Page 90 - Annual report 2021-22

Annual Report 2021-22 |

receptor type 1) by recruiting the histone acetyl-transferase p300 to the promoter of the gene in a
telomere length dependent fashion. The group found that TRF2 dependent regulation of IL1R1 alters
the NFkappa B activation in cancer cells and promotes the secretion of the key pro-inflammatory
cytokine IL1B (Interleukin 1-beta) among others. Experiments across multiple cell lines demonstrated
that TRF2 occupancy at the hTERT promoter alters with change in telomere length.
73
The infiltration of TAM (tumour associated macrophages) was telomere sensitive: Tumours with
relatively short telomeres had higher abundance of TAM and vice versa. This observation was
replicated across triple negative breast cancer (TNBC) clinical tissue, patient-derived organoids,
tumour xenografts and cancer cells with long/short telomeres. Mechanistically, his group showed that
Interleukin-1 signaling could be enhanced in TRF2-high cells through ligands IL1A/B, and abrogated by
the receptor antagonist IL1RA, supporting autocrine regulation of the TRF2-IL1R1 axis.

The non-telomeric binding of TRF2, a telomere-repeat-binding-factor, at the interleukin receptor
IL1R1 promoter directly activated IL1R1 through recruitment of the histone-acetyl-transferase p300
and consequent H3K27 acetylation. Further, specific lysine acetylation of the 293rd residue of TRF2
was found to be crucial for TRF2-dependent activation of IL1R1 through p300-mediated histone
modifications. Together, results show a heretofore unknown function of telomeres in interleukin
signaling and anti-tumour immune response through non-telomeric TRF2. These new results implicate
telomeres as a key factor in patient-specific response to cancer immunotherapy.

An Omics approach to understanding breast cancer in India
To enable targeted therapies for Indian breast cancers there is an unmet need to understand the
characteristic of this disease within the Indian population. The present study plans to do a whole
genome, epigenome and transcriptome sequencing of Indian breast cancer patients. Shantanu
Chowdhury is using next-generation whole genome and transcriptome sequencing to characterize the
landscape of genetic alterations underlying breast cancer patients. A comprehensive cancer genome
analysis will be undertaken and along with validation of data it would help identify driver alterations
and differential gene expression signatures. In parallel, the mutations will be identified in cell-free
tumor DNA from blood samples of patient volunteers. Identification of immune markers and
metabolic markers in patients with follow up of three years from blood is also planned. Ultimately, all
the data collected will be analyzed to find differential molecular signatures between patients who
responded versus patients who did not respond to treatment.
The primary focus immediately after initiation of the project has been to start processes for sample
collection including regulatory approvals with clinical partners/hospitals, currently with seven clinical
partners/hospitals while tie-ups are being established with more. Meanwhile optimization of
protocols for sample collection from hospitals, delivery to respective research partners and processing
of samples are being critically assessed and formalized. At present, 70 patient tissue samples with
respective adjacent normal have been collected along with 40 slides for IHC studies. Out of the
collected samples 33 pairs of samples have been sequenced (WGS) and 16 samples have been
processed and are ready to be sequenced. Another objective of the study includes generation of
organoids as 3D model system from patient samples. To achieve this, Shantanu’s group has optimized
the protocol for in-lab generation of organoids from tissue samples. Tumour organoids from eight
patients have been generated and are in culture currently. For characterization of organoids:
cytokeratin 19 as surface marker-based protein assay has been standardized.