Relationship between chromosomal aberrations and gene expressions in the p53 pathway in chronic lymphocytic leukemia

G Öztan; M Aktan; S Palanduz; H İşsever; S Öztürk; E Nikerel; A Uçur; G Bağatir; A Bayrak; K Çefle

Open Access

Relationship between chromosomal aberrations and gene expressions in the p53 pathway in chronic lymphocytic leukemia

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| Aug 26, 2020

Balkan Journal of Medical Genetics

Volume 23 (2020): Issue 1 (June 2020)

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Published Online: Aug 26, 2020

Page range: 15 - 24

DOI: https://doi.org/10.2478/bjmg-2020-0007

Keywords
Chronic lymphocytic leukemia (CLL), gene expression, p53 Pathway, Prognosis, RT Profiler PCR (polymerase chain reaction)Array

© 2020 Öztan G, Aktan M, Palanduz S, İşsever H, Öztürk S, Nikerel E, Uçur A, Bağatir G, Bayrak B, Çefle K, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Scatterplot comparing the normalized expression of genes between the CLL patients and healthy controls. Genes involved in CLL cell cycle and cell growth, proliferation and differentiation and apoptosis are shown. The central line indicates unchanged gene expression. Red dots represent genes with a fold regulation of >2.

Illustration of interactions between the 18 differentially-expressed genes in CLL patients (String v10, confidence view).

The mean difference values of the patient and control group according to average ᐃCt and fold change.

Gene	Average Ct		Average ᐃCt		2^-ᐃCt		Fold Change		p Value	Fold Regulation
	CLL	Control	CLL	Control	CLL	Control	CLL/ Control	95% CI		CLL/ Control
APAF1	26.57	25.28	7.72	7.54	0.004695	0.005368	0.87	0.78-0.96	0.072729	-1.14
ATM	27.85	27.91	9.01	10.17	0.001936	0.000869	2.23	1.67-2.79	<0.001	2.23
ATR	29.00	29.41	10.17	11.67	0.000871	0.000307	2.83	2.23-3.43	<0.001	2.83
BAX	25.61	25.87	6.78	8.13	0.009116	0.003578	2.55	2.15-2.95	<0.001	2.55
CASP9	27.35	27.58	8.52	9.84	0.002723	0.001091	2.50	2.06-2.94	<0.001	2.50
CDK4	26.92	27.96	8.09	10.22	0.003672	0.000839	4.38	3.20-5.56	<0.001	4.38
CDKN1A	27.59	26.82	8.75	9.08	0.002315	0.001852	1.25	0.97-1.53	0.066	1.25
CDKN2A	30.50	32.77	11.67	15.02	0.000307	0.000030	10.22	7.14-13.3	<0.001	10.22
CHEK1	31.37	31.58	12.54	13.83	0.000168	0.000068	2.45	1.98-2.92	<0.001	2.45
CHEK2	29.45	30.42	10.62	12.68	0.000638	0.000152	4.18	3.02-5.34	<0.001	4.18
E2F1	31.44	30.88	12.60	13.14	0.000161	0.000111	1.45	1.04-1.86	0.012741	1.45
E2F3	28.88	27.09	10.05	9.34	0.000944	0.001541	0.61	0.53-0.69	<0.001	-1.63
GADD45A	31.94	31.14	13.10	13.39	0.000114	0.000093	1.22	0.90-1.54	0.121	1.22
MCL1	23.34	21.85	4.51	4.11	0.043950	0.057965	0.76	0.66-0.86	<0.001	-1.32
MDM2	25.77	25.60	6.93	7.86	0.008184	0.004312	1.90	1.56-2.24	<0.001	1.90
MDM4	27.43	28.00	8.60	10.26	0.002577	0.000818	3.15	2.32-3.998	<0.001	3.15
PCNA	25.75	26.36	6.92	8.62	0.008266	0.002545	3.25	2.64-3.86	<0.001	3.25
PTEN	25.53	24.05	6.50	6.31	0.011036	0.012615	0.87	0.78-0.96	0.062542	-1.14
RB1	26.51	27.04	7.67	9.29	0.004894	0.001595	3.07	2.40-3.74	<0.001	3.07
P53	25.76	26.32	6.92	8.58	0.008229	0.002619	3.14	2.47-3.81	<0.001	3.14
PTX3	32.50	30.53	13.67	12.79	0.000077	0.000141	0.54	0.37-0.71	0.006057	-1.84
BCL2	25.94	27.94	7.11	10.20	0.007231	0.000850	8.5'	5.46-11.56	<0.001	8.51

Patient diagnostic data and FISH results.

n	Sex-Age	Prognosis	Rai Stage	Binet Stage	FISH Results				(WBC 10⁹/L)	Hb (g/dL)	Platelet (10⁹/L)
					del(13q)	del(17p)	+12	Normal Non-del(13q), del(17p), +12.
1	F-75	bad	1	B	[–]	[+]	[–]	[–]	12.6	12.7	166.0
2	M-71	good	0	A	[–]	[–]	[–]	[+]	23.0	12.0	203.0
3	M-57	good	0	A	[–]	[–]	[–]	[+]	24.8	15.1	262.0
4	M-56	good	3	A	[–]	[–]	[–]	[+]	71.4	13.2	49.0
5	F-59	bad	2	B	[–]	[+]	[–]	[–]	7.9	10.9	284.0
6	F-74	bad	2	B	[–]	[+]	[–]	[–]	108.6	10.3	190.0
7	F-63	bad	2	A	[–]	[+]	[–]	[–]	35.4	13.4	185.0
8	M-80	bad	2	A	[–]	[+]	[–]	[–]	3.6	12.9	104.0
9	F-62	bad	0	A	[–]	[–]	[+]	[–]	190.2	12.0	192.0
10	M-67	bad	2	A	[–]	[–]	[+]	[–]	142.6	11.6	81.0
11	F-65	bad	0	A	[–]	[–]	[+]	[–]	5.2	12.1	144.0
12	F-74	bad	2	A	[–]	[–]	[+]	[–]	179.7	11.9	321.0
13	F-86	bad	3	A	[–]	[–]	[+]	[–]	213.0	8.6	113.0
14	M-60	good	3	A	[–]	[–]	[–]	[+]	51.7	9.4	137.0
15	M-46	good	2	A	[–]	[–]	[–]	[+]	15.0	14.4	184.0
16	M-54	good	0	A	[–]	[–]	[–]	[+]	41.9	13.8	352.0
17	F-61	good	1	A	[–]	[–]	[–]	[+]	11.8	12.1	148.0
18	F-67	good	0	A	[–]	[–]	[–]	[+]	195.3	10.8	188.0
19	F-53	good	2	B	[–]	[–]	[–]	[+]	39.8	11.4	135.0
20	M-67	good	0	A	[+]	[–]	[–]	[–]	74.6	12.4	183.0
21	M-62	good	2	A	[+]	[–]	[–]	[–]	121.4	14.5	294.0
22	M-68	good	0	A	[+]	[–]	[–]	[–]	37.7	13.9	197.0
23	F-46	good	1	A	[+]	[–]	[–]	[–]	59.4	12.3	91.0
24	M-58	good	2	B	[+]	[–]	[–]	[–]	201.4	11.1	101.0
25	M-66	good	0	A	[+]	[–]	[–]	[–]	43.9	12.3	88.0
26	M-61	good	4	C	[+]	[–]	[–]	[–]	110.0	13.9	39.0
27	M-51	good	2	A	[+]	[–]	[–]	[–]	98.5	14.3	250.0
28	F-78	good	3	B	[+]	[–]	[–]	[–]	13.7	11.0	324.0
29	F-63	good	0	A	[+]	[–]	[–]	[–]	113.3	11.5	178.0
30	M-64	good	0	A	[+]	[–]	[–]	[–]	432.0	15.3	206.0

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Relationship between chromosomal aberrations and gene expressions in the p53 pathway in chronic lymphocytic leukemia

Article Category: Original Article

Published Online: Aug 26, 2020

Page range: 15 - 24

DOI: https://doi.org/10.2478/bjmg-2020-0007

Keywords
Chronic lymphocytic leukemia (CLL), gene expression, p53 Pathway, Prognosis, RT Profiler PCR (polymerase chain reaction)Array

© 2020 Öztan G, Aktan M, Palanduz S, İşsever H, Öztürk S, Nikerel E, Uçur A, Bağatir G, Bayrak B, Çefle K, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Figure 2

The mean difference values of the patient and control group according to average ᐃCt and fold change.

Patient diagnostic data and FISH results.

Relationship between chromosomal aberrations and gene expressions in the p53 pathway in chronic lymphocytic leukemia

Article Category: Original Article

Published Online: Aug 26, 2020

Page range: 15 - 24

DOI: https://doi.org/10.2478/bjmg-2020-0007

KeywordsChronic lymphocytic leukemia (CLL), gene expression, p53 Pathway, Prognosis, RT Profiler PCR (polymerase chain reaction)Array

© 2020 Öztan G, Aktan M, Palanduz S, İşsever H, Öztürk S, Nikerel E, Uçur A, Bağatir G, Bayrak B, Çefle K, published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Figure 2

The mean difference values of the patient and control group according to average ᐃCt and fold change.

Patient diagnostic data and FISH results.

Keywords
Chronic lymphocytic leukemia (CLL), gene expression, p53 Pathway, Prognosis, RT Profiler PCR (polymerase chain reaction)Array