In two small series of patients with myelodysplastic syndrome (MDS), treatment with a hypomethylating agent that was aimed at inducing cell differentiation resulted in induction of expression of the SALL4 oncogene in more than 30% of patients, and such expression was associated with a poorer outcome. Identifying other oncogenes that are similarly activated by treatment with hypomethylating agent and evaluation of these and SALL4 expression in larger prospective study samples are needed to validate this observation according to the study team who published the findings on 26 May 2022 in The New England Journal of Medicine.

Two hypomethylating agents, decitabine and 5-azacytidine are used clinically. There are many mechanisms of action of these drugs, including irreversibly binding to and inhibiting DNA methyltransferases, which result in hypomethylation and up-regulation of genes such as tumour suppressors. Other major mechanisms of action include incorporation of the hypomethylating agent into newly synthesized DNA, which triggers a DNA-damage response and leads to cytotoxic effects in cancer cells, as well as alteration of immune responses. Whether hypomethylating agents can also reactivate and up-regulate oncogenes is not well elucidated.

The study team hypothesized that the overall effect of treatment with hypomethylating agents would not only contribute to the demethylation of tumour-suppressor genes, but may also induce demethylation of oncogenes. To test this theory, the study team focused on candidate genes with the following features: aberrant expression in human cancers, functionally proved to be oncogenes with the use of methods such as murine models, and DNA methylation may be important for the expression of these genes. This led to the current study, in which the investigators examined the effect of hypomethylating agents on SALL4, a known oncogene that plays an important role in MDS and other cancers.

Paired bone marrow samples that were obtained from two cohorts of patients with MDS before and after treatment with a hypomethylating agent were used to explore the relationships among changes in SALL4 expression, treatment response, and clinical outcome. Leukaemic cell lines with low or undetectable SALL4 expression were used to study the relationship between SALL4 methylation and expression. A locus-specific demethylation technology, CRISPR-DiR, was used to identify the CpG island that is critical for SALL4 expression.

The study team retrospectively analyzed SALL4 expression and survival among 68 patients with MDS in 2 cohorts with distinct ethnic background (25 patients in cohort 1 and 43 patients in cohort 2) with bone marrow samples obtained before and after treatment with a hypomethylating agent. SALL4 up-regulation after treatment with hypomethylating agents was observed in 10 of 25 patients (40%) in cohort 1 and in 13 of 43 patients (30%) in cohort 2 and was associated with a worse outcome.

Using CRISPR-DiR, the study team discovered that demethylation of a CpG island within the 5′ untranslated region was critical for SALL4 expression. In cell lines and patients, they confirmed that treatment with a hypomethylating agent led to demethylation of the same CpG region and up-regulation of SALL4 expression.

The authors commented that although the up-regulation of SALL4 may be associated with a worse prognosis, it may also provide an additional treatment option on the basis of SALL4-mediated cancer vulnerability. They are currently exploring the concept that if SALL4 expression is up-regulated, a concomitant targeted therapy that directly or indirectly mitigates SALL4 expression, function, or both could be added to the treatment plan.

The authors concluded that by combining analysis of patient samples with CRISPR-DiR technology, they found that demethylation and up-regulation of an oncogene after treatment with a hypomethylating agent can occur and should be further studied.

This work was funded by Associazione Italiana per la Ricerca sul Cancro and others.


Liu Y-C, Kwon J, Fabiani E, et al. Demethylation and Up-Regulation of an Oncogene after Hypomethylating Therapy. N Engl J Med 2022; 386:1998-2010.