ACTREC, Tata Memorial Centre · Mumbaiindraneel.mittra@gmail.com
Translational Research Laboratory
ACTRECTata Memorial
CentreNavi Mumbai
Cell-Free Chromatin: Rethinking the Foundations of Biology

Research

Our Research

A New Biology emerges after cell death: The critical role of cell-free chromatin

  1. Life depends on the daily death of hundreds of billions of cells. Yet, what happens to the genetic material released from these dying cells remains one of biology's least explored questions.

  2. Our laboratory investigates the biology of cell-free chromatin particles (cfChPs)—fragments of chromatin released into the extracellular environment during cell death.

  3. We challenge the long-held view that these particles are biologically inert and instead test the hypothesis that they represent an active, previously unrecognized layer of biological regulation.

  4. Our research shows that extracellular cfChPs can readily enter healthy cells, reshape cellular function, and influence processes ranging from genomic instability and inflammation, to ageing, cancer, metastasis, and treatment-related toxicity.

  5. A major focus of our work is based on the discovery that internalized cfChPs, composed predominantly of non-coding DNA, can assemble into large DNA concatemers that behave as autonomous "satellite genomes."

  6. We investigate whether these structures can replicate, transcribe, synthesize proteins, and mobilize transposable elements, and whether they represent a previously unrecognized mechanism of horizontal gene transfer within multicellular organisms.

  7. Our studies raise fundamental questions about genome plasticity, the biological functions of non-coding DNA, and the mechanisms shaping mammalian evolution.

  8. Alongside these mechanistic investigations, we are developing a new therapeutic paradigm based on extracellular redox biology. Rather than targeting intracellular oxidative stress, we explore whether extracellular cfChPs can be selectively neutralized by reactive oxygen species generated by ultra-low doses of resveratrol and copper (R-Cu).

  9. This strategy has shown promise in preclinical and early clinical studies for reducing DNA damage, inflammation, ameliorating treatment-related toxicity, reducing the aggressive phenotype of cancer, and down-regulating the biological hallmarks of ageing.

  10. By integrating cell and molecular biology, genomics, cancer biology, immunology, ageing research, and evolutionary biology, we aim to understand how genetic material released from dying cells influences the biology of living cells—and whether this process reflects a fundamental principle that governs health, disease, and evolution.

Our Vision

Our vision is to establish cell-free chromatin biology as a new field of biomedical research.

Research Themes

Research theme 1.

Cell-free chromatin particles as drivers of evolutionary change

Together, these four papers propose that circulating cell-free chromatin particles (cfChPs) released during cell death are biologically active mobile genetic elements, not inert debris. They demonstrate that cfChPs can enter recipient cells, function as autonomous “satellite genomes,” mediate horizontal transfer of genetic information across cellular, species, and kingdom boundaries, mobilize transposable elements, and reveal evolutionary information encoded within non-coding DNA, with potential implications for genomic instability, disease, ageing, and mammalian evolution.

Publications in this theme (4)

  1. 1. Banerjee, S., Shende, S. S., Kata, L., Lopes, R. S., Praveen, S., Joshi, R., ... & Mittra, I. (2025). Horizontally transferred cell-free chromatin particles function as autonomous ‘satellite genomes’ and vehicles for transposable elements within host cells. Elife, 13, RP103771. https://elifesciences.org/articles/103771

    Video Links

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  2. 2. Mittra, I. (2015). Circulating nucleic acids: a new class of physiological mobile genetic elements. F1000Research, 4, 924. https://f1000research.com/articles/4-924/v1
  3. 3. Raghuram, G. V., Gupta, D., Subramaniam, S., Gaikwad, A., Khare, N. K., Nobre, M., ... & Mittra, I. (2017). Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries. BMC Molecular Biology, 18(1), 21. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5550992/
  4. 4. Joshi, R., Roy, A., Lopes, R., Kata, L., Selukar, R., Markam, M., ... & Mittra, I. (2025). Apoptosis uncovers human evolutionary heritage sequestered in non-coding DNA. bioRxiv, 2025-11. https://www.biorxiv.org/content/10.1101/2025.11.13.688179v2

Our Publications: this theme with summaries →

Research theme 2.

Cell-free chromatin particles as pathological entities

DNA damage and Inflammation

These studies show that cfChPs can integrate into healthy cell genomes, inducing DNA double-strand breaks, genomic instability, and inflammation. The findings link inflammatory signalling directly to genomic injury and suggest that chronic cfChP exposure contributes to aging, somatic mosaicism, cancer, and other diseases. Together, they support a unified model of cfChP-driven disease progression.

Aging and neurodegeneration

These studies identify cfChPs as endogenous drivers of biological aging by inducing DNA double-strand breaks, particularly at telomeres, thereby promoting senescence and genomic instability. Interventions such as the resveratrol-copper (R-Cu) combination suppressed hallmarks of aging and neurodegeneration in experimental models, highlighting cfChP neutralization as a potential anti-aging strategy.

Mitochondrial Damage and Oxidative Stress

These studies show that cfChPs damage both mitochondria and the genomic DNA. Following cellular uptake, cfChPs disrupt mitochondrial integrity, increasing reactive oxygen species and oxidative stress. However, cfChP-induced DNA damage can also occur independently of ROS, indicating multiple pathogenic mechanisms. This dual toxicity may contribute to inflammation, aging, neurodegeneration, and chronic disease progression.

Cellular Reprogramming

These publications suggests that cell-free chromatin particles (cfChPs) can alter cellular identity and induce stem-like properties. These studies They show that chromatin-associated factors can reprogram differentiated cells into cancer stem-like states, while recent advances indicate the potential generation of pluripotent stem cells using cfChPs. These findings imply that horizontally transferred chromatin information may influence regeneration, disease progression, and tumor initiation by promoting cellular plasticity and stemness.

Cancer Metastasis

These studies propose that metastases may arise de novo within distant organs through cfChP-mediated transformation of target cells, rather than solely by cancer cell migration. Histological differences between primary and metastatic tumors support this model. If validated, this paradigm could redefine cancer dissemination and identify cfChP blockade as a strategy to prevent metastasis.

Immune check-points

Together, the published study and the accompanying manuscript identify circulating cell-free chromatin particles (cfChPs) released from dying cells as potent endogenous immune activators. The earlier study showed that cfChPs activate immune checkpoints in human lymphocytes, contributing to immune suppression in cancer. The current manuscript extends these findings by demonstrating that cfChPs trigger a previously unrecognized biphasic STING signalling programme that precedes DNA damage and drives inflammatory responses, establishing cfChPs as mechanistic links between cell death, DNA damage, sterile inflammation, and immune dysregulation.

Publications in this theme (24)

DNA damage and Inflammation

  1. 1. Mittra, I., Nair, N. K., & Mishra, P. K. (2012). Nucleic acids in circulation: are they harmful to the host?. Journal of biosciences, 37(2), 301-312. https://www.ncbi.nlm.nih.gov/pubmed/22581336
  2. 2. Mittra, I., Khare, N. K., Raghuram, G. V., Chaubal, R., Khambatti, F., Gupta, D., ... & Dutt, A. (2015). Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes. Journal of biosciences, 40(1), 91-111. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5779614/
  3. 3. Mittra, I., Samant, U., Sharma, S., Raghuram, G. V., Saha, T., Tidke, P., ... & Dutt, A. (2017). Cell-free chromatin from dying cancer cells integrate into genomes of bystander healthy cells to induce DNA damage and inflammation. Cell Death Discovery, 3(1), 1-14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447133/
  4. 4. Basak, R., Nair, N. K., & Mittra, I. (2016). Evidence for cell-free nucleic acids as continuously arising endogenous DNA mutagens. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 793, 15-21. https://www.ncbi.nlm.nih.gov/pubmed/27768916
  5. 5. Mehrotra, S., & Mittra, I. (2020). Origin of genome instability and determinants of mutational landscape in cancer cells. Genes, 11(9), 1101. https://www.mdpi.com/2073-4425/11/9/1101
  6. 6. Chaudhary, S., Raghuram, G. V., & Mittra, I. (2018). Is inflammation a direct response to dsDNA breaks?. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 808, 48-52. https://www.ncbi.nlm.nih.gov/pubmed/29518635
  7. 7. Mittra, I., Pal, K., Pancholi, N., Tidke, P., Siddiqui, S., Rane, B., ... & Raghuram, G. V. (2020). Cell-free chromatin particles released from dying host cells are global instigators of endotoxin sepsis in mice. PLoS One, 15(3), e0229017. https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0229017
  8. 8. Mittra, I., de Souza, R., Bhadade, R., Madke, T., Shankpal, P. D., Joshi, M., ... & Badwe, R. (2020). Resveratrol and Copper for treatment of severe COVID-19: an observational study (RESCU 002). MedRxiv, 2020-07. https://www.medrxiv.org/content/10.1101/2020.07.21.20151423v1
  9. 9. Shabrish, S., & Mittra, I. (2021). Cytokine storm as a cellular response to dsDNA breaks: a new proposal. Frontiers in immunology, 12, 622738. http://journal.frontiersin.org/article/10.3389/fimmu.2021.622738/full?
  10. 10. Chaudhary, S., & Mittra, I. (2019). Cell-free chromatin: A newly described mediator of systemic inflammation. Journal of biosciences, 44(2), 32. https://link.springer.com/article/10.1007%2Fs12038-019-9849-7
  11. 11. V. Raghuram, G., Chaudhary, S., Johari, S., & Mittra, I. (2019). Illegitimate and repeated genomic integration of cell-free chromatin in the aetiology of somatic mosaicism, ageing, chronic diseases and cancer. Genes, 10(6), 407. https://www.mdpi.com/2073-4425/10/6/407
  12. 12. Shabrish, S., Patade,S., Shinde, S., Yelukar, R., Raghuram, GV., Lopes, R., Khare, NK., Mittra, I. (2026). Circulating Cell-Free Chromatin Particles Trigger a Unique Biphasic STING Signaling Program that Drives DNA Damage and Inflammation. bioRxiv 2026.07.28.741182; https://doi.org/10.64898/2026.07.28.741182

Aging and neurodegeneration

  1. 1. Tripathy, B. K., Pal, K., Shabrish, S., & Mittra, I. (2021). A new perspective on the origin of DNA double-strand breaks and its implications for ageing. Genes, 12(2), 163. https://www.mdpi.com/2073-4425/12/2/163/htm
  2. 2. Birwatkar, S., Ghosh, T., Selukar, R., Lopes, R., Khare, N. K., Raghuram, G. V., ... & Mittra, I. (2025). DsDNA breaks inflicted by cell-free chromatin particles selectively target telomeres. Scientific Reports, 15(1), 36470. https://www.nature.com/articles/s41598-025-21509-1
  3. 3. Pal, K., Raghuram, G. V., Dsouza, J., Shinde, S., Jadhav, V., Shaikh, A., ... & Mittra, I. (2022). A pro-oxidant combination of resveratrol and copper down-regulates multiple biological hallmarks of ageing and neurodegeneration in mice. Scientific Reports, 12(1), 17209. https://www.nature.com/articles/s41598-022-21388-w

Mitochondrial Damage and Oxidative Stress

  1. 1. Raghuram, G. V., Tripathy, B. K., Avadhani, K., Shabrish, S., Khare, N. K., Lopes, R., ... & Mittra, I. (2024). Cell-free chromatin particles released from dying cells inflict mitochondrial damage and ROS production in living cells. Cell death discovery, 10(1), 30. https://rdcu.be/dv20s
  2. 2. Jain, K., Raghuram, G. V., Lopes, R., Khare, N. K., Shabrish, S., & Mittra, I. (2024). Cell-free chromatin particles damage genomic DNA of healthy cells via an ROS-independent mechanism. BioRxiv, 2024-08. https://www.biorxiv.org/content/10.1101/2024.08.16.608226v1

Cellular Reprogramming

  1. 1. Mittra, I., Shabrish, S. (2026). A method, a kit and the use of pluripotent stem cells induced using cell-free chromatin particle (cfChPs). (WIPO Patent Publication No. WO/2026/078725). World Intellectual Property Organization. https://patentscope.wipo.int/search/en/WO2026078725
  2. 2. Shabrish, S., Naorem, L. D., Mohanty, S., Kumar, R., Lopes, R., Akhter, N., ... & Mittra, I. (2025). Induction of cancer stem cells from mouse fibroblasts. Scientific Reports, 15(1), 25489. https://www.nature.com/articles/s41598-025-09686-5

Cancer Metastasis

  1. 1. Singh, A., Jambhekar, N., Shet, T., Ramadwar, M., Dikshit, R., & Mittra, I. (2025). Are metastatic tumors histologically similar to the primary? Result of a retrospective blinded experiment. International Journal of Surgery Open, 63(2), 176-177. https://journals.lww.com/ijsopen/fulltext/2025/04000/are_metastatic_tumors_histologically_similar_to.21.aspx
  2. 2. Raghuram, G. V., Pal, K., Shende, S., Khare, N. K., Jadhav, V., Shinde, S., ... & Mittra, I. (2023). Evidence that metastases arise de novo as new cancers from cells of target organs. bioRxiv, 2023-08. https://www.biorxiv.org/content/10.1101/2023.08.09.552586v3
  3. 3. Raghuram, G. V., Pal, K., Sriram, G., Khan, A., Joshi, R., Jadhav, V., ... & Mittra, I. (2024). Therapeutic interventions on human breast cancer xenografts promote systemic dissemination of oncogenes. Plos one, 19(2), e0298042. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0298042

Immune check-points

  1. 1. Shabrish, S., Pal, K., Khare, N. K., Satsangi, D., Pilankar, A., Jadhav, V., ... & Mittra, I. (2024). Cell-free chromatin particles released from dying cancer cells activate immune checkpoints in human lymphocytes: implications for cancer therapy. Frontiers in immunology, 14, 1331491. https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1331491/full
  2. 2. Snehal Shabrish1,2*, Swamini Patade1,2, Roohi Yelukar1,2, Gorantla V. Raghuram1,2, Relestina Lopes1,2, Sushma Shinde1,2, Naveen Kumar Khare1,2, Indraneel Mittra1,2. Circulating Cell-Free Chromatin Particles Trigger a Unique Biphasic STING Signaling Program that Drives DNA Damage and Inflammation. https://doi.org/10.64898/2026.07.28.741182

Our Publications: this theme with summaries →

Research theme 3.

Therapeutic Strategies: Neutralisation of Cell-free Chromatin

These studies establish the scientific rationale and translational potential of the pro-oxidant combination of resveratrol and copper (R–Cu). They demonstrate that R–Cu generates reactive oxygen species that selectively deactivate extracellular cell-free chromatin particles (cfChPs), thereby preventing their pathogenic effects. Across experimental models, R–Cu reduced chemotherapy toxicity, radiation-induced bystander effects, endotoxin sepsis, ageing and neurodegeneration, and systemic dissemination of oncogenic material. Clinical studies and exploratory trials in COVID-19, oral cancer, gastric cancer, multiple myeloma, and glioblastoma showed reduced treatment-related toxicities and attenuation of malignant hallmarks, supporting cfChP deactivation as a novel therapeutic strategy.

The studies cited below represent another nanotechnology-based approach to deactivating cfChPs: pullulan nanoparticles conjugated with anti-histone antibodies selectively recognize and remove cfChPs, providing proof of principle for targeted chromatin clearance. Complementing degradation strategies such as R-Cu, these publications expand therapeutic options and strengthen the case for cfChPs as clinically relevant pathological targets.

Publications in this theme (17)

  1. 1. Subramaniam, S., Vohra, I., Iyer, A., Nair, N. K., & Mittra, I. (2016). A paradoxical relationship between resveratrol and copper (II) with respect to degradation of DNA and RNA. F1000Research, 4, 1145. https://f1000research.com/articles/4-1145/v2
  2. 2. Mittra, I. (2024). Exploiting the damaging effects of ROS for therapeutic use by deactivating cell-free chromatin: the alchemy of resveratrol and copper. Frontiers in pharmacology, 15, 1345786. https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1345786/full
  3. 3. Khanvilkar, S., & Mittra, I. (2025). Copper imparts a new therapeutic property to resveratrol by generating ROS to deactivate cell-free chromatin. Pharmaceuticals, 18(1), 132. https://pubmed.ncbi.nlm.nih.gov/39861193/
  4. 4. Mittra, I., Pal, K., Pancholi, N., Tidke, P., Siddiqui, S., Rane, B., ... & Raghuram, G. V. (2020). Cell-free chromatin particles released from dying host cells are global instigators of endotoxin sepsis in mice. PLoS One, 15(3), e0229017. https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0229017
  5. 5. Mittra, I., de Souza, R., Bhadade, R., Madke, T., Shankpal, P. D., Joshi, M., ... & Badwe, R. (2020). Resveratrol and Copper for treatment of severe COVID-19: an observational study (RESCU 002). MedRxiv, 2020-07. https://www.medrxiv.org/content/10.1101/2020.07.21.20151423v1
  6. 6. Mittra, I., Pal, K., Pancholi, N., Shaikh, A., Rane, B., Tidke, P., ... & Nair, N. K. (2017). Prevention of chemotherapy toxicity by agents that neutralize or degrade cell-free chromatin. Annals of Oncology, 28(9), 2119-2127. https://www.ncbi.nlm.nih.gov/pubmed/28911066
  7. 7. Kirolikar, S., Prasannan, P., Raghuram, G. V., Pancholi, N., Saha, T., Tidke, P., ... & Mittra, I. (2018). Prevention of radiation-induced bystander effects by agents that inactivate cell-free chromatin released from irradiated dying cells. Cell death & disease, 9(12), 1142. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6238009/
  8. 8. Agarwal, A., Khandelwal, A., Pal, K., Khare, N. K., Jadhav, V., Gurjar, M., ... & Mittra, I. (2022). A novel pro-oxidant combination of resveratrol and copper reduces transplant related toxicities in patients receiving high dose melphalan for multiple myeloma (RESCU 001). PLoS One, 17(2), e0262212. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0262212
  9. 9. Ostwal, V., Ramaswamy, A., Bhargava, P., Srinivas, S., Mandavkar, S., Chaugule, D., ... & Mittra, I. (2022). A pro-oxidant combination of resveratrol and copper reduces chemotherapy-related non-haematological toxicities in advanced gastric cancer: results of a prospective open label phase II single-arm study (RESCU III study). Medical Oncology, 40(1), 17. https://rdcu.be/cZyge
  10. 10. Juthani, R., Punatar, S., & Mittra, I. (2024). New light on chemotherapy toxicity and its prevention. BJC reports, 2(1), 41. https://www.nature.com/articles/s44276-024-00064-8
  11. 11. Pilankar, A., Singhavi, H., Raghuram, G. V., Siddiqui, S., Khare, N. K., Jadhav, V., ... & Mittra, I. (2022). A pro-oxidant combination of resveratrol and copper down-regulates hallmarks of cancer and immune checkpoints in patients with advanced oral cancer: Results of an exploratory study (RESCU 004). Frontiers in oncology, 12, 1000957. https://www.frontiersin.org/articles/10.3389/fonc.2022.1000957/full
  12. 12. Bandiwadekar, C., Naorem, L. D., Moiyadi, A. V., Singh, V., Shetty, P., Epari, S., ... & Mittra, I. (2025). Attenuation of malignant phenotype of glioblastoma following a short course of the pro-oxidant combination of Resveratrol and Copper. BJC reports, 3(1), 68. https://www.nature.com/articles/s44276-025-00177-8
  13. 13. Raghuram, G. V., Pal, K., Sriram, G., Khan, A., Joshi, R., Jadhav, V., ... & Mittra, I. (2024). Therapeutic interventions on human breast cancer xenografts promote systemic dissemination of oncogenes. Plos one, 19(2), e0298042. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0298042
  1. 14. Rekha, M. R., Pal, K., Bala, P., Shetty, M., Mittra, I., Bhuvaneshwar, G. S., & Sharma, C. P. (2013). Pullulan-histone antibody nanoconjugates for the removal of chromatin fragments from systemic circulation. Biomaterials, 34(27), 6328-6338. https://www.ncbi.nlm.nih.gov/pubmed/23746856
  2. 15. Mittra, I., Pal, K., Pancholi, N., Shaikh, A., Rane, B., Tidke, P., ... & Nair, N. K. (2017). Prevention of chemotherapy toxicity by agents that neutralize or degrade cell-free chromatin. Annals of Oncology, 28(9), 2119-2127. https://www.ncbi.nlm.nih.gov/pubmed/28911066
  3. 16. Kirolikar, S., Prasannan, P., Raghuram, G. V., Pancholi, N., Saha, T., Tidke, P., ... & Mittra, I. (2018). Prevention of radiation-induced bystander effects by agents that inactivate cell-free chromatin released from irradiated dying cells. Cell death & disease, 9(12), 1142. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6238009/
  4. 17. Raghuram, G. V., Pal, K., Sriram, G., Khan, A., Joshi, R., Jadhav, V., ... & Mittra, I. (2024). Therapeutic interventions on human breast cancer xenografts promote systemic dissemination of oncogenes. Plos one, 19(2), e0298042. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0298042

Our Publications: this theme with summaries →