An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity

Sahoo, Ajaya Kumar; Chivukula, Nikhil; Ramesh, Kundhanathan; Singha, Jasmine; Marigoudar, Shambanagouda Rudragouda; Sharma, Krishna Venkatarama; Samal, Areejit

doi:10.1016/j.scitotenv.2024.170968

Cited by 5 publications

(19 citation statements)

References 105 publications

(130 reference statements)

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“…US EPA’s ToxCast program provides high throughput in vitro bioactivity assay data for thousands of chemicals tested across several assays (Dix et al, 2007). Importantly, the ToxCast data includes assay annotations and information on associated bioprocess and genes that can aid in the identification of KEs (specifically MIEs) associated with the corresponding active chemical (Aguayo-Orozco et al, 2019; Knapen et al, 2018; Sahoo et al, 2024). First, we downloaded the latest ToxCast invitrodb version 4.1 (EPA, 2023) dataset from the US EPA repository (https://www.epa.gov/chemical-research/exploring-toxcast-data).…”

Section: Methodsmentioning

confidence: 99%

“…CGPD-tetramers, was proposed to understand the phenotypes and diseases that result from the interaction of chemicals with genes (Davis et al, 2020). Based on our previous work (Sahoo et al, 2024), we retrieved the CGPD-tetramers associated with plastic additives within CTD, and leveraged them to identify the associated KEs within AOP-Wiki.…”

Section: Methodsmentioning

confidence: 99%

“…Based on our previous work (Sahoo et al, 2024), we relied on a systematic and comprehensive data-centric integration method to identify the KEs within AOP-Wiki that are associated with plastic additives by utilizing toxicogenomics and biological endpoints data from five exposome-relevant resources: ToxCast (Dix et al, 2007), Comparative Toxicogenomics Database (CTD) (Davis et al, 2023) (https://ctdbase.org/), DEDuCT (Karthikeyan et al, 2021(Karthikeyan et al, , 2019 (https://cb.imsc.res.in/deduct/), NeurotoxKb (Ravichandran et al, 2021b) (https://cb.imsc.res.in/neurotoxkb/) and AOP-Wiki (https://aopwiki.org/).…”

Section: Identification Of Kes Associated With Plastic Additivesmentioning

confidence: 99%

“…These 28 AOPs are classified under various disease categories namely, cancer, gastrointestinal system disease, reproductive system disease, respiratory system disease, cognitive disorder, thoracic disease, and musculoskeletal system disease (Supplementary Table S9). Previously, Yang et al (Yang et al, 2022) Next, we computed the cumulative weight of evidence (WoE) for each of these 28 B[a]P-AOPs based on their KER information to assess the biological plausibility (Ravichandran et al, 2022b;Sahoo et al, 2024). We observed that 9 of these 28 B[a]P-AOPs have 'High' cumulative WoE and 6 B[a]P-AOPs have 'Moderate' cumulative WoE (Supplementary Table S11).…”

mentioning

confidence: 91%

“…Recently, we had leveraged heterogenous biological data from five exposome-relevant resources namely, ToxCast, Comparative Toxicogenomics Database (CTD) (Davis et al, 2023), DEDuCT (Karthikeyan et al, 2021, 2019), NeurotoxKb (Ravichandran et al, 2021b), and AOP-Wiki to extensively explore various toxicity pathways associated with inorganic cadmium-induced toxicity (Sahoo et al, 2024). Previously, Aguayo-Orozco et al .…”

Section: Introductionmentioning

confidence: 99%

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Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Sahoo,

Chivukula,

Madgaonkar

et al. 2024

Preprint

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Plastics are widespread pollutants found in atmospheric, terrestrial and aquatic ecosystems due to their extensive usage and environmental persistence. Plastic additives, that are utilized to achieve specific functionality in plastics, leach into the environment upon plastic degradation and pose considerable risk to ecological and human health. Limited knowledge concerning the presence of plastic additives throughout the plastic life cycle has hindered their effective regulation, thereby posing risks to product safety. In this study, we leveraged the adverse outcome pathway (AOP) framework to understand the mechanisms underlying plastic additives-induced toxicities. We first identified an exhaustive list of 6470 plastic additives from chemicals documented to be found in plastics. Next, we leveraged heterogenous toxicogenomics and biological endpoints data from five exposome-relevant resources, and identified associations between 1287 plastic additives and 322 complete and high quality AOPs within AOP-Wiki. Based on these plastic additive-AOP associations, we constructed a stressor-centric AOP network, wherein the stressors are categorized into 10 priority use sectors and AOPs are linked to 27 disease categories. We visualized the plastic additives-AOP network for each of the 1287 plastic additives and made them available in a dedicated website: https://cb.imsc.res.in/saopadditives/. Finally, we showed the utility of the constructed plastic additives-AOP network by identifying 28 highly relevant AOPs associated with benzo[a]pyrene, and thereafter, explored the associated toxicity pathways leading to respiratory and gastrointestinal system diseases in humans and developmental disorders in aquatic species. Overall, the constructed plastic additives-AOP network will enable regulatory risk assessment of plastic additives, thereby contributing towards a toxic-free circular economy for plastics.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Identification Of Kes Associated With Plastic Additivesmentioning

confidence: 99%

mentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

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Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Sahoo,

Chivukula,

Madgaonkar

et al. 2024

Preprint

Self Cite

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show abstract

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Sahoo,

Chivukula,

Madgaonkar

et al. 2024

Arch Toxicol

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Plastics are widespread pollutants found in atmospheric, terrestrial and aquatic ecosystems due to their extensive usage and environmental persistence. Plastic additives, that are intentionally added to achieve specific functionality in plastics, leach into the environment upon plastic degradation and pose considerable risk to ecological and human health. Limited knowledge concerning the presence of plastic additives throughout plastic life cycle has hindered their effective regulation, thereby posing risks to product safety. In this study, we leveraged the adverse outcome pathway (AOP) framework to understand the mechanisms underlying plastic additives-induced toxicities. We first identified an exhaustive list of 6470 plastic additives from chemicals documented in plastics. Next, we leveraged heterogenous toxicogenomics and biological endpoints data from five exposome-relevant resources, and identified associations between 1287 plastic additives and 322 complete and high quality AOPs within AOP–Wiki. Based on these plastic additive–AOP associations, we constructed a stressor-centric AOP network, wherein the stressors are categorized into ten priority use sectors and AOPs are linked to 27 disease categories. We visualized the plastic additives–AOP network for each of the 1287 plastic additives and made them available in a dedicated website: https://cb.imsc.res.in/saopadditives/. Finally, we showed the utility of the constructed plastic additives–AOP network by identifying highly relevant AOPs associated with benzo[a]pyrene (B[a]P), bisphenol A (BPA), and bis(2-ethylhexyl) phthalate (DEHP) and thereafter, explored the associated toxicity pathways in humans and aquatic species. Overall, the constructed plastic additives–AOP network will assist regulatory risk assessment of plastic additives, thereby contributing towards a toxic-free circular economy for plastics.

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Sulfide-carbonate-mineralized functional bacterial consortium for cadmium removal in flue gas

Huang,

Chen,

Liu

et al. 2024

Chemosphere

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An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity

Cited by 5 publications

References 105 publications

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Sulfide-carbonate-mineralized functional bacterial consortium for cadmium removal in flue gas

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