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Aberrant circulating epigenomic signatures: Development and validation of non-invasive biomarkers for trans-generational monitoring of air pollution associated cancers

Primary Information



Project No.


Sanction and Project Initiation

Sanction No: ***

Sanction Date: ***

Project Initiation date: 18/04/2017

Project Duration: 36

Partner Ministry/Agency/Industry

Ministry of Health and Family Welfare, Government of India


Role of partner:Presently no industry partner


Principal Investigator

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Koel Chaudhury
Indian Institute of Technology Kharagpur

Host Institute


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Pradyumna Kumar Mishra
National Institute for Research in Environmental Health (ICMR) Bhopal

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Kailash C Pandey
National Institute for Research in Environmental Health (ICMR) Bhopal

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Suresh P. Vyas
Dr. Harisingh Gour Central University, Sagar


Scope and Objectives

To develop a pragmatic molecular strategy for risk assessment of air pollution associated cancers To screen circulating epigenetic signatures for biomarker identification. To develop and validate a novel nano sensor based technology for mass screening.


The proposed approach will benefit the arena of environmental exposure-associated health hazards. Epigenetic signature based novel biomarker strategy for population based risk assessment possesses the ability to capture the entire genetic panorama of the tumoral landscape and will be helpful in the identification of past toxic exposure and upcoming diseases. In particular, use of biological fluids such as saliva and urine as sources of non-invasive biomarkers for cancer detection will be of significant impact. Moreover, development of the quantum dot based screening technique holds great clinical promise.


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Scientific Output

Organo-chloride pesticides (OCPs) have various adverse health effects, including endocrine disorders, abnormal embryonic development, altered lipid metabolism, hematological and hepatic alterations and potential carcinogenic effects. For quantitative analysis, calibration for alpha-endosulfan, beta-endosulfan, heptachlor epoxide, alpha-HCH, beta-HCH, gamma-HCH, delta-HCH was performed using Agilent Gas Chromatography-Mass Spectrometry (GC-MS) and is shown in Figure 1. Figure 1a shows the overlaid chromatogram of heptachlor epoxide with different concentrations selected (1ppm, 0.5ppm, 0.25ppm, 0.1ppm, 10ppb, 1ppb and 0.1 ppb). Figure1b shows overlaid chromatogram of alpha-endosulfan and beta-endosulfan. The concentration range for alpha-endosulfan is 0.7ppm, 0.35ppm, 0.175ppm, 0.07ppm and 0.0007ppm. The concentration range for beta-endosulfan is 0.9ppm, 0.5ppm, 0.3ppm, 0.15ppm, 0.075ppm, 0.03ppm and 0.003ppm. Figure 1c shows overlaid chromatogram of alpha-HCH, beta-HCH, gamma-HCH, delta-HCH with different concentrations ranging from 1ppm, 0.5ppm, 0.25ppm, 0.125ppm, 0.0625pm, 0.025ppm to 0.00025ppm. Figure 2 shows the calibration curve for alpha HCH, beta HCH, gamma HCH, delta HCH


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Results and outcome till date

Epigenetic modifiers not only maintain chromatin conformation but govern the dynamic state of chromatin assembly and control genomic activation. Histone acetyltransferases and Histone methyltransferases are regarded as two crucial epigenetic modifiers that are responsible for maintenance of chromatin organization to acclimatize cells and adapt to alterations in the gene-environmental interactions and developmental cues while conferring sufficient plasticity. Relative gene expression analysis (semi-quantitative reverse transcriptase PCR) was performed using cellular mRNA transcripts. For cDNA synthesis, we used a reverse transcription system that included a reverse transcriptase enzyme and an optimized set of reagents for efficient synthesis of first-strand cDNA. Subsequent amplification was done using a ready-to-use master mix containing Taq DNA Polymerase, dNTPs, MgCl2, KCI and stabilizers. Band intensity was analyzed using Image Lab software and obtained amplicons were quantitated using agarose gel electrophoresis. In our study, we observed higher expression levels of two methyltransferases in the high-risk group: (i) enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2, H3K27me modifier gene); (ii) euchromatic histone-lysine N-methyltransferase 2 (EHMT2/G9a, H3K9me1 and H3K9me2 gene) which corroborates with the levels of histone-tail modifications. Relative gene expression analysis of histone acetyltransferase (HAT), P300 also showed a similar trend. Our work enunciates the role of ROS-dependent the epigenetic modification induced by air-borne particulate matter. Studies are in progress.

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Societal benefit and impact anticipated

This study will allow rapid, economical, and repeated sampling: features that permit their use in screening programs and close monitoring of treatment response and disease progression, thereby permitting earlier intervention and dynamic therapeutic management. Consequently, this technology has the potential to radically improve current treatment regimens and therefore the outcome of cancer patients, allowing for a personalised approach for each patient.

Next steps

1. With regard to nano-biosensor development, QDs have been synthesized and characterized. Following validation of the epigenetic signatures in controlled and exposed settings, field trials will be conducted, as proposed in the original plan.

Publications and reports

1. A. Bhargava, A. Shukla, N. Bunkar, R. Shandilya, L. Lodhi, R. Kumari, P. K. Gupta, A. Rahman, K. Chaudhury, R. R. Tiwari, I. Y. Goryacheva, P. K. Mishra. Exposure to ultrafine particulate matter induces NF-kb mediated epigenetic modifications. Environmental Pollution (Elsevier, USA): 252; 39-50, 2019. IMPACT FACTOR - 5.714
2. A. Shukla, N. Bunkar, R. Kumar, A. Bhargava, R. Tiwari, K. Chaudhury, I. Y. Goryacheva, P. K. Mishra Air pollution associated epigenetic modifications: Transgenerational inheritance and underlying molecular mechanisms. Science of the Total Environment (Elsevier, USA): 656; 760-777, 2019. IMPACT FACTOR - 5.589
3. R. D. Singh, R. Shandilya, A. Bhargava, R. Kumar, R. Tiwari, K. Chaudhury, R. K. Srivastava, I. Y. Goryacheva, P. K. Mishra. Quantum dot based nano-biosensors for detection of circulating cell free miRNAs in lung carcinogenesis: from biology to clinical translation. Frontiers in Genetics (EPFL, Switzerland): 9; e616, 2018 IMPACT FACTOR - 3.789.
4. A. Bhargava, N. Bunkar, K. C. Pandey, R. R. Tiwari, K. Chaudhury, Yu I. Goryacheva, P. K. Mishra. Epigenetic biomarkers for risk assessment of particulate matter associated lung cancer. Current Drug Targets (Bentham Science, USA): 19; 1127-1147, 2018. IMPACT FACTOR - 2.642.
5. N. Bunkar, A. Bhargava, K. Chaudhury, R. S. Sharma, N. K. Lohiya, P. K. Mishra. Fetal nucleic acids in maternal plasma: from biology to clinical translation. Frontiers in Bioscience (Landmark Ed): 23; 397-431, 2018. IMPACT FACTOR - 1.52.
6. A. Bhargava, S. Tamrakar, A. Aglawe, H. Lad, R. K. Srivastava , D. K. Mishra, R. R. Tiwari, K. Chaudhury, I. Y. Goryacheva, P. K. Mishra. Ultrafine particulate matter impairs mitochondrial redox homeostasis and activates phosphatidylinositol 3-kinase mediated DNA damage responses in lymphocytes. Environmental Pollution (Elsevier, USA): 234; 406-419, 2018. IMPACT FACTOR - 5.714.
7. A. Bhargava, N. K. Khare, N. Bunkar, K. Chaudhury, K. C. Pandey, S. K. Jain, P. K. Mishra. Cell-free circulating epigenomic signatures: Non-invasive biomarker for cardiovascular and other age-related chronic diseases. Current Pharmaceutical Design (Bentham Science, USA): 23; 1175-1187, 2017. IMPACT FACTOR - 2.412.

1. N. Bunkar, K. Chaudhury, P. K. Mishra A pan-India study to isolate and characterize aberrant circulating epigenomic signatures from high-risk, mid-risk and low-risk air pollution zones. In: Proceedings of the World Congress on Cancer, Jaipur, February 3-5, 2018.
2. N. Bunkar, K. Chaudhury, P. K. Mishra. Isolation and characterization of aberrant circulating epigenomic signatures from high-risk, mid-risk and low-risk air pollution zones: A pan-India study. In: Proceedings of the 4th India International Science Festival 2018, Indira Gandhi Pratishthan, Lucknow, October 5 - 8, 2018.


In Progress

Scholars and Project Staff

1. Scientist-C at IIT-KGP
2. SRF at ICMR-NIREH, Bhopal
4. Lab Technician at ICMR-NIREH, Bhopal
5. Field Worker at ICMR-NIREH, Bhopal

Challenges faced

Inter individual variations in the levels of different signatures have been observed in two low risk zones, therefore, the investigators propose to re-sample from these two low-risk areas (subject to availability of funds). Following validation of the signatures in controlled settings, field trials will be conducted, as proposed in the original plan (subject to availability of funds).

Financial Information

  • Total sanction: Rs. 13368900

  • Amount received: Rs. 8759179

  • Amount utilised for Equipment: Rs. 3091883

  • Amount utilised for Manpower: Rs. 2816141

  • Amount utilised for Consumables: Rs. 1005543

  • Amount utilised for Contingency: Rs. 989343

  • Amount utilised for Travel: Rs. 473341

  • Amount utilised for Other Expenses: 0

  • Amount utilised for Overheads: Rs. 382928

Equipment and facilities


1. Auto-Injector Mass Hunter Data Analysis Bundle with DRS-NIST-RTL at IIT-KGP.
2. Molecular Workstation Part-1 at ICMR-NIREH, Bhopal.