Multi-omic analysis of bat versus human fibroblasts reveals altered central metabolism
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, China
- SingHealth Duke-NUS Global Health Institute, Singapore
Figures
Figure 1 with 2 supplements
RNAseq data analysis of PaLung and WI-38 cells for differential expression and pathway enrichment.
(A) Workflow of bioinformatics analysis pipeline for RNAseq data from PaLung (P. alecto) and WI-38 (H. sapiens) cells (n=3). (B) Heatmap showing the expression patterns for genes that passed our …
Figure 1—figure supplement 1
Analysis of transcriptomics data from PaLung and WI-38 cells.
(A) Principal component analysis plots showing the separation of the PaLung and WI-38 transcriptomics datasets. (B) Volcano plot showing the genes that passed our differential expression (DE) …
Figure 1—figure supplement 2
A summary of transcriptomics log fold changes (LFC) overlaid onto key metabolic reactions from central carbon metabolism.
Shown here is a network of reactions in central carbon metabolism that includes reactions from multiple pathways (glycolysis, pentose phosphate pathway, TCA cycle, fatty acid oxidation, electron …
Figure 2 with 1 supplement
Proteomic data analysis of mitochondrial fractions of PaLung and WI-38 cells for differential expression, pathway enrichment, and electron transport chain (ETC) activity.
(A) Workflow of bioinformatics analysis pipeline for proteomics data from PaLung (P. alecto) and WI-38 (H. sapiens) cells (n=3). (B) Heatmap showing the expression patterns for the 129 …
Figure 2—figure supplement 1
Proteomic analysis of PaLung and WI-38 data.
(A) Gene ontology category cellular (GO CC) enrichment using the Enrichr tool for compartmental enrichment on the 1469 genes detected in the proteomics dataset shows enrichment for the mitochondrial …
Figure 3 with 2 supplements
Metabolomic data and model-based analysis of mitochondrial metabolism in PaLung and WI-38 cells.
(A) Schematic showing the metabolic modeling pipeline. We begin with the context-specific reconstruction of a metabolic model – the process where a generic mitochondrial model (Smith et al., 2017) …
Figure 3—figure supplement 1
Schematic of the workflow for metabolic flux modeling.
(A) Left is a toy network of metabolic reactions showing a few reactions from the glycolysis pathway for illustration. This network of metabolic reactions (defined by nodes and arrows) is converted …
Figure 3—figure supplement 2
Analysis of the metabolomics data from PaLung and WI-38 cells.
(A) Principal component analysis (PCA) plot shows the separation between the three PaLung samples and the three WI-38 samples in the metabolomics data. (B–D) Bar plots of AMP (B), the ratios of …
Figure 4
PaLung cells show basal metabolism that resembles an ischemic-like state.
(A) Fold changes (mean PaLung/mean WI-38) of metabolite abundances, obtained through targeted metabolomics profiling of central carbon metabolites in PaLung and WI-38 cells. (B and C) Amino acid and …
Figure 5 with 1 supplement
Reactive oxygen species (ROS) and antioxidant system measurements in PaLung and WI-38 cells.
(A) MitoSOX measurement of PaLung and WI-38 cells with or without antimycin A treatment for 1 hr. Antimycin A is an electron transport chain (ETC) inhibitor known to induce superoxide generation. (B)…
Figure 5—figure supplement 1
Increased phosphorylation of NAD cofactors in PaLung cells.
(A) Ratio of NADP/NAD in PaLung (P) and WI-38 (W) cells. (B) Bar graphs show the expression levels of the genes involved in NAD synthesis and phosphorylation (as transcripts per million [TPM]) in …
Figure 6
PaLung cells display high resistance to ferroptosis.
(A and B) WI-38 or PaLung cells were treated with 2.5 µM erastin and/or 1 µM ferrostatin-1. Representative images were taken at 6 hr using phase contrast microscopy (A). Propidium iodide (PI) …
Appendix 1—figure 1
Gene set enrichment analysis (GSEA) enrichment plots of the same gene sets as shown in Figure 2D and E of the main text, after removing the outlier proteomic samples P1 and W1 from the analysis (n=2).
Appendix 2—figure 1
Gene set enrichment analysis (GSEA) enrichment plots of the gene sets that are biological equivalents of the gene sets shown in Figure 2D and E of the main text.
This analysis was performed using the MitoCarta 3.0 gene set list instead of the Gene Ontology Biological Process (GO BP) gene set list used to generate Figure 2D and E.
Appendix 3—figure 1
Flux sampling histograms of the P and W metabolic models in the unconstrained control (left column) and the constrained (right column) cases.
The P fluxes are in blue and the W fluxes in red. The first two rows show the constrained reactions (Complex I and O2), while the third row shows the flux histograms of the Complex II reaction.
Appendix 3—figure 2
Flux sampling histograms of the P and W metabolic models under different threshold values for constraints.
Each row corresponds to a constraint scheme (unconstrained, 20-80, 30-70, 40-60, and 50-50), and was obtained by running our script with different minFrac values. Within each panel, the P model …
Author response image 1
Histograms of coefficient-of-variation (CV) for the four protein subsets (defined by p-value and log fold change).
Each row corresponds to a different subset indicated by the title above. Within each row, the blue histogram corresponds to the CV from the 3 PaLung samples, and the red histogram corresponds to the …
Author response image 2
Histograms of log(abundance) for the four protein subsets (defined by p-value and log fold change) for WI-38 samples.
Each panel corresponds to a different subset indicated by the title above.
Author response image 3
Scatter plot of Log fold change of proteomic data vs Log fold change of transcriptomics data.
Each point represents a protein/gene that was detected in both proteomics and transcriptomics experiments. Log fold change was computed in each case as log2(PaLung /WI-38).
Author response image 4
Flux histograms showing the feasible flux distributions for the Complex I (CI) and the mitochondrial oxygen transport (O2) reactions in the P (PaLung) and W (WI-38) metabolic models.
Each column corresponds to setting constraints as per one of the four experiments described above.
Tables
Appendix 1—table 1
Table showing the top 35 gene sets enriched in the PaLung mitochondrial proteomics samples, after removing the outlier samples P1 and W1.
Columns indicate the name of the gene set, size (number of genes in gene set), normalized enrichment score, and the false discovery rate (FDR) value.
| NAME | SIZE | NES | FDR q-val |
|---|---|---|---|
| MUSCLE CONTRACTION GOBP GO:0006936 | 35 | –2.301 | 0.002 |
| NICOTINIC ACETYLCHOLINE RECEPTOR SIGNALING PATHWAY PANTHER PATHWAY P00044 | 15 | –2.191 | 0.012 |
| REGULATION OF CELL JUNCTION ASSEMBLY GOBP GO:1901888 | 15 | –2.163 | 0.011 |
| THE CITRIC ACID (TCA) CYCLE AND RESPIRATORY ELECTRON TRANSPORT REACTOME R-HSA-1428517.1 | 64 | –2.154 | 0.011 |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION MSIGDB_C2 HALLMARK_OXIDATIVE_PHOSPHORYLATION | 91 | –2.142 | 0.010 |
| COLLAGEN FORMATION REACTOME DATABASE ID RELEASE 71 1474290 | 31 | –2.096 | 0.015 |
| RESPIRATORY ELECTRON TRANSPORT, ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING, AND HEAT PRODUCTION BY UNCOUPLING PROTEINS. REACTOME R-HSA-163200.1 | 32 | –2.074 | 0.017 |
| RESPIRATORY ELECTRON TRANSPORT REACTOME R-HSA-611105.3 | 32 | –2.059 | 0.019 |
| NADH DEHYDROGENASE COMPLEX ASSEMBLY GOBP GO:0010257 | 16 | –2.059 | 0.017 |
| EPH-EPHRIN SIGNALING REACTOME DATABASE ID RELEASE 71 2682334 | 30 | –2.057 | 0.016 |
| COMPLEX I BIOGENESIS REACTOME R-HSA-6799198.1 | 16 | –2.036 | 0.018 |
| MUSCLE SYSTEM PROCESS GOBP GO:0003012 | 40 | –2.033 | 0.017 |
| RHO GTPASES ACTIVATE PKNS REACTOME DATABASE ID RELEASE 71 5625740 | 17 | –2.030 | 0.016 |
| ACTIN FILAMENT-BASED MOVEMENT GOBP GO:0030048 | 17 | –2.022 | 0.017 |
| ACTOMYOSIN STRUCTURE ORGANIZATION GOBP GO:0031032 | 21 | –2.021 | 0.016 |
| MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX I ASSEMBLY GOBP GO:0032981 | 16 | –1.999 | 0.019 |
| INTEGRIN SIGNALLING PATHWAY PANTHER PATHWAY P00034 | 44 | –1.994 | 0.019 |
| KERATINIZATION GOBP GO:0031424 | 15 | –1.976 | 0.021 |
| MITOCHONDRIAL ATP SYNTHESIS COUPLED ELECTRON TRANSPORT GOBP GO:0042775 | 26 | –1.971 | 0.021 |
| MITOCHONDRIAL ELECTRON TRANSPORT, NADH TO UBIQUINONE GOBP GO:0006120 | 15 | –1.968 | 0.021 |
| MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX ASSEMBLY GOBP GO:0033108 | 19 | –1.966 | 0.020 |
| CORNIFICATION GOBP GO:0070268 | 15 | –1.963 | 0.019 |
| SYSTEM PROCESS GOBP GO:0003008 | 77 | –1.953 | 0.021 |
| MIDBRAIN DEVELOPMENT GOBP GO:0030901 | 15 | –1.953 | 0.020 |
| COLLAGEN BIOSYNTHESIS AND MODIFYING ENZYMES REACTOME R-HSA-1650814.3 | 25 | –1.949 | 0.020 |
| KERATINIZATION REACTOME DATABASE ID RELEASE 71 6805567 | 15 | –1.936 | 0.022 |
| ELECTRON TRANSPORT CHAIN (OXPHOS SYSTEM IN MITOCHONDRIA) WIKIPATHWAYS_20191210 WP111 HOMO SAPIENS | 28 | –1.933 | 0.022 |
| NABA_CORE_MATRISOME MSIGDB_C2 NABA_CORE_MATRISOME | 34 | –1.921 | 0.025 |
| CELLULAR RESPIRATION GOBP GO:0045333 | 52 | –1.905 | 0.028 |
| HALLMARK_ESTROGEN_RESPONSE_EARLY MSIGDB_C2 HALLMARK_ESTROGEN_RESPONSE_EARLY | 16 | –1.902 | 0.028 |
| EXTRACELLULAR MATRIX ORGANIZATION REACTOME DATABASE ID RELEASE 71 1474244 | 59 | –1.895 | 0.029 |
| RHO GTPASES ACTIVATE PAKS REACTOME R-HSA-5627123.2 | 16 | –1.863 | 0.038 |
| INFLAMMATION MEDIATED BY CHEMOKINE AND CYTOKINE SIGNALING PATHWAY PANTHER PATHWAY P00031 | 30 | –1.848 | 0.043 |
| ELECTRON TRANSPORT CHAIN GOBP GO:0022900 | 31 | –1.842 | 0.044 |
| ATP SYNTHESIS COUPLED ELECTRON TRANSPORT GOBP GO:0042773 | 27 | –1.832 | 0.048 |
Appendix 2—table 1
Table showing the top gene sets enriched in the PaLung mitochondrial proteomics samples, when gene set enrichment analysis (GSEA) was performed using the MitoCarta 3.0 gene set list instead of the Gene Ontology Biological Process (GO BP) gene set.
Columns indicate the name of the gene set, size (number of genes in gene set), normalized enrichment score, and the false discovery rate (FDR) value.
| NAME | SIZE | NES | FDR q-val |
|---|---|---|---|
| OXPHOS_SUBUNITS | 34 | –2.186 | 0.002 |
| OXPHOS | 41 | –2.166 | 0.001 |
| CARBOHYDRATE_METABOLISM | 36 | –2.004 | 0.005 |
| TRANSLATION | 16 | –1.987 | 0.005 |
| COMPLEX_I | 17 | –1.966 | 0.005 |
| CI_SUBUNITS | 15 | –1.892 | 0.007 |
| FATTY_ACID_OXIDATION | 20 | –1.864 | 0.007 |
| METALS_AND_COFACTORS | 30 | –1.794 | 0.011 |
| METABOLISM | 153 | –1.782 | 0.011 |
| AMINO_ACID_METABOLISM | 33 | –1.763 | 0.011 |
| MITOCHONDRIAL_CENTRAL_DOGMA | 24 | –1.609 | 0.030 |
| TCA_CYCLE | 15 | –1.510 | 0.053 |
| LIPID_METABOLISM | 43 | –1.480 | 0.057 |
| PROTEIN_IMPORT_SORTING_AND_HOMEOSTASIS | 24 | –1.200 | 0.223 |
| PROTEIN_HOMEOSTASIS | 18 | –1.053 | 0.377 |
Appendix 3—table 1
Minimum and maximum flux values possible for the Complex I and mitochondrial O2 transport reaction when different constraints are applied to the P and W metabolic models.
| Constraint description (all follow the 30-70 protocols) | Complex 1 | Oxygen transport | ||||||
|---|---|---|---|---|---|---|---|---|
| Bat (P model) | Human (W model) | Bat (P model) | Human (W model) | |||||
| Min | Max | Min | Max | Min | Max | Min | Max | |
| Control simulation – no constraints | 0 | 41.43 | 0 | 41.44 | 0 | 19.8 | 0 | 19.8 |
| Ideal target flux range expected with the 30-70 protocol, when CI and O2 are independent of each other | 29 | 41.43 | 0 | 12.43 | 0 | 5.94 | 13.86 | 19.8 |
| Constraining only the Complex I reaction | 29 | 41.43 | 0 | 12.43 | 13.58 | 19.8 | 0 | 19.8 |
| Constraining only the O2 reaction | 0 | 13.74 | 0 | 41.43 | 0 | 5.94 | 13.86 | 19.8 |
| Constraining CI first, then constraining O2, without avoiding flux range overlap | 29 | 32.72 | 0 | 12.43 | 13.58 | 15.45 | 13.86 | 19.8 |
| Constraining CI first, then constraining O2, avoiding flux range overlap | 29 | 32.72 | 0 | 12.43 | 13.58 | 15.45 | 15.45 | 19.8 |
| Constraining O2 first, then constraining CI, without avoiding flux range overlap | 9.61 | 13.73 | 0 | 12.43 | 3.88 | 5.94 | 13.86 | 19.8 |
| Constraining O2 first, then constraining CI, avoiding flux range overlap | 9.61 | 13.73 | 0 | 9.61 | 3.88 | 5.94 | 13.86 | 19.8 |
Author response table 1
| NAME | SIZE | NES | FDR |
|---|---|---|---|
| L13A-MEDIATED TRANSLATIONAL SILENCING OF CERULOPLASMIN EXPRESSION REACTOME DATABASE ID RELEASE 71 156827 | 102 | -1.86459 | 0 |
| CAP-DEPENDENT TRANSLATION INITIATION REACTOME DATABASE ID RELEASE 71 72737 | 110 | -1.85211 | 0 |
| TRANSLATIONAL INITIATION GOBP GO:0006413 | 114 | -1.8446 | 0 |
| REGULATION OF EXPRESSION OF SLITS AND ROBOS REACTOME DATABASE ID RELEASE 71 9010553 | 153 | -1.84266 | 0 |
| NONSENSE MEDIATED DECAY (NMD) ENHANCED BY THE EXON JUNCTION COMPLEX (EJC) REACTOME R-HSA-975957.1 | 107 | -1.83796 | 0 |
| GTP HYDROLYSIS AND JOINING OF THE 60S RIBOSOMAL SUBUNIT REACTOME R-HSA-72706.2 | 103 | -1.82911 | 0 |
| NUCLEAR-TRANSCRIBED MRNA CATABOLIC PROCESS GOBP GO:0000956 | 179 | -1.82134 | 0 |
| MRNA CATABOLIC PROCESS GOBP GO:0006402 | 191 | -1.81824 | 0 |
| EUKARYOTIC TRANSLATION INITIATION REACTOME DATABASE ID RELEASE 71 72613 | 110 | -1.81618 | 0 |
| EUKARYOTIC TRANSLATION ELONGATION REACTOME R-HSA-156842.2 | 85 | -1.81611 | 0 |
| SRP-DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE REACTOME R-HSA-1799339.2 | 103 | -1.81578 | 0 |
| SELENOCYSTEINE SYNTHESIS REACTOME DATABASE ID RELEASE 71 2408557 | 84 | -1.81445 | 0 |
| NONSENSE-MEDIATED DECAY (NMD) REACTOME R-HSA-927802.2 | 107 | -1.81251 | 0 |
| TRANSLATION REACTOME DATABASE ID RELEASE 71 72766 | 278 | -1.8121 | 0 |
| RNA CATABOLIC PROCESS GOBP GO:0006401 | 214 | -1.81042 | 0 |
| PEPTIDE BIOSYNTHETIC PROCESS GOBP GO:0043043 | 313 | -1.8098 | 0 |
| FORMATION OF A POOL OF FREE 40S SUBUNITS REACTOME DATABASE ID RELEASE 71 72689 | 92 | -1.8098 | 0 |
| INFLUENZA LIFE CYCLE REACTOME DATABASE ID RELEASE 71 168255 | 129 | -1.80935 | 0 |
| RESPONSE OF EIF2AK4 (GCN2) TO AMINO ACID DEFICIENCY REACTOME DATABASE ID RELEASE 71 9633012 | 92 | -1.80856 | 0 |
| VIRAL MRNA TRANSLATION REACTOME DATABASE ID RELEASE 71 192823 | 81 | -1.80841 | 0 |
| PEPTIDE CHAIN ELONGATION REACTOME R-HSA-156902.2 | 81 | -1.80743 | 0 |
| NONSENSE MEDIATED DECAY (NMD) INDEPENDENT OF THE EXON JUNCTION COMPLEX (EJC) REACTOME R-HSA-975956.1 | 87 | -1.80499 | 0 |
| INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION REACTOME DATABASE ID RELEASE 71 168273 | 121 | -1.80381 | 0 |
| PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM GOBP GO:0070972 | 119 | -1.80193 | 0 |
| NUCLEAR-TRANSCRIBED MRNA CATABOLIC PROCESS, NONSENSE-MEDIATED DECAY GOBP GO:0000184 | 107 | -1.79958 | 0 |
| SIGNALING BY ROBO RECEPTORS REACTOME R-HSA-376176.4 | 193 | -1.79657 | 0 |
| INFLUENZA INFECTION REACTOME R-HSA-168254.2 | 139 | -1.79422 | 0 |
| TRANSLATION GOBP GO:0006412 | 296 | -1.79232 | 0 |
| EUKARYOTIC TRANSLATION TERMINATION REACTOME R-HSA-72764.4 | 85 | -1.79057 | 0 |
| SELENOAMINO ACID METABOLISM REACTOME DATABASE ID RELEASE 71 2408522 | 105 | -1.7747 | 0 |
| MAJOR PATHWAY OF RRNA PROCESSING IN THE NUCLEOLUS AND CYTOSOL REACTOME R-HSA-6791226.3 | 170 | -1.77321 | 0 |
| ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM GOBP GO:0072599 | 100 | -1.76931 | 0 |
| COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE GOBP GO:0006613 | 90 | -1.7682 | 0 |
| RRNA PROCESSING IN THE NUCLEUS AND CYTOSOL REACTOME R-HSA-8868773.3 | 180 | -1.76363 | 2.64E-05 |
| PROTEIN TARGETING TO MEMBRANE GOBP GO:0006612 | 134 | -1.76038 | 2.57E-05 |
| CYTOPLASMIC RIBOSOMAL PROTEINS WIKIPATHWAYS_20191210 WP477 HOMO SAPIENS | 82 | -1.75783 | 4.97E-05 |
| PROTEIN TARGETING TO ER GOBP GO:0045047 | 97 | -1.75446 | 7.25E-05 |
| VIRAL GENE EXPRESSION GOBP GO:0019080 | 122 | -1.75351 | 7.06E-05 |
| SRP-DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE GOBP GO:0006614 | 85 | -1.75031 | 6.88E-05 |
| VIRAL TRANSCRIPTION GOBP GO:0019083 | 105 | -1.74701 | 6.71E-05 |
| ACTIVATION OF THE MRNA UPON BINDING OF THE CAP-BINDING COMPLEX AND EIFS, AND SUBSEQUENT BINDING TO 43S REACTOME R-HSA-72662.3 | 56 | -1.74344 | 8.72E-05 |
| AMIDE BIOSYNTHETIC PROCESS GOBP GO:0043604 | 383 | -1.74084 | 8.51E-05 |
| NUCLEOBASE-CONTAINING COMPOUND CATABOLIC PROCESS GOBP GO:0034655 | 322 | -1.73596 | 1.04E-04 |
| CYTOPLASMIC TRANSLATION GOBP GO:0002181 | 54 | -1.73436 | 1.02E-04 |
| RRNA PROCESSING REACTOME DATABASE ID RELEASE 71 72312 | 189 | -1.73364 | 9.96E-05 |
| TRANSLATION INITIATION COMPLEX FORMATION REACTOME DATABASE ID RELEASE 71 72649 | 55 | -1.73183 | 9.75E-05 |
| RIBOSOMAL SCANNING AND START CODON RECOGNITION REACTOME R-HSA-72702.3 | 55 | -1.71426 | 2.11E-04 |
| PROTEIN TARGETING GOBP GO:0006605 | 283 | -1.70904 | 2.62E-04 |
| FORMATION OF THE TERNARY COMPLEX, AND SUBSEQUENTLY, THE 43S COMPLEX REACTOME DATABASE ID RELEASE 71 72695 | 48 | -1.70325 | 4.03E-04 |
| CELLULAR NITROGEN COMPOUND CATABOLIC PROCESS GOBP GO:0044270 | 345 | -1.69784 | 4.66E-04 |
| ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE GOBP GO:0072594 | 325 | -1.69391 | 6.33E-04 |
| AROMATIC COMPOUND CATABOLIC PROCESS GOBP GO:0019439 | 347 | -1.6925 | 6.90E-04 |
| PEPTIDE METABOLIC PROCESS GOBP GO:0006518 | 392 | -1.69196 | 6.94E-04 |
| CELLULAR RESPONSES TO STRESS REACTOME DATABASE ID RELEASE 71 2262752 | 456 | -1.67591 | 0.001561 |
| HETEROCYCLE CATABOLIC PROCESS GOBP GO:0046700 | 343 | -1.66849 | 0.00217 |
| ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE GOBP GO:0090150 | 215 | -1.66714 | 0.00226 |
| CELLULAR RESPONSES TO EXTERNAL STIMULI REACTOME DATABASE ID RELEASE 71 8953897 | 459 | -1.66708 | 0.002236 |
| ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS GOBP GO:1901361 | 365 | -1.64869 | 0.004763 |
| CALNEXIN CALRETICULIN CYCLE REACTOME R-HSA-901042.2 | 23 | -1.60474 | 0.022972 |
| N-GLYCAN TRIMMING IN THE ER AND CALNEXIN CALRETICULIN CYCLE REACTOME DATABASE ID RELEASE 71 532668 | 32 | -1.59981 | 0.026341 |
| RIBOSOMAL LARGE SUBUNIT BIOGENESIS GOBP GO:0042273 | 64 | -1.58547 | 0.041181 |
| OXYGEN-DEPENDENT PROLINE HYDROXYLATION OF HYPOXIA-INDUCIBLE FACTOR Α REACTOME DATABASE ID RELEASE 71 1234176 | 61 | -1.58214 | 0.045084 |
| ER QUALITY CONTROL COMPARTMENT (ERQC) REACTOME DATABASE ID RELEASE 71 901032 | 18 | -1.57559 | 0.054216 |
| RIBOSOME ASSEMBLY GOBP GO:0042255 | 49 | -1.56563 | 0.071338 |
| AMINO ACID AND DERIVATIVE METABOLISM REACTOME R-HSA-71291.6 | 282 | -1.56487 | 0.071759 |
| CITRIC ACID CYCLE (TCA CYCLE) REACTOME DATABASE ID RELEASE 71 71403 | 22 | -1.56128 | 0.078243 |
| TRANSLATION FACTORS WIKIPATHWAYS_20191210 WP107 HOMO SAPIENS | 48 | -1.55985 | 0.079794 |
| REGULATION OF TP53 DEGRADATION REACTOME R-HSA-6804757.1 | 31 | -1.55649 | 0.086393 |
| VIRAL PROCESS GOBP GO:0016032 | 259 | -1.5553 | 0.08777 |
| SIGNALING BY FGFR4 REACTOME R-HSA-5654743.2 | 27 | -1.55424 | 0.088823 |
| REGULATION OF CALCIUM-MEDIATED SIGNALING GOBP GO:0050848 | 47 | -1.55084 | 0.095609 |
| NEGATIVE REGULATION OF G0 TO G1 TRANSITION GOBP GO:0070317 | 36 | -1.54615 | 0.106841 |
| CYCLIN D ASSOCIATED EVENTS IN G1 REACTOME R-HSA-69231.7 | 40 | -1.54534 | 0.107785 |
| G1 PHASE REACTOME DATABASE ID RELEASE 71 69236 | 40 | -1.54481 | 0.107951 |
| INSULIN PROCESSING REACTOME R-HSA-264876.2 | 20 | -1.54226 | 0.114012 |
| ERROR-PRONE TRANSLESION SYNTHESIS GOBP GO:0042276 | 19 | -1.53741 | 0.126991 |
| TRANSLESION SYNTHESIS BY POLH REACTOME R-HSA-110320.1 | 18 | -1.53506 | 0.132554 |
| SMOOTH MUSCLE CONTRACTION REACTOME R-HSA-445355.3 | 29 | -1.53357 | 0.136112 |
| CELLULAR RESPONSE TO HYPOXIA REACTOME R-HSA-1234174.2 | 69 | -1.53084 | 0.143644 |
| INTERSPECIES INTERACTION BETWEEN ORGANISMS GOBP GO:0044419 | 322 | -1.53011 | 0.144136 |
| DUAL INCISION IN TC-NER REACTOME R-HSA-6782135.1 | 62 | -1.53011 | 0.142368 |
| TCA CYCLE (AKA KREBS OR CITRIC ACID CYCLE) WIKIPATHWAYS_20191210 WP78 HOMO SAPIENS | 18 | -1.52732 | 0.149964 |
| SYMBIONT PROCESS GOBP GO:0044403 | 316 | -1.52634 | 0.151093 |
| REGULATION OF TP53 EXPRESSION AND DEGRADATION REACTOME R-HSA-6806003.1 | 32 | -1.5262 | 0.149924 |
| ERROR-FREE TRANSLESION SYNTHESIS GOBP GO:0070987 | 19 | -1.52572 | 0.149766 |
| TRANSCRIPTIONAL REGULATION BY E2F6 REACTOME DATABASE ID RELEASE 71 8953750 | 34 | -1.52515 | 0.150193 |
| MITOPHAGY REACTOME DATABASE ID RELEASE 71 5205647 | 25 | -1.52402 | 0.152274 |
| GAP-FILLING DNA REPAIR SYNTHESIS AND LIGATION IN TC-NER REACTOME DATABASE ID RELEASE 71 6782210 | 62 | -1.52125 | 0.161169 |
| ER-PHAGOSOME PATHWAY REACTOME DATABASE ID RELEASE 71 1236974 | 69 | -1.52107 | 0.159943 |
| SYNTHESIS OF ACTIVE UBIQUITIN: ROLES OF E1 AND E2 ENZYMES REACTOME R-HSA-8866652.2 | 29 | -1.52027 | 0.160681 |
| FCERI MEDIATED NF-ΚB ACTIVATION REACTOME R-HSA-2871837.2 | 71 | -1.51881 | 0.164231 |
| SIGNALING BY Fgfr1 REACTOME DATABASE ID RELEASE 71 5654736 | 32 | -1.51836 | 0.164082 |
| CENTRAL NERVOUS SYSTEM NEURON DEVELOPMENT GOBP GO:0021954 | 29 | -1.51808 | 0.163292 |
| REGULATION OF TP53 ACTIVITY THROUGH METHYLATION REACTOME DATABASE ID RELEASE 71 6804760 | 17 | -1.51684 | 0.166234 |
| AUF1 (HNRNP D0) BINDS AND DESTABILIZES MRNA REACTOME DATABASE ID RELEASE 71 450408 | 50 | -1.51593 | 0.167798 |
| B CELL ACTIVATION REACTOME DATABASE ID RELEASE 71 983705 | 92 | -1.5138 | 0.173984 |
| CYTOPLASMIC PATTERN RECOGNITION RECEPTOR SIGNALING PATHWAY GOBP GO:0002753 | 32 | -1.51365 | 0.172791 |
| IKK COMPLEX RECRUITMENT MEDIATED BY RIP1 REACTOME DATABASE ID RELEASE 71 937041 | 18 | -1.51332 | 0.172421 |
| VIRION ASSEMBLY GOBP GO:0019068 | 35 | -1.51249 | 0.173743 |
| ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT (ESCRT) REACTOME R-HSA-917729.1 | 27 | -1.5117 | 0.174884 |
| INFECTIOUS DISEASE REACTOME DATABASE ID RELEASE 71 5663205 | 379 | -1.51083 | 0.176457 |
| CHONDROITIN SULFATE METABOLIC PROCESS GOBP GO:0030204 | 26 | -1.50909 | 0.181727 |
| PROTEIN LOCALIZATION TO MEMBRANE GOBP GO:0072657 | 357 | -1.5088 | 0.18113 |
| I-KAPPAB KINASE/NF-KAPPAB SIGNALING GOBP GO:0007249 | 51 | -1.50817 | 0.181788 |
| TICAM1, RIP1-MEDIATED IKK COMPLEX RECRUITMENT REACTOME R-HSA-168927.3 | 17 | -1.50722 | 0.183755 |
| RIBOSOME BIOGENESIS GOBP GO:0042254 | 227 | -1.50672 | 0.183798 |
| VESICLE-MEDIATED TRANSPORT BETWEEN ENDOSOMAL COMPARTMENTS GOBP GO:0098927 | 21 | -1.50447 | 0.190799 |
| DEGRADATION OF GLI2 BY THE PROTEASOME REACTOME R-HSA-5610783.1 | 56 | -1.50387 | 0.191333 |
| CITRATE METABOLIC PROCESS GOBP GO:0006101 | 29 | -1.50382 | 0.189784 |
| ATP METABOLIC PROCESS GOBP GO:0046034 | 136 | -1.50016 | 0.202786 |
| PRADER-WILLI AND ANGELMAN SYNDROME WIKIPATHWAYS_20191210 WP3998 HOMO SAPIENS | 31 | -1.49851 | 0.20778 |
| MYD88-INDEPENDENT TOLL-LIKE RECEPTOR SIGNALING PATHWAY GOBP GO:0002756 | 27 | -1.49841 | 0.206341 |
| ANTIGEN PROCESSING AND PRESENTATION OF PEPTIDE ANTIGEN VIA MHC CLASS I GOBP GO:0002474 | 80 | -1.49762 | 0.207835 |
| STABILIZATION OF P53 REACTOME R-HSA-69541.5 | 53 | -1.49515 | 0.216427 |
| DOWNSTREAM TCR SIGNALING REACTOME R-HSA-202424.3 | 76 | -1.49442 | 0.217854 |
| THE ROLE OF GTSE1 IN G2 M PROGRESSION AFTER G2 CHECKPOINT REACTOME DATABASE ID RELEASE 71 8852276 | 57 | -1.49062 | 0.233181 |
| ABC TRANSPORTER DISORDERS REACTOME DATABASE ID RELEASE 71 5619084 | 64 | -1.49037 | 0.232277 |
| GAP-FILLING DNA REPAIR SYNTHESIS AND LIGATION IN GG-NER REACTOME R-HSA-5696397.1 | 24 | -1.48948 | 0.234394 |
| TNFR2 NON-CANONICAL NF-ΚB PATHWAY REACTOME R-HSA-5668541.2 | 80 | -1.48934 | 0.233057 |
| CLEC7A (DECTIN-1) SIGNALING REACTOME R-HSA-5607764.1 | 89 | -1.4891 | 0.232317 |
| REGULATION OF G0 TO G1 TRANSITION GOBP GO:0070316 | 38 | -1.48792 | 0.235624 |
| NEGATIVE REGULATION OF FGFR4 SIGNALING REACTOME DATABASE ID RELEASE 71 5654733 | 19 | -1.48738 | 0.236268 |
| VIF-MEDIATED DEGRADATION OF APOBEC3G REACTOME DATABASE ID RELEASE 71 180585 | 50 | -1.48711 | 0.235552 |
| G1 S DNA DAMAGE CHECKPOINTS REACTOME R-HSA-69615.2 | 63 | -1.48708 | 0.233782 |
| GLI3 IS PROCESSED TO GLI3R BY THE PROTEASOME REACTOME R-HSA-5610785.1 | 56 | -1.48693 | 0.232652 |
| RESPIRATORY ELECTRON TRANSPORT, ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING, AND HEAT PRODUCTION BY UNCOUPLING PROTEINS. REACTOME R-HSA-163200.1 | 107 | -1.48672 | 0.231731 |
| REGULATION OF TP53 ACTIVITY THROUGH PHOSPHORYLATION REACTOME DATABASE ID RELEASE 71 6804756 | 85 | -1.48642 | 0.231313 |
| BUDDING AND MATURATION OF HIV VIRION REACTOME DATABASE ID RELEASE 71 162588 | 24 | -1.48594 | 0.231623 |
| SIGNALING BY FGFR REACTOME R-HSA-190236.2 | 61 | -1.48574 | 0.230753 |
| PHOSPHODIESTERASES IN NEURONAL FUNCTION WIKIPATHWAYS_20191210 WP4222 HOMO SAPIENS | 29 | -1.48396 | 0.237066 |
| P53-DEPENDENT G1 DNA DAMAGE RESPONSE REACTOME DATABASE ID RELEASE 71 69563 | 61 | -1.48333 | 0.237846 |
| PINK PARKIN MEDIATED MITOPHAGY REACTOME R-HSA-5205685.2 | 20 | -1.48228 | 0.24089 |
| MFAP5 EFFECT ON PERMEABILITY AND MOTILITY OF ENDOTHELIAL CELLS VIA CYTOSKELETON REARRANGEMENT WIKIPATHWAYS_20191210 WP4560 HOMO SAPIENS | 16 | -1.48205 | 0.240132 |
| FC EPSILON RECEPTOR (FCERI) SIGNALING REACTOME DATABASE ID RELEASE 71 2454202 | 108 | -1.48203 | 0.238453 |
| OXIDATIVE STRESS INDUCED SENESCENCE REACTOME R-HSA-2559580.4 | 65 | -1.48099 | 0.241159 |
Author response table 2
| NAME | SIZE | NES | FDR |
|---|---|---|---|
| MUSCLE CONTRACTION GOBP GO:0006936 | 35 | -2.29 | 0.008034 |
| NICOTINIC ACETYLCHOLINE RECEPTOR SIGNALING PATHWAY PANTHER PATHWAY P00044 | 15 | -2.17947 | 0.018238 |
| REGULATION OF CELL JUNCTION ASSEMBLY GOBP GO:1901888 | 15 | -2.17782 | 0.012159 |
| THE CITRIC ACID (TCA) CYCLE AND RESPIRATORY ELECTRON TRANSPORT REACTOME R-HSA-1428517.1 | 64 | -2.13697 | 0.015138 |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION MSIGDB_C2 HALLMARK_OXIDATIVE_PHOSPHORYLATION | 91 | -2.12375 | 0.013852 |
| COLLAGEN FORMATION REACTOME DATABASE ID RELEASE 71 1474290 | 31 | -2.11295 | 0.013374 |
| MUSCLE SYSTEM PROCESS GOBP GO:0003012 | 40 | -2.07522 | 0.017172 |
| EPH-EPHRIN SIGNALING REACTOME DATABASE ID RELEASE 71 2682334 | 30 | -2.06553 | 0.016753 |
| ACTIN FILAMENT-BASED MOVEMENT GOBP GO:0030048 | 17 | -2.05773 | 0.017006 |
| RESPIRATORY ELECTRON TRANSPORT REACTOME R-HSA-611105.3 | 32 | -2.0515 | 0.016612 |
| RHO GTPASES ACTIVATE PKNS REACTOME DATABASE ID RELEASE 71 5625740 | 17 | -2.0504 | 0.015369 |
| COLLAGEN BIOSYNTHESIS AND MODIFYING ENZYMES REACTOME R-HSA-1650814.3 | 25 | -2.03023 | 0.018264 |
| RESPIRATORY ELECTRON TRANSPORT, ATP SYNTHESIS BY CHEMIOSMOTIC COUPLING, AND HEAT PRODUCTION BY UNCOUPLING PROTEINS. REACTOME R-HSA-163200.1 | 32 | -2.0253 | 0.017967 |
| COMPLEX I BIOGENESIS REACTOME R-HSA-6799198.1 | 16 | -2.02379 | 0.016892 |
| MITOCHONDRIAL RESPIRATORY CHAIN COMPLEX I ASSEMBLY GOBP GO:0032981 | 16 | -2.01705 | 0.01673 |
| INTEGRIN SIGNALLING PATHWAY PANTHER PATHWAY P00034 | 44 | -2.00758 | 0.017239 |
| NADH DEHYDROGENASE COMPLEX ASSEMBLY GOBP GO:0010257 | 16 | -1.99919 | 0.017902 |
| MITOCHONDRIAL ATP SYNTHESIS COUPLED ELECTRON TRANSPORT GOBP GO:0042775 | 26 | -1.99497 | 0.01756 |
| ACTOMYOSIN STRUCTURE ORGANIZATION GOBP GO:0031032 | 21 | -1.98512 | 0.018578 |
| KERATINIZATION GOBP GO:0031424 | 15 | -1.96272 | 0.024099 |
Author response table 3
Gene sets enriched in phenotype P (3 samples).
| GS follow link to MSigDB | GS DETAILS | SIZE | ES | NES | NOM p-val | FOR q-val | FWER p-val | |
|---|---|---|---|---|---|---|---|---|
| OXPHOS SUBUNITS | Details. | 34 | -0.55 | -2.19 | o.ooo | 0.002 | 0.001 | |
| 2 | OXPHOS | Details. | 41 | -0.53 | -2.17 | o.ooo | 0.001 | 0.001 |
| 3 | CARBOHYDRATE METABOLISM | Details. | 36 | -0.50 | -2.00 | o.ooo | 0.005 | 0.009 |
| 4 | TRANSLATION | Details. | 16 | -0.62 | -1.99 | 0.002 | 0.005 | 0.011 |
| 5 | COMPLEX I | Details. | 17 | -0.60 | -1.97 | 0.004 | 0.005 | 0.013 |
| 6 | Cl SUBUNITS | Details. | 15 | -0.62 | -1.89 | 0.004 | 0.007 | 0.024 |
| 7 | FATTY ACID OXIDATION | Details. | 20 | -0.55 | -1.86 | 0.008 | 0.007 | 0.030 |
| 8 | METALS AND COFACTORS | Details. | 30 | -0.47 | 1.79 | 0.006 | 0.011 | 0.051 |
| 9 | METABOLISM | Details. | 153 | -0.34 | 1.78 | 0.002 | 0.011 | 0.058 |
| 10 | AMINO ACID METABOLISM | Details. | 33 | -0.46 | 1.76 | 0.011 | 0.011 | 0.066 |
| 11 | MITOCHONDRIAL CENTRAL DOGMA | Details. | -0.45 | -1.61 | 0.012 | 0.030 | o. 181 | |
| 12 | TCA CYCLE | Details. | 15 | -0.48 | -1.51 | 0.052 | 0.053 | 0.310 |
| 13 | LIPID METABOLISM | Details. | 43 | -0.36 | -1.48 | 0.032 | 0.057 | 0.359 |
| 14 | PROTEIN IMPORT SORTING AND HOMEOSTASIS | Details. | 24 | -0.34 | -1.20 | 0.205 | 0.223 | 0.846 |
Additional files
-
Supplementary file 1
Genes that pass our differential expression cutoffs (false discovery rate [FDR] < 0.05; |log fold change| > 1) in PaLung vs WI-38 samples from whole-cell transcriptomics data.
Differential expression analysis was performed using the DESeq2 pipeline. Fold changes are indicated as PaLung/WI-38.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp1-v1.xlsx
-
Supplementary file 2
Biological pathways upregulated in PaLung cells from gene set enrichment analysis (GSEA) of transcriptomics data.
GSEA was performed on the transcriptomics data using (PI) value as a metric. The table below lists the pathways detected as upregulated in PaLung cells (compared to WI-38 cells) and associated enrichment metrics.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp2-v1.xlsx
-
Supplementary file 3
Biological pathways upregulated in WI-38 cells from gene set enrichment analysis (GSEA) of transcriptomics data.
GSEA was performed on the transcriptomics data using (PI) value as a metric. The table below lists the pathways detected as upregulated in WI-38 cells (compared to PaLung cells) and associated enrichment metrics.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp3-v1.xlsx
-
Supplementary file 4
Differentially expressed (DE) mitochondrial proteins in PaLung vs WI-38 samples from mitochondrial proteomics data.
405 DE proteins were first identified using a Student’s t-test on median-corrected protein abundances from the mitochondrial samples of PaLung and WI-38. Of the 405 DE proteins, 127 were identified to be core mitochondrial proteins (as defined by MitoCarta and IMPI datasets) and are listed in this sheet. Fold changes are indicated as PaLung/WI-38.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp4-v1.xlsx
-
Supplementary file 5
Biological pathways upregulated in PaLung cells from gene set enrichment analysis (GSEA) of proteomics data.
GSEA was performed on the proteomics data using protein abundances as input. The table below lists the pathways detected as upregulated in PaLung cells (compared to WI-38 cells) and associated enrichment metrics.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp5-v1.xlsx
-
Supplementary file 6
Biological pathways upregulated in WI-38 cells from gene set enrichment analysis (GSEA) of proteomics data.
GSEA was performed on the proteomics data using protein abundances as input. The table below lists the pathways detected as upregulated in WI-38 cells (compared to PaLung cells) and associated enrichment metrics.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp6-v1.xlsx
-
Supplementary file 7
Metabolic model for PaLung cells.
A metabolic flux model was constructed for the central carbon metabolism of PaLung cells by overlaying proteomic and transcriptomic information onto the existing mitocore model from literature.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp7-v1.xlsx
-
Supplementary file 8
Metabolic model for WI-38 cells.
A metabolic flux model was constructed for the central carbon metabolism of WI-38 cells by overlaying proteomic and transcriptomic information onto the existing mitocore model from literature.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp8-v1.xlsx
-
Supplementary file 9
Flux sampling results comparing flux distributions in the constrained PaLung and WI-38 models.
Flux sampling was performed with 5000 flux vectors for the PaLung and WI-38 metabolic models each. The flux histograms for each reaction were compared across the two models and the following statistics were extracted from the histograms.
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp9-v1.xlsx
-
Supplementary file 10
Absolute metabolite quantification in PaLung and WI-38 cells.
Absolute concentrations of metabolites detected in PaLung and WI-38 cells by Human Metabolome Technologies (HMT).
- https://cdn.elifesciences.org/articles/94007/elife-94007-supp10-v1.xlsx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/94007/elife-94007-mdarchecklist1-v1.docx
