Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia

PURPOSE

In acute myeloid leukemia (AML), somatic mutations (commonly missense, nonsense, and frameshift indels) in RUNX1 are associated with a dismal clinical outcome. Inherited RUNX1 mutations cause familial platelet disorder. As approximately 5%-10% of germline RUNX1 mutations are large exonic deletions, we hypothesized that such exonic RUNX1 aberrations may also be acquired during the development of AML.

EXPERIMENTAL DESIGN

Sixty patients with well-characterized AML were analyzed with multiplex ligation-dependent probe amplification (n = 60), microarray (n = 11), and/or whole-genome sequencing (n = 8).

RESULTS

In total, 25 (42% of the cohort) RUNX1-aberrant patients (defined by the presence of classical mutations and/or exonic deletions) were identified. Sixteen patients (27%) carried only exonic deletions, 5 (8%) carried classical mutations, and 4 (7%) carried both exonic deletions and mutations. No significant difference was observed between patients with classical RUNX1 mutations and RUNX1 exonic deletions in median overall survival (OS, 53.1 vs. 38.8 months, respectively, P = 0.63). When applying the European Leukemia Net (ELN) classification including the RUNX1-aberrant group, 20% of the patients initially stratified as intermediate-risk (5% of the whole cohort) were reassigned to the high-risk group, which improved the performance of ELN classification regarding OS between intermediate- and high-risk groups (18.9 vs. 9.6 months, P = 0.09).

CONCLUSIONS

Somatic RUNX1 exonic deletions constitute a novel recurrent aberration in AML. Our findings have important clinical implications regarding AML classification, risk stratification, and treatment decision. Moreover, they argue in favor of further investigating such genomic aberrations not only in RUNX1 but also in other genes implicated in cancer biology and management. See related commentary by Chakraborty and Stengel, p. 2742.

Familial platelet disorder due to germline exonic deletions in RUNX1: a diagnostic challenge with distinct alterations of the transcript isoform equilibrium

Germline pathogenic variants in RUNX1 are associated with familial platelet disorder with predisposition to myeloid malignancies (FPD/MM) with intragenic deletions in RUNX1 accounting for almost 7% of all reported variants. We present two new pedigrees with FPD/MM carrying two different germline RUNX1 intragenic deletions. The aforementioned deletions encompass exons 1-2 and 9-10 respectively, with the exon 9-10 deletion being previously unreported. RNA sequencing of patients carrying the exon 9-10 deletion revealed a fusion with LINC00160 resulting in a change in the 3' sequence of RUNX1. Expression analysis of the transcript isoform demonstrated altered RUNX1a/b/c ratios in carriers from both families compared to controls. Our data provide evidence on the impact of intragenic RUNX1 deletions on transcript isoform expression and highlight the importance of routinely performing copy number variant analysis in patients with suspected MM with germline predisposition.

Standardization of molecular monitoring of CML: results and recommendations from the European treatment and outcome study

Standardized monitoring of BCR::ABL1 mRNA levels is essential for the management of chronic myeloid leukemia (CML) patients. From 2016 to 2021 the European Treatment and Outcome Study for CML (EUTOS) explored the use of secondary, lyophilized cell-based BCR::ABL1 reference panels traceable to the World Health Organization primary reference material to standardize and validate local laboratory tests. Panels were used to assign and validate conversion factors (CFs) to the International Scale and assess the ability of laboratories to assess deep molecular response (DMR). The study also explored aspects of internal quality control. The percentage of EUTOS reference laboratories (n = 50) with CFs validated as optimal or satisfactory increased from 67.5% to 97.6% and 36.4% to 91.7% for ABL1 and GUSB, respectively, during the study period and 98% of laboratories were able to detect MR^4.5 in most samples. Laboratories with unvalidated CFs had a higher coefficient of variation for BCR::ABL1^IS and some laboratories had a limit of blank greater than zero which could affect the accurate reporting of DMR. Our study indicates that secondary reference panels can be used effectively to obtain and validate CFs in a manner equivalent to sample exchange and can also be used to monitor additional aspects of quality assurance.

Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics

BACKGROUND

We have evaluated an NGS-based method to detect recurrent gene fusions of diagnostic and prognostic importance in hematological malignancies. Our goal was to achieve a highly specific assay with a simple workflow, short turnaround time and low cost.

METHOD

The assay uses a commercially available anchored multiplex PCR panel for target enrichment and library preparation, followed by sequencing using a MiSeq instrument. The panel includes all recurrent gene fusions in AML and ALL and is designed to detect gene-specific fusions without prior knowledge of the partner sequence or specific break points. Diagnostic RNA samples from 27 cases with hematological malignancies encompassing 23 different transcript variants were analyzed. In addition, 12 cases from a validation cohort were assessed.

RESULT

All known fusion transcripts were identified with a high degree of confidence, with a large number of reads covering the breakpoints. Importantly, we could identify gene fusions where conventional methods had failed due to cryptic rearrangements or rare fusion partners. The newly-identified fusion partners were verified by RT-PCR and transcript-specific qPCR was designed for patient-specific follow-up. In addition, 12 cases were correctly assessed in a blind test, without prior knowledge of molecular cytogenetics or diagnosis.

CONCLUSION

In summary, our results demonstrate that targeted RNA sequencing using anchored multiplex PCR can be implemented in a clinical laboratory for the detection of recurrent and rare gene fusions in hematological diagnostic samples.

Prognostic scoring systems and comorbidities in chronic myelomonocytic leukaemia: a nationwide population-based study

Outcomes in chronic myelomonocytic leukaemia (CMML) are highly variable and may be affected by comorbidity. Therefore, prognostic models and comorbidity indices are important tools to estimate survival and to guide clinicians in individualising treatment. In this nationwide population-based study, we assess comorbidities and for the first time validate comorbidity indices in CMML. We also compare the prognostic power of: the revised International Prognostic Scoring System (IPSS-R), CMML-specific prognostic scoring system (CPSS), MD Anderson Prognostic Scoring System (MDAPS) and Mayo score. In this cohort of 337 patients with CMML, diagnosed between 2009 and 2015, the median overall survival was 21·3 months. Autoimmune conditions were present in 25% of the patients, with polymyalgia rheumatica and Hashimoto's thyroiditis being most common. Of the tested comorbidity indices: the Charlson Comorbidity Index (CCI), Haematopoietic cell transplantation-specific Comorbidity Index (HCT-CI) and Myelodysplastic Syndrome-Specific Comorbidity Index (MDS-CI), CCI had the highest C-index (0·62) and was the only comorbidity index independently associated with survival in multivariable analyses. When comparing the prognostic power of the scoring systems, the CPSS had the highest C-index (0·69). In conclusion, using 'real-world' data we found that the CCI and CPSS have the best prognostic power and that autoimmune conditions are overrepresented in CMML.

Prognostic scoring systems for myelodysplastic syndromes (MDS) in a population-based setting: a report from the Swedish MDS register

The myelodysplastic syndromes (MDS) have highly variable outcomes and prognostic scoring systems are important tools for risk assessment and to guide therapeutic decisions. However, few population-based studies have compared the value of the different scoring systems. With data from the nationwide Swedish population-based MDS register we validated the International Prognostic Scoring System (IPSS), revised IPSS (IPSS-R) and the World Health Organization (WHO) Classification-based Prognostic Scoring System (WPSS). We also present population-based data on incidence, clinical characteristics including detailed cytogenetics and outcome from the register. The study encompassed 1329 patients reported to the register between 2009 and 2013, 14% of these had therapy-related MDS (t-MDS). Based on the MDS register, the yearly crude incidence of MDS in Sweden was 2·9 per 100 000 inhabitants. IPSS-R had a significantly better prognostic power than IPSS (P < 0·001). There was a trend for better prognostic power of IPSS-R compared to WPSS (P = 0·05) and for WPSS compared to IPSS (P = 0·07). IPSS-R was superior to both IPSS and WPSS for patients aged ≤70 years. Patients with t-MDS had a worse outcome compared to de novo MDS (d-MDS), however, the validity of the prognostic scoring systems was comparable for d-MDS and t-MDS. In conclusion, population-based studies are important to validate prognostic scores in a 'real-world' setting. In our nationwide cohort, the IPSS-R showed the best predictive power.

Search for Pompe disease among patients with undetermined myopathies

OBJECTIVE

Pompe disease is a rare treatable glycogen storage disease with in adults - a limb-girdle muscle weakness. Muscle biopsy may fail to show the typical vacuolar myopathy. We asked if we had un-diagnosed patients with Pompe disease in western Sweden.

MATERIAL AND METHODS

We searched the muscle biopsy registry during the time period 1986 until 2006 including 3665 biopsies and included patients at our Neuromuscular Center with unspecified myopathy or limb-girdle muscular dystrophy. The dry blood spot test was used to identify patients with Pompe disease.

RESULTS

A total of 82 patients (46 from the biopsy register and 36 from our center) were seen and dry blood spot test was obtained. No patient with Pompe disease was found. The dry blood spot test was low in three cases (11, 16, and 18% of normal) but a second blood sample showed a normal result based on GAA enzyme activity in lymphocytes in all three patients. In one patient with low normal result of the analysis in lymphocytes a genetic test showed no pathogenic mutations. Further investigation gave a definite diagnose of another myopathy in 12 patients.

CONCLUSIONS

The prevalence of Pompe disease in western Sweden (3 in 1.27 million or 0.24 per 100.000 inhabitants) is lower than in the Netherlands and New York. Re-evaluation of patients with myopathies but without definite diagnosis is rewarding since 12 of 82 patients in our study had a definite molecular diagnosis after workup.

Sarcoplasmic body myopathy--a rare hereditary myopathy with characteristic inclusions

OBJECTIVES

To characterise a Swedish family with a rare hereditary myopathy with unique sarcoplasmic inclusion bodies in the muscle biopsy.

MATERIALS AND METHODS

Part of the pedigree was described in 1980. Nine new members of the included and the phenotype further characterised through clinical, neurophysiological and radiological investigations.

RESULTS

Six of the nine subjects displayed clinical and/or laboratory evidence of myopathy with sarcoplasmic inclusions.

CONCLUSIONS

Sarcoplasmic body myopathy is distinguished from other distal myopathies by a more malignant course and early involvement of thenar muscles and hand flexors. Five to ten years after onset the affected subjects develop distal, as well as proximal, weakness and atrophy and the majority require a wheelchair after ten to fifteen years of disease. The disorder is manifested through elevated creatine kinase levels and the presence of the pathognomonic sarcoplasmic inclusions prior to clinical signs and symptoms.

Oral sugar clearance and other caries-related factors in patients with myotonic dystrophy

The aim of the investigation was to try to explain why patients with myotonic dystrophy (MD) have a high caries prevalence. Seventeen MD patients, 15 of whom had been examined 8 years earlier, and 17 matched, healthy controls participated. In connection with this follow-up examination, the oral sugar clearance was evaluated after chewing a glucose tablet. A paraffin-stimulated whole saliva sample was collected for determination of secretion rate, buffer capacity, and numbers of mutans streptococci and lactobacilli. Dietary score, plaque index, oral muscular coordination, and self-cleaning ability were also recorded. For all factors, the MD patients showed less favorable mean values than the controls; the differences between the groups were statistically significant, except for the bacterial counts and the salivary buffer capacity. Thus, the high caries prevalence in MD patients may be explained by longer oral sugar clearance time, lower salivary secretion rate, higher intake frequency of sugar-containing products, higher plaque index, and less pronounced oral muscular coordination and self-cleaning ability than in healthy individuals.

Ultrasound imaging of the masseter muscle in myotonic dystrophy patients

Ultrasound technique was applied to measure the thickness and examine the internal structure of the masseter muscle in a group of 16 adult patients (nine women and seven men) with myotonic dystrophy (MyD) and 16 healthy individuals matched in age, sex and number of occluding teeth. The masseter thickness was measured bilaterally under both relaxed conditions and during maximal clenching. The error of measurement was found to be small, not exceeding 0.45 mm. The imaging characteristics of the masseter in most of the MyD patients was an obvious atrophy of the muscle with increased echointensity of the intramuscular tissue and loss of the internal structure concerning tendons and fasciae. The mean masseter thickness (+/- SD) in the MyD group was 10.4 (+/- 2.2) mm under relaxed conditions and 11.1 (+/- 2.4) mm during maximal clenching, compared with 13.3 (+/- 2.2) mm and 14.1 (+/- 2.4) mm, respectively, in the healthy group (P < 0.001). In conclusion, our results indicate that, in most of the myotonic dystrophy patients, the masseter muscle is atrophic with obvious signs of degeneration. Ultrasound is a useful method for both qualitative and quantitative evaluation of the condition of the masseter muscle.

Geographical and temporal distribution of Ockelbo disease in Sweden

The incidence of Ockelbo disease and the prevalence of Ockelbo virus neutralizing antibodies were investigated in a sample of the Swedish population. The disease occurs throughout most of Sweden but with higher incidence and antibody prevalence rates in the central part of the country. It generally affects middle-aged men and women, with equal incidence between sexes, and is uncommon in people younger than 20 years of age. The disease occurs during a short period each year between the third week of July and the first week of October, with a peak during the second half of August. During the 8 years studied (1981-8), an average of 31 Ockelbo patients/year were diagnosed. The antibody prevalence rates in the oldest age groups were 20-40 times higher than the accumulated life-risk of being diagnosed and reported as an Ockelbo disease patient, which suggests that many cases are asymptomatic and/or unreported.