Gene expression-based biodosimetry for radiological incidents: assessment of dose and time after radiation exposure

Figures & data

Figure 1. Schematic representation of the experimental procedures.

Table 1. Donor information.

Donor	Gender	Age	Smoking status	Recent viral/bacterial infection	Reference/blind sample
D1	Male	24	No	No	Reference
D2	Female	24	No	No	Reference
D3	Male	29	No	No	Reference
D4	Male	23	No	Yes	Reference
D5	Female	28	No	No	Reference
D6	Female	27	No	No	Reference
D7	Female	46	No	No	Reference
D8	Male	56	Recently stopped	No	Blind
D9	Male	58	No	No	Blind
D10	Male	54	No	No	Blind
D11	Male	49	No	No	Blind
D12	Male	40	No	No	Blind
D13	Male	56	Yes	No	Blind
D14	Male	30	No	Yes	Blind

Table 2. Information on doses and time points assigned to blind samples.

Donor	Code	Dose, mGy	Time point, h
D8	B	0	8
D8	R	200	8
D8	P	900	12
D9	I	700	8
D9	C	60	12
D9	L	0	24
D10	S	1200	12
D10	A	30	24
D11	W	100	8
D11	F	1600	36
D11	M	0	48
D12	Q	60	36
D12	T	200	36
D12	G	2000	36
D13	Y	400	24
D13	U	400	48
D13	D	1200	48
D14	E	100	12
D14	J	0	24
D14	O	700	48

Figure 2. Comparison of RNA extraction protocols. (A) Quantity of RNA extracted following each protocol. Statistical comparison performed using two-tailed paired t-test. In case two bars are mark with the same letter(s) the difference is not statistically significant (p > .05), if the letters are different the difference between two conditions is statistically significant. (B) Quality of RNA extracted following each protocol. Statistical comparison performed using two-tailed paired t-test. In case two bars are mark with the same letter(s) the difference is not statistically significant (p > .05), if the letters are different the difference between two conditions is statistically significant. (C) Levels of contamination of RNA extracted from whole blood samples with PAXgene and QIAmp kits with excessive globin mRNA assessed as expression of α- and β-globin coding genes. Statistical comparison performed using unpaired t-test. SP: standard protocol; MP: modified protocol. Bars represent the mean of five measurement, error bars represent SD. **p < .005, ***p < .001.

Figure 3. (A–E) Heatmaps showing the average of expression levels in seven donors (relative to control samples per time point, log₂ transformed) for all the 25 genes (shown in rows) included in the qPCR arrays in response to exposure to different doses (shown in columns) at five time points. (F) Heatmap showing the relative expression levels in sham-irradiated samples from seven donors relative to sham-irradiated samples at 8 h for all the 25 genes (shown in rows) at five time points (shown in columns).

Table 3. Dose and time point prediction results for blind samples.

Sample code (with remark)	True time point, h	Predicted time point, h	Error, h	True dose, mGy	Predicted dose, mGy	Error, mGy
A	24	23.3	–0.7	30	20	–10
B (ex-smoker)	8	9.5	+1.5	0	20	+20
C	12	10.2	–1.8	60	20	–40
D (smoker)	48	44.0	–4.0	1200	900	–300
E (infection)	12	8.9	–3.1	100	30	–70
F	36	39.6	+3.4	1600	1370	–230
G	36	43.2	+7.2	2000	1370	–630
I	8	4.5	–3.5	700	410	–290
J (infection)	24	22.1	–1.9	0	20	+20
L	24	15.5	–8.5	0	20	+20
M	48	42.7	–5.3	0	120	+120
O (infection)	48	43.9	–4.1	700	900	+200
P (ex-smoker)	12	14.0	+2.0	900	1370	+470
Q	36	39.0	+3.0	60	120	+60
R (ex-smoker)	8	10.5	+2.5	200	420	+220
S	12	18.4	+6.4	1200	420	–780
T	36	40.1	+4.1	200	120	–80
U (smoker)	48	41.0	–7.0	400	900	+500
W	8	10.0	+2.0	100	230	+130
Y (smoker)	24	21.4	–2.6	400	410	+10

Bold: time point predictions with more than 4 h difference from the true time point and dose predictions with more than 500 mGy difference from the true dose.

Figure 4. (A–C) Changes in expression of FDXR, DDB2 and TNFRSF10B relative to sham-irradiated samples at 8 h time point. Bars represent the average of samples from seven donors irradiated in vitro with doses from 0 to 2000 mGy and fixed at 5 time points after exposure. (D–F) Changes in expression of FDXR, DDB2 and TNFRSF10B relative to sham-irradiated samples per time point. Bars represent the average of samples from seven donors irradiated in vitro with doses from 0 to 2000 mGy and fixed at 5 time points after exposure.

Figure 5. The decision tree for the REPTree model built for dose prediction, ending with 11 leaves (for each the dose prediction is calculated).

Figure 6. The decision tree for the M5Base model built for time point prediction, ending with 23 leaves (for each a linear model named LM1-LM23 has been calculated).

Figure 7. Dose (A) and time point (B) prediction results for the blind samples. CC: correlation coefficient.