Deletional HPFH Vs. Delta Beta Thalassemia: Closing in on a Possible Hb F Silencer Location

Background: The control of hemoglobin F (Hb F) expression has proven an elusive puzzle with several postulated but not mutually exclusive hypotheses.  A silencing mechanism hypothesis, which predicts the existence of a regulatory element that suppresses HbF expression, has been supported by recent investigations into a 3.5 kb region upstream from the delta globin gene (HBD). To test this hypothesis, we have investigated our historical case files in a tertiary care high-throughput clinical laboratory and compared the patient phenotype (Hgb, MCV, MCH, RDW, Hb F %, and flow cytometry Hb F distribution) with the status of this 3.5 kb region.

Methods: A query of clinical testing patient files from Mayo Clinic Metabolic Hematology Laboratory yielded 179 patients confirmed by Multiplex Ligation-dependent Probe Amplification (MLPA) to contain large deletions located within the epsilon through beta globin genes.  Of these, 27 unrelated patients with breakpoints between the pseudobeta (HBBP1) and HBD genes were identified. Four additional MLPA probe pairs were placed in this region and the patient phenotypes were compared.

Results: The interior two (of the four added) probes between HBBP1 and HBD stratified all 27 cases.  The other two (flanking) probes were never discriminatory, thus refining the area of interest to 2.4 kb. Sixteen cases showed breakpoints within hg19 g.5260154-5259135 (5' region) and eleven cases showed breakpoints within hg19 g.5259136-5257692 (3' region) upstream of HBD. Patients who displayed a phenotype of HPFH (n = 9) contained breakpoints in the 5' region whereas those with a delta beta thalassemia (DBT) phenotype (n = 11) were associated with breakpoints in the 3' region.  A subset (n = 7) with breakpoints in the 5' region had indefinite phenotypic features, but of these, all but one showed homocellular Hb F distribution.

Conclusion: Our molecular and phenotypic correlation of 27 patients with large deletional breakpoints between HBBP1 and HBD supports the hypothesis of a silencing element located upstream of HBD and further narrows the area that segregates many HPFH and DBT patient phenotypes from 3.5 kb to 2.4 kb. Several potential silencing effectors with binding sites in this region include HDAC1, GATA1 and H3K27me3; interestingly, the BCL11A binding site may be outside of the regulatory area.

   

Table 1: Phenotypic data of patients with deletions between HBBP1 and HBD.
Case	Age/Sex		Hb F	Hb A2	Hb X		Hgb	RBC		MCV	MCH	MCHC	RDW		Hb F Flow
	(Y)		(%)	(%)	(%)		(g/dL)	( 10^12/L)		(fL)	(pg/cell)	(hg/cell)	(%)
3' Region
1	47 M		25.5	2.1			16.7	6.3		81.4	26.7	32.8	15.7		H
2	5 M		28.3	2.4			12.5	4.9		74.6	25.4	34	15.9		H
3	24 F		30.3	1.7			11.6	4.23		92.7	27.4	29.6	15.2		H
4	9 F		36.3	2.2	S = 62		13.1	5.2		69.9	NA	NA	14.8
5	24 F		37.3	2.1	C = 61		12.9	5.1		72.9	25.5	35	14.3
6	3 M		39.7	2.1			12.4	4.4		88.7	28.1	31.7	16.3
7	27 F		40.2	3.4	S = 56		12.2	4.4		79.7	27.8	34.9	15
8	16 M		43.7	2.2	S = 54		15.9	6.8		71.5	23.5	32.9	14.1
9	7m M		100.0*	0.0			12.8	4.8		76	26.5	34.9	16.8
3' Region
10	28 F		20.9	2			10.11	4.4		70.9	22.7	32.1	19		H
11	64 M		21.4	2.3			10.51	4.1		81.1	25.8	31.8	18.1
12	2.5 M		24	2.1			10.21	5.3		59.4	19.3	32.5	20.9		H
13	58 F		24	2.1			9.51	4.4		72.2	21.5	29.8	17.7		H
14	14 F		25.4	1.5			10.81	4.9		69.4	22	31.8	17.6		H
15	52 F		26.9	1.8			8.42	3.6		72	23.5	32.7	19.4		T
16	34 M		38.7	1.7	S = 60		11.4	4.7		71.6	NA	NA	21.6
5' Region
17	24 F		2.7	2.9			12.3	6.1		62.2	20	32.2	18.2
18	32 F		6.1	2.7			10.2	5.1		61.3	19.9	32.5	19.3
19	27 F		7.2	2.9			11	5.1		72.9	21.7	29.8	19.9
20	29 F		7.8	2.7			10.2	4.7		72.2	21.7	30	20.5
21	15 M		7.8	2.5			12.7	6.2		64.7	20.4	31.5	21.2
22	42 M		7.8	3.1			10.6	4.9		75.1	21.5	28.6	23.7
23	60 M		10.1	2.5			11	4.5		74.8	24.7	33	23.4
24	41 M		10.7	2.8			8.6	4.1		73.3	21.2	29	26.8
25	30 F		11.5	2.7			12.1	5.5		67.4	21.9	32.5	21.8
26	25  F		13.2	2.8			12.1	5.3		68.4	22.8	33.3	21.6
27	3 F		18.3	2.6			11.9	5.79		63.6	20.6	32.3	22.7		T
Normal values			<1	2-3.3	0
H = homocellular; T= heterocellular; I = indeterminate;  *homozygous deletion
-- = no deletion; + = deletion present (all alpha deletions were single -3.7 kb ‘rightward' deletions)
1  = Suspected Fe deficiency; 2 = recent transfusion