Table 2.
Cell or tissue-specific GEMs developed using omics data. Abbreviations G, T, P, M, and F denote gene expression (microarray), transcriptomics (NGS), proteomics, metabolomics, and fluxomics, data, respectively. CVD, NAFLD, AD, T2D, T1D, MTB, IEMs, PBMCs, and HEK denote cardiovascular disease, non-alcoholic fatty liver disease, Alzheimer’s disease, type 2 diabetes, type 1 diabetes, and Mycobacterium tuberculosis, inborn errors of metabolism, peripheral blood mononuclear cells, and human embryonic kidney, respectively.
| Tissue or Cell-Type | Human Metabolic Reconstructions Used for the Contextualization | Omics or Diet Data Type(s) | Phenotypes Modeled | References |
|---|---|---|---|---|
| Liver | HepatoNet1 | G | Liver metabolism | [113] |
| HMR2 (iHepatocytes2322) |
T, P, and M | NAFLD | [6] | |
| HMR2 | T and M | NAFLD | [8] | |
| Recon1 | T, M, and F | NAFLD | [98] | |
| Adipocytes | HMR1 (iAdipocytes1809) |
T, P, and F | Adipocyte metabolism | [28] |
| Skeletal muscles | HMR2 (iMyocyte2419) |
T and P | T2D | [29] |
| –– | T and P | CVD | [105] | |
| Heart | Recon1 (CardioNet) |
G | Cardiac metabolism | [114] |
| Brain | Astrocyte metabolic network | T | Ischemic and normal conditions | [115] |
| Recon3D | T and M | AD | [103,104] | |
| Recon1 (iNL403) |
G and P | AD | [101] | |
| Kidney | –– | T and P | Focal segmental glomerulosclerosis | [116] |
| Kidney | Recon2 (HEK cell culture) |
–– | Metabolism of HEK cells | [117] |
| Alveolar macrophage | Recon1 (iAB-AMØ-1410) |
G | Host-pathogen interactions in MTB | [118] |
| CD4+ T-cells | HMR2 | G, T, and M | CD4+ T-cells activation and differentiation | [7] |
| PBMCs | HMR2 | G, T, and M | T1D | [119] |
| Human small intestinal epithelial cells | Recon1 (hs_sIEC611) |
American diet and a balanced diet | Intestinal metabolism and IEMs | [106] |
| Whole-body metabolic reconstructions | Recon3D (WBM) |
T, P, and M | Human metabolism and host-microbiome co-metabolism | [120] |