Hypoxia and 3D Culture

This vignette from the R package canprot reproduces calculations of compositional oxidation state and hydration state that are described in a paper published in PeerJ (Dick, 2017).


U937 (acute promonocytic leukemic cells), B104 (rat neuroblastoma cells), DU145 (prostate carcinoma cells), SK-N-BE(2)c; IMR-32; SH-SY5Y (neuroblastoma cells), H9C2 (rat heart myoblast), MCF-7 (breast cancer cells), THP-1 (macrophages), A431 (epithelial carcinoma cells), Hx48 (hypoxia 48 h), Hx72 (hypoxia 72 h), ReOx (hypoxia 48 h followed by reoxygenation for 24 h), -S (supernatant fraction), -P (pellet fraction), SPH (spheroids), HepG2/C3A (hepatocellular carcinoma cells), U87MG (glioblastoma), 786-O (renal clear cell carcinoma cells), HCT116; HT29 (colon cancer cells), SC (stem cells), SAL (salidroside).

Summary Table

This table compares the chemical compositions of groups of proteins that are relatively down- and up-expressed (n1 and n2, respectively) in cells grown in hypoxia or 3D culture compared to control conditions.

datasets <- pdat_hypoxia()
comptab <- lapply_canprot(datasets, function(dataset) {
  pdat <- get_pdat(dataset, "pdat_hypoxia")
  ZC_nH2O(pdat, plot.it=FALSE)
}, varlist="pdat_hypoxia")
set reference (description) n1 n2 MD ES p-value MD ES p-value
a HXS+06 (U937) 37 24 -0.027 31 1e-02 0.029 62 1e-01
b BRA+10 (placental secretome) 41 22 -0.027 38 1e-01 0.011 54 6e-01
c DPL+10 (B104) 71 19 -0.021 37 9e-02 0.001 51 9e-01
d BMJ+11 (DU145) 87 28 0.014 61 8e-02 0.000 49 9e-01
e CBW+11 (SK-N-BE(2)c; IMR-32) 29 21 0.004 51 9e-01 0.001 50 1e+00
f LAR+12 (H9C2) 53 65 -0.007 51 8e-01 -0.066 35 6e-03
g MHG+12 (MCF-7 SPH P5) 409 337 -0.027 40 1e-06 -0.008 47 2e-01
h MHG+12 (MCF-7 SPH P2) 248 214 -0.025 42 2e-03 -0.003 48 5e-01
i MVC+12 (SPH perinecrotic) 48 52 -0.006 47 6e-01 -0.025 44 3e-01
j MVC+12 (SPH necrotic) 101 186 -0.023 38 9e-04 -0.029 43 6e-02
k FWH+13 (THP-1) 56 40 0.003 53 6e-01 0.011 54 5e-01
l RHD+13 (A431 Hx48) 178 77 0.012 53 4e-01 -0.017 46 4e-01
m RHD+13 (A431 Hx72) 69 54 -0.025 38 2e-02 -0.048 40 5e-02
n RHD+13 (A431 ReOx) 48 36 0.001 51 8e-01 0.003 56 4e-01
o VTMF13 (SH-SY5Y) 141 64 -0.021 39 1e-02 0.024 59 3e-02
p DYL+14 (A431 Hx48-S) 65 34 0.033 65 2e-02 -0.032 37 3e-02
q DYL+14 (A431 Hx72-S) 137 61 -0.006 49 8e-01 -0.012 45 2e-01
r DYL+14 (A431 ReOx-S) 56 49 0.037 67 4e-03 -0.050 33 2e-03
s DYL+14 (A431 Hx48-P) 74 44 -0.002 52 8e-01 -0.008 46 5e-01
t DYL+14 (A431 Hx72-P) 67 53 -0.013 46 4e-01 -0.015 43 2e-01
u DYL+14 (A431 ReOx-P) 41 31 0.021 64 4e-02 -0.035 37 6e-02
v RKP+14 (CRC-derived SPH) 113 154 0.012 55 2e-01 0.005 50 1e+00
w WRK+14 (HepG2/C3A SPH) 127 292 -0.032 39 4e-04 -0.029 43 2e-02
x BSA+15 (HeLa) 53 72 0.004 53 6e-01 -0.003 50 1e+00
y HWA+16 (U87MG and 786-O) 137 164 -0.001 49 8e-01 -0.026 42 2e-02
z LCS16 (HCT116 transcription) 129 141 -0.004 47 4e-01 0.024 57 4e-02
A LCS16 (HCT116 translation) 469 1024 -0.028 39 1e-11 -0.025 43 2e-05
B RSE+16 (adipose-derived SC) 66 50 0.031 67 2e-03 -0.011 45 3e-01
C XCJ+16 (cardiomyocytes CoCl2) 65 27 -0.025 41 2e-01 -0.012 46 6e-01
D XCJ+16 (cardiomyocytes SAL) 35 69 0.014 58 2e-01 -0.004 46 5e-01
E YLW+16 (HT29 SPH) 116 225 -0.053 29 2e-10 -0.018 45 2e-01

Data Sources

a. 2% O2 vs normoxic conditions. Source: Table 1 of Han et al. (2006). b. 1% vs 6% O2. Source: Tables 2 and 3 of Blankley et al. (2010). c. The comparisons here use expression ratios HYP/LSC (oxygen deprivation / low serum control) >1.2 or <0.83, calculated from the reported ratios. Source: extracted from Suppl. Table 2 of Datta et al. (2010), including proteins with p-value <0.05 and EF <1.4. d. Translationally regulated genes. Source: Suppl. Tables 1–4 of Beucken et al. (2011). e. 1% O2 for 72 h vs standard conditions. Source: Suppl. Table 1(a) of Cifani et al. (2011). f. Hypoxic vs control conditions for 16 h. Source: Suppl. Table S5 of Li et al. (2012). g. h. Tumourspheres (50 to 200 μm diameter) at passage 5 (P5) or 2 (P2) compared to adherent cells. Source: Sheets 2 and 3 in Table S1 of Morrison et al. (2012). i. j. Perinecrotic and necrotic regions compared to surface of multicell spheroids (~600 μm diameter). The comparisons here use expression ratios <0.77 or >1.3. Source: Suppl. Table 1C of McMahon et al. (2012). k. Incubation for several days under hypoxia (1% O2). Source: Suppl. Table 2A of Fuhrmann et al. (2013) (control virus cells). l. m. n. Source: extracted from Suppl. Table 1 of Ren et al. (2013), including proteins with iTRAQ ratios <0.83 or >1.2 and p-value <0.05. o. 5% O2 vs atmospheric levels of O2. The comparisons here include proteins with a normalized expression ratio of >1.2 or <0.83. Source: SI table of Villeneuve et al. (2013). p. q. r. s. t. u. The comparisons here include proteins with p <0.05. Source: Suppl. Table S1 of Dutta et al. (2014). v. Organotypic spheroids (~250 μm diameter) vs lysed CRC tissue. Source: extracted from Table S2 of Rajcevic et al. (2014), filtered as follows: at least two of three experiments have differences in spectral counts, absolute overall fold change is at least 1.5, and p-value is less than 0.05. w. SPH vs classical cell culture (2D growth). Standard concentrations of gases used for tissue culture (5% CO2, 95% air) were used in both cases. The comparisons here include proteins that have a log2 fold change of at least ±1. Source: P1_Data sheet in the SI of Wrzesinski et al. (2014). x. 1% vs 19% O2. Source: Table S1 of Bousquet et al. (2015). y. 1% O2 for 24 hr. The comparisons here include proteins with a fold change of <0.5 or >1 and proteins that were detected in only hypoxic or only normoxic conditions. Source: Table S1 of Ho et al. (2016). z. A. Microarray analysis of differential gene expression in the transcriptome (total rRNA) and translatome (polysomal / total RNA ratio) of cells grown in normal and hypoxic (1% O2) conditions. Source: data file supplied by Dr. Ming-Chih Lai (Lai, Chang & Sun (2016)). B. ASC from 3 donors cultured for 24 hr. in hypoxic (1% O2) vs normoxic (20% O2) conditions. Source: Tables 1 and 2 of Riis et al. (2016). C. D. Rat cardiomyocytes treated with CoCl2 (hypoxia mimetic) vs control or with SAL (anti-hypoxic) vs CoCl2. Source: SI Tables 1S and 2S of Xu et al. (2016). E. 800 μm spheroids vs 2D monolayers. Source: Tables S1a–b of Yue et al. (2016).

Mean Differences

The reoxygenation or anti-hypoxic, tumor spheroid, and adipose-derived stem cell datasets are highlighted in blue, red, and orange, respectively.

col <- rep("black", length(datasets))
col[grepl("ReOx", datasets)] <- "blue"
col[grepl("=SPH", datasets)] <- "red"
col[grepl("=ASC", datasets)] <- "orange"
diffplot(comptab, col=col)


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