Cinzia Pultrone 1, Giulia Minnucci1, Giulia Amicarelli1, Elena D’Agostini1, Veronica Tettamanzi1, Chiara Boroni2, Orietta Spinelli2, Francesco Colotta1, Alessandro Rambaldi2

1DiaSorin SpA, Gerenzano (VA), Italy; 2Ospedali Riuniti di Bergamo, Bergamo, Italy.

The molecular detection of the BCR-ABL fusion transcripts is necessary for the genetic confirmation of Chronic Myeloid Leukemia (CML) diagnosis and for the risk classification of Acute Lymphoblastic Leukemia (ALL) [1,2].

The molecular techniques currently used for this purpose are based on conventional RT-PCR [3]; the main limitations are time-consuming and multi-step procedures that slow down the diagnostic labs routine and require highly specialized personnel. We developed an innovative non-PCR assay based on Loop mediated isothermal AMPlification [4] reaction for multiplex detection of BCR-ABL p190 and p210 fusion transcripts and of the endogenous GUSb mRNA.

INTRODUCTION

MATERIALS AND METHODS

RESULTS

CONCLUSIONS

p190 Positive Cell Line (TOM-1)

serially diluted into Negative Cell Line

(HL-60)

Replicates %

of p190 detection

Positive control not diluted

19 100%

10-1 5 100%

10-2 7 100%

10-3 64 100%

10-4 46 74%

Total 141

p210 Positive Cell Line (K-562)

serially diluted into Negative Cell Line

(HL-60)

Replicates %

of p210 detection

Positive control not diluted

17 100%

10-1 5 100%

10-2 23 100%

10-3 30 100%

10-4 64 100%

10-5 40 57.5%

Total 179

Negative Cell Lines

Replicates Percentage of

GUSb detection

HL-60 71 100%

MV-4 9 100%

NB-4 12 100%

RS4-11 3 100%

REH 8 100%

697 9 100%

KASUMI 9 100%

Total 121 100%

Analytical Specificity

The analytical specificity was established on seven BCR-ABL wild type cell lines: no false positive results have been obtained on 121 replicates (Table 1). All negative results have been validated by amplification of the Internal Control (GUSb) (Figure 1).

The analytical sensitivity was established on 500ng RNA extracted from p210 and p190 positive cell lines serially diluted into negative cell line RNA. The assay detects p210 and p190 dilutions down to 10-5 and 10-4, respectively (Table 2). All the samples tested produced melting peaks perfectly superimposed to the ones of positive control (Figure 2).

Analytical Sensitivity

Figure 2

Table 2

100% specificity

RNA EXTRACTION 40’

RESULTS: 50’

BCR-ABL RT-LAMP REACTION

Role of Internal Control (IC): • control the RNA extration procedure • control the quality of RNA extracted • control the correct reaction condition • control of the presence of inhibitors

= ensure the absence of false negative results

Conventional RT-PCR (Biomed protocol [3])

RETROTRANSCRIPTION

PCR

GEL SEPARATION

TRIPLEX assay

F3

FIP

F3 FIP

BIP B3

BIP B3

BCR

BCR

ABL

ABL

F3 FIP

BIP B3 GUSb

p190

p210

IC

INTERCALATING DYE Use of intercalating dye (Yo-Pro-1, Invitrogen) for a real-time reaction

monitoring

Real time fluorescent detection +

Annealing analysis:

the amplified products are characterized by three distinct Melting Temperatures for p190, p210 and GUSb, respectively.

Housekeeping Control Gene

(ABL)

p190 p210 Onset

Results by conventional RT-PCR (Biomed)

p190* p210§

Negative^ Tot

Results by RT-LAMP

p190* 29 - - 29

p210§ - 33 - 33

Negative^ - - 52 52

Tot 29 33 52 114

*(29 B-ALL)

§ (30 CML+3 B-ALL)

^ (22 Ph Negative diseases (13 B-CLL; 5 AML; 1 ALL; 3 PV; 2 HES; 2 TE) + 28 healthy donors)

100% concordance on 126 clinical samples

Table3: RT-LAMP was validated on clinical samples previously diagnosed by conventional RT-PCR in Ospedali Riuniti di Bergamo. The two methods showed 100% concordance on 114 clinical samples

REFERENCES: [1] National Comprehensive Cancer Network 2010 [2] National Cancer Institute 2010 [3] Van Dongen JJM et al. Leukemia (1999) 13, 1901-1928 [4] Notomi T et al. NAR (2000) 15: 28 (12): E63 [5] Gabert J. et al. Leukemia (2003) 17,

2318-2357.

CLINICAL VALIDATION: Comparison with PCR

Follow-Up

Table 4: RT-LAMP was also validated on CML follow up samples previously diagnosed and quantified by quantitative RT-PCR[5] in Ospedali Riuniti di Bergamo.

The triplex p190-p210-GUSb RT-LAMP assay detects the major and minor BCR-ABL transcripts in a single step procedure reducing time-to-results, risk of contaminations and errors, costs and assay set-up complexity. RT-LAMP overcomes the main limitations of the conventional RT-PCR techniques and can also be considered for long term monitoring of CML patients in molecular remission. Furthermore, thanks to the role of the internal control, allows to invalidate the results if the quality of target RNA is low, thus avoiding risk of false negative results.

The results are fully concordant and the high sensitivity of RT-LAMP allowed the detection of very low NCN (Normalyzed Copy Number samples)

RESULTS

60’ 60’ 60’ 30’

High Sensitive Molecular Detection of the BCR-ABL Major and Minor Fusion Transcripts in a Multiplex, Close-Tube Format by Isothermal Loop Mediated Amplification Reaction (RT-LAMP)

RNA 500ng/rx

Consists in:

ONE ENZYME DNA polymerase with RT and strand-

displacement activities

INCUBATION AT CONSTANT TEMPERATURE

65°C FOR 50 min

65°C

Results Melting Temperature Range (°C)

positive, p190 93.2 ± 0.8

positive, p210 89.2 ± 1

negative, GUSb 86.2 ± 1.2

Figure 1

Table 1

Clinical sample

Results by p210 Quantitative PCR[5] (NCN)

Results by RT-LAMP

1 positive (14)

positive p210

2 positive (13)

3 positive (99)

4 positive (7)

5 positive (301)

6 positive (12)

7 positive (648)

8 positive (22)

9 positive (2)

10 positive (13)

11 negative negative

12 negative negative

Results on Clinical Sample degradated

6 clinical samples resulted invalid (no amplification of BCR-ABL, nor of IC GUSb) by RT-LAMP. The quality of RNA was therefore tested by Agilent 2100 Bioanalyzer , resulting highly degradated.

Retrotranscription, amplification and signal

detection in ONE HOMOGENOUS STEP

Absence of annealing peaks determines

invalid run