# Genomic Impacts of Biological Exposures

**Authors:** Amalia S. Parra, Christopher A. Johnston

PMC · DOI: 10.3390/jdb14010012 · Journal of Developmental Biology · 2026-03-05

## TL;DR

This paper reviews how biological exposures affect gene expression and health, highlighting new ways to track and understand these effects for better disease prevention and precision medicine.

## Contribution

The paper introduces recent advances in exposure biology and their potential for identifying novel biomarkers and improving biological security.

## Key findings

- Extrinsic factors in the exposome significantly influence gene expression and tissue homeostasis.
- Integrating exposure research with new technologies can improve threat prediction and disease understanding.
- Precision medicine benefits from understanding interactions between genetic and nongenetic factors.

## Abstract

Development and maintenance of complex tissues depends on a number of coordinated steps from early development through adulthood. These processes are fundamentally controlled by highly regulated gene expression patterns. Although critical contributors during development, intrinsic changes in gene expression alone cannot fully explain the complicated pathways that control tissue homeostasis. Rather, tissues are continuously exposed to extrinsic factors that also influence essential cellular processes. These external environmental factors are collectively known as the exposome. Notably, how different exposures impact gene expression and protein function, as well as how certain exposures lead to disease states, is not well understood. To understand how internal and external factors influence organismal development and homeostasis, it is necessary to consider how genetic and nongenetic components interact to direct critical biochemical pathways. Doing so presents new avenues for precision medicine, understanding disease progression, identifying biological threats, and improving biological security concerns. In this review, we present recent advances in exposure biology, focusing on how these innovations can help identify novel biomarkers to better understand changing exposome components. We also discuss the need to integrate technologies and exposure research to better identify and predict threats.

## Full-text entities

- **Genes:** KDM6A (lysine demethylase 6A) [NCBI Gene 7403] {aka KABUK2, UTX, bA386N14.2}, Nfkb1 (nuclear factor kappa B subunit 1) [NCBI Gene 81736] {aka EBP-1, NF-kB, NFKB-p50, p50}, GDNF (glial cell derived neurotrophic factor) [NCBI Gene 2668] {aka ATF, ATF1, ATF2, HFB1-GDNF, HSCR3}, SDF4 (stromal cell derived factor 4) [NCBI Gene 51150] {aka Cab45, SDF-4}, IDH1 (isocitrate dehydrogenase (NADP(+)) 1) [NCBI Gene 3417] {aka HEL-216, HEL-S-26, IDCD, IDH, IDP, IDPC}, HUS1 (HUS1 checkpoint clamp component) [NCBI Gene 3364] {aka hHUS1}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, CDK2 (cyclin dependent kinase 2) [NCBI Gene 1017] {aka CDKN2, p33(CDK2)}, CDK1 (cyclin dependent kinase 1) [NCBI Gene 983] {aka CDC2, CDC28A, P34CDC2}, CSF2 (colony stimulating factor 2) [NCBI Gene 1437] {aka CSF, GMCSF}, KDM6B (lysine demethylase 6B) [NCBI Gene 23135] {aka JMJD3, NEDCFSA, NEDSST}, HLA-A (major histocompatibility complex, class I, A) [NCBI Gene 3105] {aka HLAA}, TIMP2 (TIMP metallopeptidase inhibitor 2) [NCBI Gene 7077] {aka CSC-21K, DDC8}, PADI4 (peptidyl arginine deiminase 4) [NCBI Gene 23569] {aka PAD, PAD4, PADI5, PDI4, PDI5}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, IL18 (interleukin 18) [NCBI Gene 3606] {aka IGIF, IL-18, IL-1g, IL1F4}, MMP2 (matrix metallopeptidase 2) [NCBI Gene 4313] {aka CLG4, CLG4A, MMP-2, MMP-II, MONA, TBE-1}, PCNA (proliferating cell nuclear antigen) [NCBI Gene 5111] {aka ATLD2}, CCND1 (cyclin D1) [NCBI Gene 595] {aka BCL1, D11S287E, PRAD1, U21B31}, CYP2C9 (cytochrome P450 family 2 subfamily C member 9) [NCBI Gene 1559] {aka CPC9, CYP2C, CYP2C10, CYPIIC9, P450-2C9, P450IIC9}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, Il6 (interleukin 6) [NCBI Gene 24498] {aka ILg6, Ifnb2}, GSR (glutathione-disulfide reductase) [NCBI Gene 2936] {aka CNSHA10, GR, GSRD, HEL-75, HEL-S-122m}, ACHE (acetylcholinesterase (Yt blood group)) [NCBI Gene 43] {aka ACEE, ARACHE, N-ACHE, YT}, Il1b (interleukin 1 beta) [NCBI Gene 24494] {aka IL-1F2}, PON1 (paraoxonase 1) [NCBI Gene 5444] {aka ESA, MVCD5, PON}, WNT2 (Wnt family member 2) [NCBI Gene 7472] {aka INT1L1, IRP}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, TIMP1 (TIMP metallopeptidase inhibitor 1) [NCBI Gene 7076] {aka CLGI, EPA, EPO, HCI, TIMP, TIMP-1}, MMP9 (matrix metallopeptidase 9) [NCBI Gene 4318] {aka CLG4B, GELB, MANDP2, MMP-9}, FCGR1A (Fc gamma receptor Ia) [NCBI Gene 2209] {aka CD64, CD64A, FCG1, FCGR1, FCRI, FcgammaRI}, GH1 (growth hormone 1) [NCBI Gene 2688] {aka GH, GH-N, GHB5, GHN, IGHD1A, IGHD1B}
- **Diseases:** mitochondrial malfunction (MESH:D028361), diabetes (MESH:D003920), gastrointestinal dysfunction (MESH:D005767), nervous system disorders (MESH:D009422), neurological disease (MESH:D020271), developmental defects (MESH:D000094602), glomerulonephritis (MESH:D005921), GI disturbances (MESH:D014832), neurodegeneration (MESH:D019636), blood disorders (MESH:D006402), rheumatoid arthritis (MESH:D001172), Toxicity (MESH:D064420), cardiovascular disease (MESH:D002318), system (MESH:D015619), gut dysbiosis (MESH:D064806), cognitive dysfunction (MESH:D003072), sleep disturbances (MESH:D012893), Parkinson's (MESH:D010300), miscarriage (MESH:D000022), diseases (MESH:D004194), cardiac dysfunction (MESH:D006331), fungal (MESH:D009181), scoliosis (MESH:D012600), demyelination (MESH:D003711), abnormal birth weight (MESH:D001724), injury to (MESH:D014947), nausea (MESH:D009325), bleeding (MESH:D006470), congenital heart disease (MESH:D006330), ALS (MESH:D000690), coma (MESH:D003128), chronic kidney disease (MESH:D051436), carcinogens (MESH:D011230), genetic defects (MESH:D030342), vomiting (MESH:D014839), endothelial dysfunction (MESH:D014652), seizures (MESH:D012640), thrombosis (MESH:D013927), inflammation (MESH:D007249), hypoxic (MESH:D002534), spinal defect (MESH:D013122), necrosis (MESH:D009336), MS (MESH:D009103), diabetic nephropathy (MESH:D003928), fibrosis (MESH:D005355), cancer (MESH:D009369), lung adenocarcinoma (MESH:D000077192), metabolic dysfunctions (MESH:D008659), melanoma (MESH:D008545), autoimmune conditions (MESH:D001327)
- **Chemicals:** Aflatoxin (MESH:D000348), BPA (MESH:C006780), trichothecenes (MESH:D014255), gold (MESH:D006046), Zinc oxide (MESH:D015034), TiO2 (MESH:C009495), metoprolol (MESH:D008790), arsenic (MESH:D001151), oxygen (MESH:D010100), Heavy metal (MESH:D019216), infliximab (MESH:D000069285), ochratoxins (MESH:D009793), patulin (MESH:D010365), deoxynivalenol (MESH:C007262), Alternaria toxins (-), cadmium (MESH:D002104), adalimumab (MESH:D000068879), graphene (MESH:D006108), metal (MESH:D008670), titanium (MESH:D014025), OTA (MESH:C025589), warfarin (MESH:D014859), lead (MESH:D007854), ROS (MESH:D017382), Organophosphates (MESH:D010755)
- **Species:** Drosophila melanogaster (fruit fly, species) [taxon 7227], Homo sapiens (human, species) [taxon 9606], C. elegans [taxon 328850], Danio rerio (leopard danio, species) [taxon 7955], Mus musculus (house mouse, species) [taxon 10090], Staphylococcus aureus (species) [taxon 1280], Rattus norvegicus (brown rat, species) [taxon 10116]
- **Mutations:** rs1801274, rs396991, GG > CC, rs2308321, -308 A/G, -174G/C, AA > GG, c.-1639: G > A, rs2241880, rs12777823
- **Cell lines:** Caco-2 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0025)

## Full text

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## Figures

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## References

162 references — full list in the complete paper: https://tomesphere.com/paper/PMC13028019/full.md

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Source: https://tomesphere.com/paper/PMC13028019