Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression

Progression from myelodysplastic syndromes (MDS) to secondary acute myeloid leukemia (AML) is associated with the acquisition and expansion of subclones. Our understanding of subclone evolution during progression, including the frequency and preferred order of gene mutation acquisition, remains incomplete. Sequencing of 43 paired MDS and secondary AML samples identified at least one signaling gene mutation in 44% of MDS and 60% of secondary AML samples, often below the level of standard sequencing detection. In addition, 19% of MDS and 47% of secondary AML patients harbored more than one signaling gene mutation, almost always in separate, coexisting subclones. Signaling gene mutations demonstrated diverse patterns of clonal evolution during disease progression, including acquisition, expansion, persistence, and loss of mutations, with multiple patterns often coexisting in the same patient. Multivariate analysis revealed that MDS patients who had a signaling gene mutation had a higher risk of AML progression, potentially providing a biomarker for progression.

SIGNIFICANCE

Subclone expansion is a hallmark of progression from MDS to secondary AML. Subclonal signaling gene mutations are common at MDS (often at low levels), show complex and convergent patterns of clonal evolution, and are associated with future progression to secondary AML. See related article by Guess et al., p. 316 (33). See related commentary by Romine and van Galen, p. 270. This article is highlighted in the In This Issue feature, p. 265.

Genome Sequencing as an Alternative to Cytogenetic Analysis in Myeloid Cancers

BACKGROUND

Genomic analysis is essential for risk stratification in patients with acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS). Whole-genome sequencing is a potential replacement for conventional cytogenetic and sequencing approaches, but its accuracy, feasibility, and clinical utility have not been demonstrated.

METHODS

We used a streamlined whole-genome sequencing approach to obtain genomic profiles for 263 patients with myeloid cancers, including 235 patients who had undergone successful cytogenetic analysis. We adapted sample preparation, sequencing, and analysis to detect mutations for risk stratification using existing European Leukemia Network (ELN) guidelines and to minimize turnaround time. We analyzed the performance of whole-genome sequencing by comparing our results with findings from cytogenetic analysis and targeted sequencing.

RESULTS

Whole-genome sequencing detected all 40 recurrent translocations and 91 copy-number alterations that had been identified by cytogenetic analysis. In addition, we identified new clinically reportable genomic events in 40 of 235 patients (17.0%). Prospective sequencing of samples obtained from 117 consecutive patients was performed in a median of 5 days and provided new genetic information in 29 patients (24.8%), which changed the risk category for 19 patients (16.2%). Standard AML risk groups, as defined by sequencing results instead of cytogenetic analysis, correlated with clinical outcomes. Whole-genome sequencing was also used to stratify patients who had inconclusive results by cytogenetic analysis into risk groups in which clinical outcomes were measurably different.

CONCLUSIONS

In our study, we found that whole-genome sequencing provided rapid and accurate genomic profiling in patients with AML or MDS. Such sequencing also provided a greater diagnostic yield than conventional cytogenetic analysis and more efficient risk stratification on the basis of standard risk categories. (Funded by the Siteman Cancer Research Fund and others.).

Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells

HOX genes are highly expressed in many acute myeloid leukemia (AML) samples, but the patterns of expression and associated regulatory mechanisms are not clearly understood. We analyzed RNA sequencing data from 179 primary AML samples and normal hematopoietic cells to understand the range of expression patterns in normal versus leukemic cells. HOX expression in AML was restricted to specific genes in the HOXA or HOXB loci, and was highly correlated with recurrent cytogenetic abnormalities. However, the majority of samples expressed a canonical set of HOXA and HOXB genes that was nearly identical to the expression signature of normal hematopoietic stem/progenitor cells. Transcriptional profiles at the HOX loci were similar between normal cells and AML samples, and involved bidirectional transcription at the center of each gene cluster. Epigenetic analysis of a subset of AML samples also identified common regions of chromatin accessibility in AML samples and normal CD34(+) cells that displayed differences in methylation depending on HOX expression patterns. These data provide an integrated epigenetic view of the HOX gene loci in primary AML samples, and suggest that HOX expression in most AML samples represents a normal stem cell program that is controlled by epigenetic mechanisms at specific regulatory elements.

Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci

Genome-wide association studies (GWAS) have identified >500 common variants associated with quantitative metabolic traits, but in aggregate such variants explain at most 20–30% of the heritable component of population variation in these traits. To further investigate the impact of genotypic variation on metabolic traits, we conducted re-sequencing studies in >6,000 members of a Finnish population cohort (The Northern Finland Birth Cohort of 1966 [NFBC]) and a type 2 diabetes case-control sample (The Finland-United States Investigation of NIDDM Genetics [FUSION] study). By sequencing the coding sequence and 5′ and 3′ untranslated regions of 78 genes at 17 GWAS loci associated with one or more of six metabolic traits (serum levels of fasting HDL-C, LDL-C, total cholesterol, triglycerides, plasma glucose, and insulin), and conducting both single-variant and gene-level association tests, we obtained a more complete understanding of phenotype-genotype associations at eight of these loci. At all eight of these loci, the identification of new associations provides significant evidence for multiple genetic signals to one or more phenotypes, and at two loci, in the genes ABCA1 and CETP, we found significant gene-level evidence of association to non-synonymous variants with MAF<1%. Additionally, two potentially deleterious variants that demonstrated significant associations (rs138726309, a missense variant in G6PC2, and rs28933094, a missense variant in LIPC) were considerably more common in these Finnish samples than in European reference populations, supporting our prior hypothesis that deleterious variants could attain high frequencies in this isolated population, likely due to the effects of population bottlenecks. Our results highlight the value of large, well-phenotyped samples for rare-variant association analysis, and the challenge of evaluating the phenotypic impact of such variants.

Abnormal serum levels of various metabolites, including measures relevant to cholesterol, other fats, and sugars, are known to be risk factors for cardiovascular disease and type 2 diabetes. Identification of the genes that play a role in generating such abnormalities could advance the development of new treatment and prevention strategies for these disorders. Investigations of common genetic variants carried out in large sets of research subjects have successfully pinpointed such genes within many regions of the human genome. However, these studies often have not led to the identification of the specific genetic variations affecting metabolic traits. To attempt to detect such causal variations, we sequenced genes in 17 genomic regions implicated in metabolic traits in >6,000 people from Finland. By conducting statistical analyses relating specific variations (individually and grouped by gene) to the measures for these metabolic traits observed in the study subjects, we added to our understanding of how genotypes affect these traits. Our findings support a long-held hypothesis that the unique history of the Finnish population provides important advantages for analyzing the relationship between genetic variations and biomedically important traits.

Effect of repair strategy on hospital cost for infants with tetralogy of Fallot

OBJECTIVE

This study compares the total hospital cost (HC) for one-stage versus "two-stage" repair of tetralogy of Fallot (TOF) in infants younger than 1 year of age.

SUMMARY BACKGROUND DATA

Total (one-stage) correction of TOF is now being performed with excellent results in infancy. Alternatively, a two-stage approach, with palliation of infants in the first year of life, followed by complete repair at a later time can be used. In some institutions, the two-stage approach is standard practice for infants younger than 1 year of age or is used selectively in patients with an anomalous coronary artery across the right ventricular outflow tract (RVOT), "small pulmonary arteries," multiple congenital anomalies, critical illnesses (CI), which increase the risk of bypass (e.g., sepsis or DIC), or severe hypercyanotic spells (HS) at the time of presentation. The cost implications of these two approaches are unknown.

METHODS

The authors reviewed 22 patients younger than 1 year of age who underwent repair of TOF at their institution between 1993 and 1995. Eighteen patients had one-stage (1 degree) repair (mean age, 3.4 +/- 3.1 months; range, 3 days-9 months) and 4 patients were treated by a staged approach with initial palliation (1.6 +/- 0.4 month; range, 1.5-2 months) followed by later repair (14.75 +/- 1.5 months; range, 13-16 months). The reasons for palliation were severe HS at time of presentation (two patients), anomalous coronary artery (one patient) and CI (one patient). In the 18 patients undergoing 1 degree repair, 3 (16.6%) presented with HS, 6 (33.3%) had a transanular repair, and 6 (33.3%) were able to be repaired through an entirely transatrial approach (youngest patient, 1.5 months). The HC (1996 dollars) and hospital length of stay (LOS; days) were evaluated for all patients. The HCs were calculated using transition I, which is a cost accounting system used by our medical center since July 1992. Transition I provides complete data on all direct and indirect hospital-based, nonprofessional costs.

RESULTS

There was no mortality in either group. The group undergoing 1 degree repair had an average LOS of 14.5 +/- 11.2 days compared to an average LOS for palliation of 14 +/- 6.4 days. When the palliated group returned for complete repair, the average LOS was 28.8 +/- 25 days, yielding a total LOS for the two-stage strategy of 43 +/- 30.8 days (p = 0.003 compared to 1 degree repair). The HC for 1 degree repair was $32,541 +/- $15,968 compared to $25,737 +/- $1900 for palliation (p = not significant compared to 1 degree repair) and $54,058 +/- $39,395 for subsequent complete repair (p = not significant compared to 1 degree repair) (total two-stage repair HC = $79,795 +/- $40,625; p = 0.001 compared to 1 degree repair). The LOS and HC for the two-stage group combine a total of palliation plus later repair and, as such, reflect two separate hospitalizations and convalescent periods. To eliminate cost outliers, a best-case analysis was performed by eliminating 50% of patients from each group. Using this analysis, the two-stage approach resulted in an average (total) LOS of 16.5 +/- 2.1 days compared to 8.5 +/- 1.4 days for the 1 degree group. Total cost for the two-stage strategy in this best-case group was $44,660 +/- $3645 compared to $22,360 +/- $3331 for 1 degree repair (p = 0.00001).

CONCLUSIONS

The data from this review show that palliation alone generates HC similar to that from 1 degree infant repair of TOF, and total combined HC and LOS for palliation plus eventual repair of TOF (two-stage approach) are significantly higher than from 1 degree repair. Furthermore, these data do not include additional costs for care delivered between palliation and repair (e.g., outpatient visits, cardiac catheterization, serial echocardiography). Although there may be occasions when a strategy using initial palliation followed by later repair may seem prudent, the cost is clearly higher and use of health care resources greater.