Association of HLA Class I and Class II genes with bcr-abl transcripts in leukemia patients with t(9;22) (q34;q11)

Asymmetric Hairpins DNA Encapsulated Silver Nanoclusters for In Situ Fluorescence Imaging of Fusion Gene Isoforms in Bone Marrow

Rapid and accurate imaging of the BCR/ABL fusion gene isoforms (e.g., e13a2, e14a2 and co-expression type) of chronic myeloid leukemia (CML) is of vital importance to first-line drug selection, but there is no assay that meets clinical needs (e.g., clinical kits > 18 h without isoforms information). Herein, an in situ imaging platform is developed for the rapid and accurate detection of CML fusion gene isoforms using asymmetric sequence-enhanced hairpins DNA encapsulated silver nanoclusters (ADHA) and catalyzed hairpin assembly (CHA). The specific detection of e13a2 and e14a2 fusion gene isoforms with detection limits of 19.2 am (11.558 copies µL-1 ) and 32.56 am (19.601 copies µL-1 ) in one-pot is achieved. The feasibility of the developed assay for real-world applications are demonstrated by one-step fluorescence imaging (40 min) of e13a2, e14a2 and co-expression type in bone marrow quantitatively (International Standard: 15.66%-168.878%) and further validated by cDNA-sequencing. This work suggests that the developed imaging platform holds great potential for rapid identification of the fusion gene isoforms and isoform related treatment monitoring.

One-Pot Identification of BCR/ABLp210 Transcript Isoforms Based on Nanocluster Beacon

The BCR/ABL^p210 fusion gene is a classic biomarker of chronic myeloid leukemia, which can be divided into e13a2 and e14a2 isoforms according to different breakpoints. These two isoforms showed distinct differences in clinical manifestation, treatment effect, and prognosis risk. Herein, a strategy based on nanocluster beacon (NCB) fluorescence was developed to identify the e13a2 and e14a2 isoforms in one-pot. Because the fluorescence of AgNCs can be activated when they are placed in proximity to the corresponding enhancer sequences, thymine-rich (T-rich) or guanine-rich (G-rich). In this work, we explored an ideal DNA-AgNCs template as an excellent molecular reporter with a high signal-to-noise ratio. After recognition with the corresponding isoforms, the AgNCs can be pulled closer to the T-rich or G-rich sequences to form a three-way junction structure and generate fluorescence with corresponding wavelengths. Therefore, by distinguishing the corresponding wavelengths of AgNCs, we successfully identified two isoforms in one tube with the limitation of 16 pM for e13a2 and 9 pM for e14a2. Moreover, this strategy also realized isoform identification in leukemia cells and newly diagnosed CML patients within 40 min, which provides a powerful tool to distinguish fusion gene subtypes at the same time.

Highly sensitive fluorescence biosensing of BCR-ABL1 fusion gene based on exponential transcription-triggered hemin catalysis

Simple, sensitive and specific detection of the transcription level of BCR-ABL1 mRNA possesses vital clinical significance in diagnosis and treatment of chronic myeloid leukemia (CML). In this study, an innovative fluorescence biosensing methodology has been developed for sensitive and specific detection of BCR-ABL1 mRNA by integrating high-efficiency of exponential transcription and superior catalytic performance of DNA-grafted hemin. Exponential transcription was triggered by BCR-ABL1 mRNA to produce plenty of RNA products. They can specifically hybridize with circular dual-labeled hemin (DLH) probe to dissociate the intramolecular hemin dimmers into highly active hemin monomers for catalyzing fluorescence substrate tyramine. This exponential transcription-triggered hemin catalysis (ET-HC) strategy showed highly sensitive and specific for BCR-ABL1 detection with a limit of detection at 0.5 aM and a good linear range from 2 aM to 200 fM. This method was successfully applied to directly detect as low as 0.001% e13a2 transcript isoforms from complex genomic RNA extraction. Compared with clinical routine, the overall process is a thermostatic reaction and eliminates additional reverse transcription operation. Therefore, the developed ET-HC strategy might provide a promising alternative tool for precise diagnosis and personalized treatment of CML.

Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations

Cancer is known to result from a combination of a small number of genetic defects. However, the specific combinations of mutations responsible for the vast majority of cancers have not been identified. Current computational approaches focus on identifying driver genes and mutations. Although individually these mutations can increase the risk of cancer they do not result in cancer without additional mutations. We present a fundamentally different approach for identifying the cause of individual instances of cancer: we search for combinations of genes with carcinogenic mutations (multi-hit combinations) instead of individual driver genes or mutations. We developed an algorithm that identified a set of multi-hit combinations that differentiate between tumor and normal tissue samples with 91% sensitivity (95% Confidence Interval (CI) = 89-92%) and 93% specificity (95% CI = 91-94%) on average for seventeen cancer types. We then present an approach based on mutational profile that can be used to distinguish between driver and passenger mutations within these genes. These combinations, with experimental validation, can aid in better diagnosis, provide insights into the etiology of cancer, and provide a rational basis for designing targeted combination therapies.

Association of HLA antigens and BCR-ABL transcripts in leukemia patients with the Philadelphia chromosome

Objective

This study aimed to verify the association between human leukocyte antigens and the bcr-abl fusion protein resulting from t(9;22)(q34;q11) in chronic leukemia myeloid and acute lymphoblastic leukemia patients.

Methods

Forty-seven bcr-abl positive individuals were evaluated. Typing was performed bymicrolymphocytotoxicity and molecular biological methods (human leukocyte antigens Class I and Class II). A control group was obtained from the data of potential bone marrow donors registered in the Brazilian Bone Marrow Donor Registry (REDOME).

Results

Positive associations with HLA-A25 and HLA-B18 were found for the b2a2 transcript, as well as a tendency towards a positive association with HLA-B40 and a negative association with HLA-A68. The b3a2 transcript showed positive associations with HLA-B40 and HLA-DRB1*3.

Conclusion

The negative association between human leukocyte antigens and the BCR-ABL transcript suggests that binding and presentation of peptides derived from the chimeric protein are effective to increase a cytotoxic T lymphocyte response appropriate for the destruction of leukemic cells.

Analysis of HLA-A, HLA-B and HLA-DRB1 alleles in Chinese patients with lung cancer

The primary function of the human leukocyte antigen (HLA) system is to regulate the immune response. Because of its important role in the immune response and its high degree of polymorphism, the HLA system is associated with many diseases. We examined the polymorphisms of HLA-A, B and DRB1 alleles in 100 unrelated patients with lung carcinoma and in 438 unrelated normal controls of Han nationality from North China, using sequence-based typing and PCR with sequence-specific primers. We found that the frequencies of HLA-A*0201, A*2601, B*1518, B*3802, DRB1*0401, DRB1*0402, and DRB1*1201 were higher in the lung carcinoma group than in the normal control group. The P values were 0.035, 0.040, 0.001, 0.017, 0.014, 0.004, and 0.019, respectively, and the odds ratio values were 1.052, 3.513, 4.047, 3.054, 4.237, 19.397, and 2.128, respectively. The frequency of HLA-DRB1*1302 was lower in the lung carcinoma group than in the normal control group (P = 0.046, odds ratio = 0.168). We concluded that patients with lung cancer and healthy controls of Han nationality from North China differ in the frequencies of various HLA alleles.

Human leukocyte antigens in Indian patients with chronic myeloid leukemia

In chronic myeloid leukemia (CML), experimental studies using synthetic peptides identical to the bcr-abl fusion region have revealed the capability of specific peptides to bind to human leukocyte antigen (HLA) class I molecules (HLA-A2, A3, A11, B8) and class II molecules (HLA-DR1, DR2, DR3, DR4 and DR11). Individuals expressing HLA-A3, B8 or DR4 have a diminished risk for the development of CML in Caucasian populations. A statistically significant increase in the frequency of Cw3 and Cw4 antigens in Caucasians and European CML patients has been reported. However, HLA associations in CML have not been reported in India. In lieu of the allelic diversity of HLA in the Indian population, the present study assessed the possibility of an association of HLA molecules in Indian patients with CML. HLA A, B, C and DRB1 antigen associations in 180 clinically diagnosed Indian CML patients (aged 17 - 54 years) were analysed and compared with age-matched (n = 100) healthy individuals from the same ethnic background. In the HLA class I antigen distribution, a significant decrease was observed in HLA-A11 (25.6% versus 39%; P = 0.027, odds ratio (OR) = 0.54, 95% confidence interval (CI) = 0.31 - 0.94) and HLA-Cw6 (7.8% versus 20%; P = 0.005, OR = 0.34, 95% CI = 0.15 - 0.74). Among the DRB1 alleles, HLA-DRB1*13 (7.8% versus 17%; P = 0.031, OR = 0.41, 95% CI = 0.18 - 0.93) was decreased in CML patients. However, the differences for HLA-A11 (P(c) = 0.351) and DRB1*13 (P(c) = 0.403) did not remain significant after the application of a correction factor for the P-value. These results suggest that the development of CML is apparently associated with HLA phenotypes specific to each population and indicate that expression of HLA-Cw6 may result in a protective effect on CML acquisition in the Indian population.

The biological basis for immunotherapy in patients with chronic myelogenous leukemia

BACKGROUND

Chronic myelogenous leukemia (CML) has long been recognized as an entity responsive to immunotherapeutic interventions. Despite the success of the tyrosine kinase inhibitors (TKIs) in this disease, CML remains incurable. Only allogeneic bone marrow transplantation can provide long-term eradication of CML.

METHODS

This review summarizes the recent advances in the field of immunology in CML, specifically in tumor antigen discovery, that have been incorporated into the design of new clinical trials.

RESULTS

Multiple vaccine approaches are currently under clinical investigation. Recent laboratory and clinical data also point to a unique interaction of TKIs with the immune system.

CONCLUSIONS

A better understanding of these interactions combined with advances in the field of immunotherapy will likely lead to incorporation of TKIs in future therapeutic interventions to develop a cure for this disease.

Association with the presence of naive T cells in chronic myeloid leukemia patients after allogeneic human stem cell transplantation and the lower incidence of chronic graft-versus host disease and relapse

INTRODUCTION

Allotransplantation in chronic myeloid leukemia (CML) patients offers long-lasting remissions, which largely depend on immunologic surveillance of alloreactivity. Alloreactivity in CML patients has a durable potential. However a large proportion of relapsing patients, who have to undergo donor lymphocyte treatment is still abundant.

METHODS

We studied a group of 31 CML patients post allogeneic transplantation for their level of T-cell receptor excision circles (TREC) and proportion of naive and memory/effector T cells in the peripheral blood (PB). TREC numbers were determined by quantitative PCR (qPCR) and T-cell subsets CD4(+)CD27(+)CD45RO(-), CD4(+)CD27(-)CD24RO(+), CD4(+)CCR7(+), and CD4(+)CCR7(-) by flow cytometry. Patients were analyzed for posttransplant chimerism, type of bcr-abl transcripts, and number of TREC in association with the presence of chronic graft-versus-host disease (cGVHD) and relapse. CML patients with TREC+ in PB had a higher proportion of CD4(+)CD27(+)CD45RO(-) cells (3.54 vs 2.45%; P = .105) and CD4(+)CCR7(+) cells (4.85 vs 2.67%; P = .007), and a lower proportion of CD4(+)CD27(-)CD45RO(+) cells (5.55 vs 9.09%; P = .037). The incidence of cGvHD was reduced among TREC+ CML patients (3/14 vs 11/17; P = .006).

RESULTS

The 5 out of 31 CML patients who relapsed were characterized by the presence of b2a2, b3/a2 or both type of transcripts, a lack of TREC in the blood, and a lower proportion of naïve and effector/memory T cells. No association was observed between any of HLA specificities, type of bcr-abl transcripts and incidence of relapse.

CONCLUSION

The presence of TREC is affected by chronic GvHD; TREC negativity may constitute a risk of mixed chimerism and relapse.

Association of HLA class II allele and haplotype frequencies with chronic myelogenous leukemia and age-at-onset of the disease

Chronic myelogenous leukemia (CML) is characterized by the presence of Philadelphia chromosome resulting from bcr/abl translocation. To clarify the association between HLA class II allele and haplotype frequencies in CML, 50 patients referred to Hematology Oncology and Bone Marrow Transplantation (BMT) center, Shariaty Hospital, Tehran, Iran, were randomly selected and compared with a group of 80 unrelated healthy blood donor subjects. HLA class II alleles were determined by PCR-SSP method. The results showed that the frequencies of DQB1*03011 (P=0.01) and DQA1*0505 (P=0.05) were higher, while that of DQB1*03032 (P=0.04) was lower in patients than in the controls. Regarding age-at-onset, the frequency of HLA-DRB1*07 (P=0.03) and -DQA1*0201 (P=0.03) alleles were higher in patients younger than 35 years. The most frequent haplotypes in our CML patients were HLA-DRB1*11/-DQB1*03011/-DQA1*0505 (P=0.01) and HLA-DRB1*04/-DQB1*0302/-DQA1*03011 (P=0.02). In conclusion, it is suggested that positive and negative association in certain HLA alleles and haplotypes exist in Iranian patients with CML.

Comprehensive analysis of BCR-ABL transcript types in Korean CML patients using a newly developed multiplex RT-PCR

Diagnosis of chronic myeloid leukemia (CML) is based on the detection of BCR-ABL gene or Philadelphia chromosome (Ph chromosome), and fusion proteins with different sizes are encoded depending on the breakpoint in the BCR gene. In general, 3 breakpoint cluster regions in the BCR gene have been described: major (M-bcr), minor (m-bcr), and micro (mu-bcr). This study was designed to determine the frequency of BCR-ABL transcripts using one-step multiplex reverse transcription polymerase chain reaction (RT-PCR). Bone marrow (BM) or peripheral blood (PB) samples at diagnosis from 548 patients were obtained with a referring diagnosis of Ph-positive (Ph+) CML, and multistep RT-PCR and newly developed one-step multiplex RT-PCR were applied on each sample. Compared with the previous multistep RT-PCR, one-step multiplex RT-PCR with the primers is the more rapid and accurate method to identify the BCR-ABL breakpoints. Most patients (538/548, 98.18%) were found to have b3a2 or b2a2, and total frequency of occurrence of c3a2, e1a2, b2a3, b1a1, and e1a3 or coexpression of b2a2 and b3a2 was less than 2.00%. No differences were observed between women and men. As the multiplex RT-PCR technique distinguishes BCR-ABL transcripts in all samples with high sensitivity and specificity, it easily could be applied at early stages of diagnosis. The incidence of one or the other rearrangement in CML patients varies in different reported series, and the frequency in each type of BCR-ABL transcript in Korean CML patients seems to be different from those of Western countries.

BCR-ABL fusion regions as a source of multiple leukemia-specific CD8+ T-cell epitopes

For immunotherapy of residual disease in patients with Philadelphia-positive leukemias, the BCR-ABL fusion regions are attractive disease-specific T-cell targets. We analyzed these regions for the prevalence of cytotoxic T lymphocyte (CTL) epitopes by an advanced reverse immunology procedure. Seventeen novel BCR-ABL fusion peptides were identified to bind efficiently to the human lymphocyte antigen (HLA)-A68, HLA-B51, HLA-B61 or HLA-Cw4 HLA class I molecules. Comprehensive enzymatic digestion analysis showed that 10 out of the 28 HLA class I binding fusion peptides were efficiently excised after their C-terminus by the proteasome, which is an essential requirement for efficient cell surface expression. Therefore, these peptides are prime vaccine candidates. The other peptides either completely lacked C-terminal liberation or were only inefficiently excised by the proteasome, rendering them inappropriate or less suitable for inclusion in a vaccine. CTL raised against the properly processed HLA-B61 epitope AEALQRPVA from the BCR-ABL e1a2 fusion region, expressed in acute lymphoblastic leukemia (ALL), specifically recognized ALL tumor cells, proving cell surface presentation of this epitope, its applicability for immunotherapy and underlining the accuracy of our epitope identification strategy. Our study provides a reliable basis for the selection of optimal peptides to be included in immunotherapeutic BCR-ABL vaccines against leukemia.