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NGS IDs Cause of Exceptional Response to Cancer Drug in ALL Patient

NEW YORK (GenomeWeb) – Researchers have used next-generation sequencing in a patient with refractory early T-cell progenitor acute lymphoblastic leukemia (ETP-ALL) to figure out why he responded so well to a gamma-secretase inhibitor.

Researchers from the Dana-Farber Cancer Institute, Stanford University, and the Brigham and Women's Hospital reported the case study this week in Cold Spring Harbor Molecular Case Studies.

The male patient first presented at the Dana-Farber Cancer Institute at age 53 with relapsed refractory ETP-ALL. He was treated with chemotherapy and appeared to be in remission, but a follow-up examination showed early evidence of relapse.

The patient was enrolled in a Bristol-Myers Squibb clinical trial of a gamma-secretase inhibitor, which targets the Notch pathway. After two four-week cycles of the drug, the patient showed no signs of cancer. His peripheral blood counts had normalized and his bone marrow appeared normal, and testing for minimal residual disease came up negative.

While the gamma-secretase inhibitor had previously shown some benefit, the drug had not elicited such exceptional response in patients, so the researchers wanted to see if they could figure out the molecular reason for the patient's response.

The team performed both targeted sequencing of 137 genes and whole-exome sequencing. Both analyses identified driver mutations in NOTCH1, PTPN11, and DNMT3A, while exome sequencing uncovered an additional driver mutation in a gene not included in the panel, CSF3R.

The NOTCH1 mutation was predicted to create a substitution in a regulatory region of the gene, which is the most common site for gain-of-function mutations in T-ALL and ETP-ALL, although the patient's specific mutation had not been described before.

The DNMT3A mutation was predicted to be a nonsense mutation causing the DNMT3A to lose function. Both the PTPN11 and CSF3F mutations were heterozygous and predicted to be gain of function. "Gain-of-function CSF3R and PTPN11 mutations and loss of function DNMT3A mutations have been described in ETP-ALL," the authors reported.

Examining copy number data, the researchers identified a copy gain on chromosome 9 that encompassed the NOTCH1 locus, a CNV that previously has been reported in T-ALL. The duplicated region included the mutated NOTCH1 allele.

"In line with these observations, studies performed in vitro prior to initiation of [gamma-secretase inhibitor] therapy showed that the leukemic blasts contained high levels of activated NOTCH1 that were markedly decreased by treatment," the authors wrote.

Next the researchers performed exome sequencing on the bone marrow from the patient after he went into remission. The NOTCH1, PTPN11, and CSF3R mutations were no longer present, although the DNMT3A mutation was still there, but heterozygous. The team then confirmed that the mutation was not a germline mutation.

"These findings are consistent with a scenario in which ETP-ALL arose out of a background of clonal hematopoiesis associated with a heterozygous DNMT3A mutation," the authors wrote.

Next, the researchers did RNA-seq on the leukemic cells treated with gamma-secretase inhibitor and found that the genes that were the most sensitive, as expected, were those targeted by Notch. Although surprisingly, MYC, which is an "important Notch target gene in cortical T-ALL, was not downregulated."

The researchers also tried to create a mouse xenograft of the patient's tumor to further understand the impact of the drug, but were unable to establish a stable model.

"To our knowledge, this is the first patient with ETP-ALL who has been treated with a [gamma-secretase inhibitor]," the authors wrote. In addition, "relapsed refractory disease is rarely curable, even with stem cell transplantation, highlighting the exceptional nature of this case" and suggesting that further attempts should be made to target Notch in Notch-mutated ETP-ALL.