Study Findings Support Use of FISH to Identify Chromosomal Abnormalities in CML

In an interview with Oncology Learning Network, Zhenya Tang, MD, PhD, Associate Professor, Department of Hematopathology, The University of Texas MD Anderson Cancer Center in Houston, answered some questions about the findings and clinical significance of a study he led on the use of fluorescence in situ hybridization (FISH) to identify chromosomal abnormalities in patients with chronic myeloid leukemia (CML; Mod Pathol. 2020;33[10]:2035-2045).

What existing data led you and your co-investigators to conduct this research?

During our daily practice, we encountered some cases of CML without a typical Philadelphia (Ph) chromosome derived from the classic t(9;22)(q34.1;q11.2), but subsequently consequent BCR-ABL1 fusion was detected by various laboratory tests, such as FISH and reverse-transcription PCR (RT-PCR).

Several terms, such as “masked Ph”, “cryptic Ph”, “variant Ph”, and “complex Ph” have been used to describe this phenomenon in the literature, but none of these terms fit all of the cases we have encountered. More importantly, certain criteria used currently for CML risk prediction and/or response to treatment do not apply for some of these cases. For example, one CML case had a normal karyotype, but was positive for BCR-ABL1 by FISH with a complicated signal pattern.

These results suggest that complicated chromosomal aberrations should not be classified based only on the karyotype results as standard risk for prognosis, and the cytogenetic response criteria recommend by National Comprehensive Cancer Network do not apply for monitoring responses to treatment in this case. Therefore, my colleagues and I teamed up to conduct studies to further characterize this distinctive group of CML cases.

Please briefly describe your study and its findings. Were any of the outcomes particularly surprising?

In this study published in Modern Pathology in July 2020, we focused on a group of 41 CML cases that a BCR-ABL1 fusion derived by insertion instead of the classic t(9;22) (q34.1;q11.2),  confirmed by intensive laboratory testing.

Different from most CML cases with a classic Ph chromosome, these 41 cases showed a wide spectrum of chromosomal analysis results, such as normal karyotype, abnormal karyotype with morphologically normal chromosomes 9 and 22, and abnormal karyotype with morphologically abnormal chromosome 9 and/or chromosome 22.

Although the BCR-ABL1 FISH results were all positive in these cases, the signal patterns were highly variable and unrelated to their karyotype results. We divided these cases into 2 groups, complex karyotype (CK) and non-CK following the current guidelines for risk stratification. No significant difference for overall survival was observed between these 2 groups (P = .97).

We incorporated BCR-ABL1 FISH findings into the chromosomal abnormalities in each case and then re-categorized these cases into two new groups, one group with simple chromosomal abnormalities and another group with complex chromosomal abnormalities, based on all positive findings by both chromosomal analysis and FISH tests. Interestingly, a statistically significant difference for overall survival was observed between these 2 new groups (P = .004).

What are the possible real-world applications of these findings in clinical practice?

We have shown that some CML cases through a non-classic BCR-ABL1 rearrangement, e.g., an insertion instead of a translocation, might have a “normal” karyotype, but actually possess complex chromosomal abnormalities that might be overlooked by conventional chromosomal analysis, but more easily identified by various FISH tests. The complex chromosomal abnormalities recognizing by incorporating FISH findings into chromosomal analysis can better predict outcomes in these patients.

Therefore, while encountering a case with a potential insertion-derived BCR-ABL1 fusion, a normal or non-CK obtained by conventional cytogenetics can be misleading in terms of risk stratification, response categorization and clinical follow-up. Instead, intensive FISH studies, to explore or exclude complex chromosomal abnormalities are necessary, at least at the time of initial diagnosis.

Do you and your co-investigators intend to expand upon this research?

We are expanding this study to additional CML cases with isolated t(9;22)(q34.1;q11.2), but BCR-ABL1 FISH indicates more complicated chromosomal abnormalities.

Is there anything else pertaining to your research and findings that you would like to add?

FISH testing has been applied to provide definitive information (eg, positive vs negative result for the target; BCR-ABL1 fusion for establishment of CML diagnosis) in most patients. However, additional information provided by FISH testing (eg, unexpected location of target, atypical and/or complicated signal patterns that indicate for complicated chromosomal abnormalities) can be sometimes overlooked.

Incorporating all additional findings obtained by FISH as well as other tests into chromosomal analysis is helpful for better understanding the underlying genetic changes and more accurate risk stratification and prognosis prediction of CML patients. We assume that this concept may apply for other hematologic malignancies with recurrent chromosomal abnormalities/gene rearrangement, such as acute myeloid leukemia with t(8;21)/RUNX1T1-RUNX1; inv(16)/CBFB/MYH11 and t(15;17)/PML-RARA.