Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts.

BACKGROUND: Myelodysplastic syndromes are a diverse and common group of chronic hematologic cancers. The identification of new genetic lesions could facilitate new diagnostic and therapeutic strategies. METHODS: We used massively parallel sequencing technology to identify somatically acquired point mutations across all protein-coding exons in the genome in 9 patients with low-grade myelodysplasia. Targeted resequencing of the gene encoding RNA splicing factor 3B, subunit 1 (SF3B1), was also performed in a cohort of 2087 patients with myeloid or other cancers. RESULTS: We identified 64 point mutations in the 9 patients. Recurrent somatically acquired mutations were identified in SF3B1. Follow-up revealed SF3B1 mutations in 72 of 354 patients (20%) with myelodysplastic syndromes, with particularly high frequency among patients whose disease was characterized by ring sideroblasts (53 of 82 [65%]). The gene was also mutated in 1 to 5% of patients with a variety of other tumor types. The observed mutations were less deleterious than was expected on the basis of chance, suggesting that the mutated protein retains structural integrity with altered function. SF3B1 mutations were associated with down-regulation of key gene networks, including core mitochondrial pathways. Clinically, patients with SF3B1 mutations had fewer cytopenias and longer event-free survival than patients without SF3B1 mutations. CONCLUSIONS: Mutations in SF3B1 implicate abnormalities of messenger RNA splicing in the pathogenesis of myelodysplastic syndromes. (Funded by the Wellcome Trust and others.).

High-density single nucleotide polymorphism array analysis and ASXL1 gene mutation screening in chronic myeloid leukemia during disease progression.

We have undertaken a genome-wide single nucleotide polymorphism (SNP) array analysis of 41 chronic myeloid leukemia (CML) patients. In total, 44 regions of uniparental disomy (UPD) >3 Mb were identified in 24 of 32 patients in chronic phase (CP), and 21 regions of UPD >3 Mb were identified in 13 of 21 patients in blast crisis (BC). Chromosome 8 had the highest frequency of UPD regions in both CP and BC samples. Eight recurrent regions of UPD were observed among the 41 patients, with chromosome 8 showing the highest frequency. Ten regions of copy number change (CNC) >3 Mb were observed in 4 of 21 patients in BC, whereas none were observed in CP. We have identified several recurrent regions of UPD and CNC in CML that may be of pathogenetic importance. Overrepresentation of genomic aberrations (UPD and copy number gain) mapping to chromosome 8 was observed. Selected candidate genes mapping within the aberrant genomic regions were sequenced and mutation of the TP53 gene was observed in one case in BC and of the ASXL1 gene in 6 of 41 cases in CP or BC. Mutation of ASXL1 represents an important new molecular abnormality in CML.

Deregulated gene expression pathways in myelodysplastic syndrome hematopoietic stem cells.

To gain insight into the molecular pathogenesis of the myelodysplastic syndromes (MDS), we performed global gene expression profiling and pathway analysis on the hematopoietic stem cells (HSC) of 183 MDS patients as compared with the HSC of 17 healthy controls. The most significantly deregulated pathways in MDS include interferon signaling, thrombopoietin signaling and the Wnt pathways. Among the most significantly deregulated gene pathways in early MDS are immunodeficiency, apoptosis and chemokine signaling, whereas advanced MDS is characterized by deregulation of DNA damage response and checkpoint pathways. We have identified distinct gene expression profiles and deregulated gene pathways in patients with del(5q), trisomy 8 or -7/del(7q). Patients with trisomy 8 are characterized by deregulation of pathways involved in the immune response, patients with -7/del(7q) by pathways involved in cell survival, whereas patients with del(5q) show deregulation of integrin signaling and cell cycle regulation pathways. This is the first study to determine deregulated gene pathways and ontology groups in the HSC of a large group of MDS patients. The deregulated pathways identified are likely to be critical to the MDS HSC phenotype and give new insights into the molecular pathogenesis of this disorder, thereby providing new targets for therapeutic intervention.

hTERT, the catalytic component of telomerase, is downregulated in the haematopoietic stem cells of patients with chronic myeloid leukaemia.

Telomere shortening is associated with disease progression in chronic myeloid leukaemia (CML). To investigate the biology and regulation of telomerase in CML, we evaluated expression of the telomerase components, its regulators and several telomeric-associated proteins. Quantitative real-time-polymerase chain reaction (PCR) was used to compare gene expression in the CD34+/leukaemic blast cells of 22 CML patient samples to the CD34+ cell population of healthy individuals. hTERT, the catalytic component of telomerase, was downregulated in eight of 12 chronic phase (CP) patients (P = 0.0387). Furthermore, hTERT was significantly downregulated in two of three patients in accelerated phase (AP) and seven of seven patients in blast crisis (BC), P = 0.0017. Expression of hTR and telomeric-associated proteins TEP1, TRF1, TRF2, tankyrase and PinX1 was high in the majority of CP and AP patients. With the exceptions of TEP1 and hTR, expression of these factors was highest in CP and decreased during disease progression. Expression of c-Myc, a positive regulator of hTERT transcription, correlated with hTERT expression and decreased with disease progression, falling below control levels in BC. hTERT levels were increased in CP patients following successful treatment with imatinib, relative to untreated CP patients. We suggest that reduced hTERT expression directly causes the shortened telomeres observed in CML.

The 5q- syndrome.

The 5q- syndrome is a distinct hematological disorder with typical laboratory, morphological, cytogenetic, molecular, and prognostic features. It is defined as a myelodysplastic syndrome with a medullary blast count <5% and an isolated interstitial deletion of the long arm of chromosome 5, including bands q31-q33. The molecular basis of this disease has not yet been fully elucidated, but there is evidence that a commonly deleted region of 1.5 Mb harbors one or several tumor suppressor genes, the loss of which being the basic event leading to disease activity. The 5q- deletion has been demonstrated in very early hematopoietic precursors, including CD34+CD133+ and CD34+CD38-Thyl+ cells. Analysing data of 60 patients with the 5q- syndrome that were followed over a period of up to 28 years, we found a median age at diagnosis of 66.8 years and a female preponderance with a male to female ratio of 1:1.5. Anemia is usually macrocytic and combined with low reticulocyte counts and high erythropoetin levels. Three types of cytogenetic deletion are most prevalent: del(5)(q13q33), del(5)(q13q31) and del(5)(q22q33). The 5q- syndrome has a good prognosis with a median overall survival of 107 months at a median follow-up of 53 months, and a low probability of transformation to AML. An increase of the medullary blast count to > or =5% or the addition of one karyotypic anomaly severely reduces median overall survival. The most promising therapeutic approach is the novel thalidomide analogue CC5013 that is currently evaluated in an international phase II study.

Quantitation of circulating DNA in the serum of breast cancer patients by real-time PCR.

The purpose of this study was to quantify the level of serum DNA in different groups of primary breast cancer patients and in healthy controls using real-time quantitative PCR in order to determine whether such measurements have diagnostic or prognostic value. A total of 96 serum samples of patients with primary breast cancer before surgery (with positive or negative lymph nodes and with high or low relapse-free survival) as well as 24 healthy controls were analysed. DNA concentrations in the serum of the patients differed significantly from the concentration of serum DNA in the controls (medians were 221 and 63 ng x ml(-1), respectively, P<0.001 M-W test). However, no statistically significant difference was observed between the patient groups (P=0.87, M-W test). The serum DNA levels were elevated independently of the size of primary tumour or lymph node metastases. The overall survival of patients with serum DNA concentrations >221 ng x ml(-1) was better than patients with serum DNA concentration

Technical optimization of RhD zygosity determination by real-time quantitative polymerase chain reaction: implication for fetal RhD status determination by maternal plasma.

We have recently reported the development of a multiplex, real-time quantitative polymerase chain reaction (PCR) assay for RhD zygosity determination based on the coamplification and quantification of RHD-specific sequences in relation to a reference gene, albumin. This paper discusses the optimization procedure and technical parameters of this multiplex assay.

Detection of mammaglobin mRNA in the plasma of breast cancer patients.

It has been suggested that mammaglobin may be a useful marker for breast cancer clinical research. Studies investigating the detection of mRNA by RT-PCR from circulating carcinoma cells in the peripheral blood of breast cancer patients have shown that mammaglobin is a highly specific marker and correlates with several prognostic factors, such as lymph node involvement. We aimed to detect cell-free mammaglobin mRNA in the plasma of breast cancer patients and to investigate whether it can be used as a marker for diagnosis of breast cancer.

Detection of Plasmodium falciparum DNA in plasma.

We present a new application in the field of circulating nucleic acids in plasma: the detection of parasite DNA in plasma. We have investigated the presence of Plasmodium falciparum (P. falciparum) DNA in the blood cells and plasma of patients with malaria. Ten blood samples from malaria patients and 9 blood samples from healthy volunteers were collected. Plasma was separated and DNA was extracted from both plasma and blood cells. DNA samples were subjected to a nested polymerase chain reaction (PCR) for the small subunit rRNA gene of P. falciparum and a control amplification of the human rRNA gene. All 6 cases positive by microscopy for P. falciparum were positive by PCR on DNA extracted from blood cells and plasma. Two cases negative by microscopy for malaria were positive by PCR--the blood samples were taken from one of the cases at 7 days after successful treatment of malaria and the other case at the onset of the malaria illness. Two other cases were negative by microscopy and by PCR on blood cells and plasma, both after successful treatment of malaria. The quantitation of Plasmodium DNA in plasma may prove to be a useful prognostic measurement in malaria, and the detection of P. falciparum DNA in archival stored plasma samples may allow the reconstruction of the recent historic evolution of the parasite genome.

A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de novo childhood acute myeloid leukemia.

The recurrent translocation t(5;11)(q35;p15.5) associated with a 5q deletion, del(5q), has been reported in childhood acute myeloid leukemia (AML). We report the cloning of the translocation breakpoints in de novo childhood AML harboring a cryptic t(5;11)(q35;p15.5). Fluorescence in situ hybridization (FISH) analysis demonstrated that the nucleoporin gene (NUP98) at 11p15.5 was disrupted by this translocation. By using 3'--rapid amplification of complementary DNA ends (3'-RACE) polymerase chain reaction, we identified a chimeric messenger RNA that results in the in-frame fusion of NUP98 to a novel gene, NSD1. The NSD1 gene has 2596 amino acid residues and a 85% homology to the murine Nsd1 with the domain structure being conserved. The NSD1 gene was localized to 5q35 by FISH and is widely expressed. The reciprocal transcript, NSD1-NUP98, was also detected by reverse transcriptase--polymerase chain reaction. This is the first report in which the novel gene NSD1 has been implicated in human malignancy. (Blood. 2001;98:1264-1267)

Determination of RhD zygosity: comparison of a double amplification refractory mutation system approach and a multiplex real-time quantitative PCR approach.

BACKGROUND: Rh isoimmunization and hemolytic disease of the newborn still occur despite the availability of Rh immunoglobulin. For the prenatal investigation of sensitized RhD-negative pregnant women, determination of the zygosity of the RhD-positive father has important implications. The currently available molecular methods for RhD zygosity assessment, in general, are technically demanding and labor-intensive. Therefore, at present, rhesus genotype assessment is most commonly inferred from results of serological tests. The recent elucidation of the genetic structure of the prevalent RHD deletion in Caucasians, as well as the development of real-time PCR, allowed us to explore two new approaches for the molecular determination of RhD zygosity. METHODS: Two methods for RhD zygosity determination were developed. The first was based on the double Amplification Refractory Mutation System (double ARMS). The second was based on multiplex real-time quantitative PCR. For the double ARMS assay, allele-specific primers were designed to directly amplify the most prevalent RHD deletion found in RhD-negative individuals in the Caucasian population. The multiplex real-time quantitative PCR assay, on the other hand, involved coamplification and quantification of RHD-specific sequences in relation to a reference gene, albumin, in a single PCR reaction. A ratio, DeltaCt, based on the threshold cycle, was then determined and reflects the RHD gene dosage. RESULTS: The allele-specific primers of the double ARMS assay reliably amplified the RHD-deleted allele and therefore accurately distinguished homozygous from heterozygous RhD-positive samples. The results were in complete concordance with serological testing. For the multiplex real-time quantitative PCR assay, the DeltaCt values clearly segregated into two distinct populations according to the RHD gene dosage, with mean values of 1.70 (SD, 0.17) and 2.62 (SD, 0.29) for the homozygous and heterozygous samples, respectively (P: <0.001, t-test). The results were in complete concordance with the results of serological testing as well as with the double ARMS assay. CONCLUSION: Double ARMS and real-time quantitative PCR are alternative robust assays for the determination of RhD zygosity.

Physical mapping of the human ATX1 homologue (HAH1) to the critical region of the 5q- syndrome within 5q32, and immediately adjacent to the SPARC gene.

The 5q- syndrome is a myelodysplastic syndrome with the 5q deletion as the sole karyotypic abnormality. The human ATX1 homologue (HAH1), encodes a copper-binding protein with a role in antioxidant defence. We have mapped this gene to the 3 Mb critical region of gene loss of the 5q- syndrome within 5q32, flanked by the genes for ADRB2 and IL12B, using gene dosage analysis. Fine physical mapping of the HAH1 gene within this genomic interval was then performed by screening YAC and BAC contigs spanning the critical region of the 5q- syndrome using PCR amplification. The HAH1 gene maps immediately adjacent to the SPARC gene at 5q32, and is flanked by the genetic markers D5S1838 and D5S1419. The HAH1 gene is expressed in haematological tissues and plays a role in antioxidant defence. Antioxidant levels are low in most cancers and the importance of antioxidant enzymes in cancer genesis is well recognised. Genomic localisation, function and expression would suggest that the HAH1 gene represents a candidate gene for the 5q-syndrome.

Combined immunophenotyping and FISH identifies the involvement of B-cells in 5q- syndrome.

The 5q- syndrome is a distinct subtype of myelodysplastic syndrome (MDS) characterized by refractory anemia, deletion of the long arm of chromosome 5, del(5q), as the sole cytogenetic abnormality, and a low frequency of transformation to acute leukemia. Using combined immunophenotyping and fluorescence in situ hybridization (FISH), studies were carried out on bone marrow smears of three 5q- syndrome cases to identify the cell lineages carrying the 5q deletion. In all three cases, the granulocytic, monocytic, and erythroid lineages possessed the del(5q) clonal marker, whereas the T-lymphocytes did not. Interestingly, in one case, cells of B-lymphoid lineage also showed the presence of the del(5q). This is the first report to date showing involvement of an acquired 5q deletion associated with MDS in B-cells. This result suggests that in some cases, MDS arises in a multipotent cell with a capacity to differentiate into both myeloid and lymphoid cells.