Hematopathology and Molecular Diagnostics Case Study: A 63 Year Old Man with Fatigue

The following case is an interesting overlap of Hematopathology and Molecular Diagnostics, and shows the utility of sequencing to detect a cancer before biopsy could.

A 63 year old gentleman presented to a heme/onc physician with six months of intractable anasarca, fatigue, and a recent mild thrombocytopenia (Table 1). They were otherwise in healthy condition. The physician initiated a lymphoma work-up that included a bone marrow biopsy. The tests were negative for M-protein.

Table 1. Summary of symptoms and relevant abnormal labs.

The bone marrow biopsy was somewhat limited, but the core contained multiple marrow elements. After a thorough review by a Hematopathologist, no evidence of dysplasia or other irregularities could be detected (Image 1). Flow cytometry detected no aberrant blast population. Cytogenetics detected 20del [16/20] and 5del [3/20]. These findings did not clearly indicate a specific diagnosis.

Image 1. 40x view of the bone marrow specimen at the initial presentation. No evidence of dysplasia was found.

As the clinical suspicion for a malignancy was high, the bone marrow specimen was sent for sequencing on a 1385-gene panel test. The test included tumor-normal matched DNA sequencing (“tumor” sample: bone marrow, normal: saliva), RNA whole transcriptome sequencing on the bone marrow, and Copy Number Variant (CNV) analysis. Tumor-normal matched sequencing helps rule out variants that are normal and present in the patient.

Somatic mutations were determined as those that were present in the “tumor” sample and not in the matched normal sample. The somatic variants found are listed below with their variant allele frequency (VAF) in parenthesis. Recall that a VAF of 40% means that a mutation is present in the heterozygous state in 80% of cells.

  • IDH2 (p.R140Q, 46%)
  • SRSF2 (p.P95T, 51%)
  • CBL (p.R499*, 47%)
  • KRAS (p.K117N, 12%)
Figure 1. View of IGV, which displays the NGS reads for IDH1 along with the variant allele highlighted in red. The color of the bars indicates the direction of the reads (forward in red and reverse in blue). This reflects the allele frequency of approximately 50%.

The mutations in these genes are commonly found in myeloid cancers including myselodysplastic syndrome. Activating mutation in IDH2 (isocitrate dehydrogenase 2) increase the production of the oncometabolite 2-HG, which alters methylation in cells taking them to an undiffereitiated state. SRSF2 (Serine And Arginine Rich Splicing Factor 2) is a part of the spliceosome complex, which regulates how sister chromatids separate from each other. Failures in the proper function of the complex creates genomic instability. CBL (Casitas B-lineage Lymphoma) is a negative regulator of multiple signaling pathways, and loss of function mutations (as seen here) lead to increased growth signals through several tyrosine kinase receptors. KRAS (Kirsten RAt Sarcoma virus) is an upstream mediator of the RAS pathway, which acquires mutations that lead to constitutive activation and sends growth signals to cells causing them to proliferate.

Furthermore the CNV analysis also found the heterozygous loss of chromosome 20 as reported in cytogenetics. CNV analysis did not detect chromosome 5 deletion, as it was below the limit of detection (20% for CNV analysis).

Figure 2. This plot shows the normalized read frequency of genes across each of the chromosomes is shown here. The drop at chromosome 20 is shown in a pale brown color on the right side of the graph. This is consistent with the cytogenetic findings. The loss of 5q isn’t seen as it is below the limit of detection of 30%.

These mutations are all individually common in MDS, but the co-occurance of each gives very strong evidence that MDS is the diagnosis (Figure 3). There have also been studies that provide prognostic implications for several of the genetic mutations present. Some mutations like SRSF2 or CBL at high VAF (>10%) indicate a poor prognosis, but mutations in IDH2 or TP53 at any frequency have not only a high chance of progression, but also a faster time to onset of disease. Another non-genetic risk factor for developing MDS is an elevated RDW, which we saw in our patient.

Figure 3. From Becker et al 2016.

All of these high-risk factors together led us to push for a diagnosis of MDS based off of molecular findings, and the patient was started on treatment with Azacitadine. Our assessment was confirmed 3 months later when, the patient’s follow up bone marrow biopsy showed significant progression with megakaryocytic and erythroid dysplasia and hyperplasia and reticulin fibrosis MF2 (Image 2). Aberrant blasts were detected (1-2%), but not elevated. This demonstrates how molecular findings predicted and predated the patient’s rapid progression to morphologic disease.

Image 2. Dysplastic, hyperplastic megakaryocytes and erythroid lineage.

In summary, multiple molecular mutations indicative of MDS were found in a symptomatic patient’s unremarkable bone marrow biopsy months before a rapid progression to MDS.

References

  1. Steensma DP, Bejar R, Jaiswal S et al. Blood 2015;126(1):9-16.
  2. Sellar RS, Jaiswal S, and Ebert BL. Predicting progression to AML. Nature Medicine 2018; 24:904-6.
  3. Abelson S, Collord G et al. Prediction of acute myeloid leukemia risk in healthy individuals. Nature 2018; 559:400-404.
  4. Desai P, Mencia-Trinchant N, Savenkov O et al. Nature Medicine 2018; 24:1015-23.
  5. Becker PM. Clonal Hematopoiesis: The Seeds of Leukemia or Innocuous Bystander? Blood.2016 13(1)

-Jeff SoRelle, MD is a Chief Resident of Pathology at the University of Texas Southwestern Medical Center in Dallas, TX. His clinical research interests include understanding how the lab intersects with transgender healthcare and improving genetic variant interpretation.

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