the human ETS (erythroblast transformation-specific)-Related Gene, also known as ERG. The misexpression of this gene due to chromosomal rearrangements and gene fusions in many cell types makes it oncogenic. It causes cancers of diverse lineages like prostate cancer (PCa), Ewing sarcoma, and acute myeloid leukemia. Several oncogenic targets, including Notch (N), Wnt, and the epigenetic regulator EZH2, are upregulated in ERG-induced tumors. These prior findings, however, do not explain why misexpression of the ERG master transcription factor-turned-oncoprotein selectively targets a small number of common targets across cells of different lineages. We hypothesized that whereas downstream effector genes and signaling pathways are conserved across cell types, ERG’s primary/direct targets will likely be cell type-specific. In other words, this line of thinking also implies that after over three decades of study, the identities of critical cell type-specific targets of ERG have eluded discovery.
Our study aimed to pinpoint ERG’s enigmatic target(s) via its gain in the fruit fly, Drosophila. The concept of deep homology underpins this strategy by positing that evolutionarily conserved genomic toolkits, including master transcription factors, are of paramount importance. Hence, it is likely that Drosophila shares a functional homology with human ERG and its target. Our findings display the fallout of this strategy and reveal Chip, a LIM domain-binding protein-encoding gene, as a novel target of human ERG in Drosophila. First, we demonstrated that the gain of ERG in Drosophila results in direct repression of Chip transcription.
Furthermore, ERG upregulates E(z), a Drosophila homolog of mammalian EZH2, which also epigenetically silences Chip. ERG-induced repression of Chip then activates N and Wnt signaling in only select cell types like the future adult thorax (notum) primordium in Drosophila, giving rise to extra wings: an instance of a developmental program gone awry. We also showed that ERG gain displayed cooperative tumorigenesis in Drosophila via this Chip loss-mediated deregulation paradigm of an essential development program. Finally, we demonstrated that a human homolog of Drosophila Chip, LDB1, is also repressed in an ERG-positive human prostate cancer cell line.
These findings provide novel insights into the mechanisms by which ERG induces cancer and demonstrate the efficacy of a deep homology-based method in the hunt for elusive targets of a human oncoprotein in Drosophila.
The human ERG oncoprotein is involved in a wide range of tumor types. Tens of thousands of research articles using high throughput technologies have helped narrow down Notch, Wingless (Wg/Wnt), and enhancer of zeste, EZH2, as its oncogenically essential targets in ERG-induced cancers. Yet, notwithstanding these advances over the past three decades, a crucial question of why the gain of the ERG master transcription factor causes malignancies in cells of disparate lineages remains unanswered. This conundrum raises an obvious concern: do existing methods for identifying ERG targets miss functionally crucial ones?
We looked into the outcome of its gain in Drosophila as an alternative method to discover ERG’s lineage-specific consequences. More specifically, we benefited from the fact that fly and human development utilize similar genetic toolkits. Therefore, we reasoned that the gain of human ERG in Drosophila would also affect putative ERG targets with deep homology. Despite the evident lack of complexity in this reasoning, the advances highlighted below demonstrate the validity of this method in discovering oncoprotein targets and understanding the developmental basis of cancer mechanisms.
The fact that ERG targets the highly conserved cell lineage regulator Chip/LDB1 drastically alters our previous understanding of ERG-induced carcinogenesis. Chip/LDB1 is a transcriptional co-activator that regulates and recruits lineage-specific DNA binding protein and controls cell fate in various cell types and tissues. The specificity of its targeting explains ERG’s ability to induce malignancies in diverse cell types. We further show that ERG-driven carcinogenesis is a telling example of ‘cancer as development has gone awry’ by revealing how it hijacks a primary developmental mechanism for carcinogenesis in a spatial context.
“We show that ERG-driven carcinogenesis is a telling example of ‘cancer as development has gone awry’ by revealing how it hijacks a primary developmental mechanism for carcinogenesis in a spatial context.”
“We cannot solve a problem with the ways of thinking that created it.”
Hybrid research. We used an oncogene from humans and expressed it in a tiny organism, Drosophila; to our astonishment, the result was a fly with four wings instead of two. That was the most thrilling part for us, perhaps. Information on a human oncoprotein target was obtained from a far-off fly, demonstrating the need to take a multidisciplinary approach when resolving issues. Based on what we know now, our findings illustrate the above adage.
What a fantastic adventure this has been! The most excellent part was gazing at the images you obtained after spending several hours on the confocal microscope.
My Ph.D. journey has given me invaluable expertise, and I plan to use it to establish a career in academia or a related field.
The inspiring phrase “Until it has been done, anything is theoretically impossible.” motivated budding science inside me. My deepest gratitude goes to my mentors, Prof. Pradip Sinha, Prof. Bushra Ateeq, and Dr. Anjali Bajpai, for providing me with invaluable wisdom and motivation throughout my Ph.D. journey.
That science should be one of India’s top priorities is something I feel very strongly about. India’s potential as a hub of cutting-edge scientific thinking is enormous. However, I feel that in order to advance Indian science, we researchers and the government will need to work together. Indian scientists need better access to resources and more significant opportunities to work with peers worldwide and in industry.
Bharti, M., Bajpai, A., Rautela, U., Manzar, N., Ateeq, B., & Sinha, P. (2023). Human ERG oncoprotein represses a Drosophila LIM domain binding protein–coding gene Chip. Proceedings of the National Academy of Sciences, 120(2), e2211189119. https://www.pnas.org/doi/abs/10.1073/pnas.2211189119
Ph.D. candidate at Rice University
Kshipra has completed Bachelor’s in Biomedical engineering from University of Mumbai where she was the recipient of institute gold medal and university bronze medal for obtaining the highest GPA in her cohort. She received her master’s degree in Electrical and Computer Engineering at Rice University. She is currently a Ph.D. candidate at Rice University, where she is working with Prof. Raghu Kalluri in the field of exosomes. Specifically she is interested in dissecting the exosome heterogeneity between healthy and cancer cells-derived nanovesicles and advancing the understanding of exosomes classes in cancer. In her spare time, Kshipra enjoys keeping fit, cooking, calligraphy and family & friends.
Kshipra is also involved in various professional development programs and as a first generation-PhD student is helping amplify the voices and stories of minorities in her field via the global organization she is part of snevresearch where she manages the events.
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