Co-existence of PHF6 and NOTCH1 mutations in adult T-cell acute lymphoblastic leukemia

Abstract

T-cell acute lymphoblastic leukemia (T-ALL) results from the collaboration of multiple genetic abnormalities in the transformation of T-cell progenitors. Plant homeodomain finger protein 6 (PHF6) has recently been established as a key tumor suppressor, which is mutated in T-ALL; however, the clinical significance of PHF6 mutations has not been fully determined in adult T-ALL. In the present study, amplification of the PHF6 exons was performed, followed by DNA sequencing to identify the genomic mutations and examine the expression of PHF6 in adult patients with T-ALL. The correlation between PHF6 mutations and clinical features was also analyzed using a χ2 test, and between PHF6 mutations and survival curve using the Kaplan-Meier methods. PHF6 mutations were detected in 27.1% of the Chinese adults with T-ALL (16/59), 10 of which were found to be novel mutations. A significantly lower expression level of PHF6 was observed in T-ALL patients with PHF6 mutations compared with those without mutations. Of the observed mutations in PHF6, 6/16 were frame-shift mutations, indicating a PHF6 dysfunction in those patients. Of note, PHF6 mutations were found to be significantly associated with older age, lower hemoglobin levels, higher frequency of CD13 positivity and higher incidence of splenomegaly or lymphadenopathy. Furthermore, PHF6 mutations were found to be significantly correlated with Notch homolog 1, translocation-associated (Drosophila) (NOTCH1) mutations. The patients with T-ALL with co-existence of the two mutations had a significantly shorter event-free survival and a poor prognosis. The present results indicated that PHF6 is inactivated in adult T-ALL, due to its low expression and mutations. The present data indicated the synergistic effect of PHF6 and NOTCH1 mutations, as well as their co-existence, on the oncogenesis of adult T-ALL, and their potential as a prognostic marker for the disease.

Genetic mutational analysis of pediatric acute lymphoblastic leukemia from a single center in China using exon sequencing

“…In our cohort, NOTCH1 mutations occurred in 23.1% of T-ALL cases, which was significantly lower than previously reported values [26,29]. However, it is interesting that 2 cases with PHF6 mutations co-occurred with NOTCH1 mutations and were significantly correlated with the NOTCH1 mutation in Chinese adult T-ALL (PHF6 mutNOTCH1mut vs PHF6 wtNOTCH1mut, 75.0% vs 44.2%; P = 0.035) [37]. This discrepancy could be caused by the limited number of T-ALL cases enrolled in this study (n = 26), or possible coverage bias impairing ability to call gene sequence [38], and the detection of sequence mutations in ALL was insufficient.…”

Novel dynamin 2 mutations in adult T-cell acute lymphoblastic leukemia

“…The primers for PCR amplification of DNM2 exons were as follows: exon 2 forward, TGC AAG ACA GAG TTG CTC CAC and reverse, TGT GTA AGT GTT CAC TGA GCCG; exon 3 forward, CCA GCC TGG GTC ATT ACT TTC and reverse, ACA CAG GCT CAC CCA TAG CAC; exon 4 forward, GTG GTT CAG GCA GAG TGT CAG and reverse, GAC TTG GAA CCA AGG ATG CTG; exon 5 forward, CTG TGA GAT CAG GGC TGT GAC and reverse, GGA GAA GCA ATG ACT TCC AGG; exon 6 forward, TAC TTG AAT CTT GCC CAT CCC and reverse, CTG AAA CAA GTG CCA GTG AGG; exon 7 forward, ATA GTG GCA CCC TGG TGT TG and reverse, GTG GAC GAG TGA TGA GTG GTG; exon 8 forward, GTA AAC CCT GGC TTG ACT TGG and reverse, CTT GAG ACC TTA TTG CCT GGG; exon 9 forward, GTG TGA GCC ACT GTA TCT GGC and reverse, GGA CTC AGA GGT GTG GGT GAC; exon 10 forward, CAA CCT TCA TTC CTT GTT GGG and reverse, CTG GGA GCC TGA TAC CAA ACC; exon 12 forward, TCT TCT GCT CTT AGC TCC CAG and reverse, TGT CAG CAT GCA CAG AAC AGT; exon 13 forward, TCT GTT GCC TAT GAG GGT GTG and AAT CCC AAC TCA GTC ACC TCC; exon 14 forward, CTA CCT GTG GCT GCT CAC TTG and reverse, TAG AGA GAG CAG ATG GCC TGG; exon 16 forward, GGG CTG GAG GTG TCT CTA TTG and reverse, GCA GTG ACT GAG TTC TGC CC; exon 17 forward, TCA TAT ACA GCA GCG ACC AGC and reverse, GTG CTC AGT GCT CAG TGA AGG; exon 18 forward, CTA GAG CCC ATT CCT CTC GG and reverse, CAT GAT TTC AGA GAC TCC TGGC; exon 19 forward, TAG GGC AGA TGG TTT CCA GAG and reverse, CTC CTT AGC TCG TGA TCC GC; exon 20 forward, CCC GCC CTG TGA GAG ATG and reverse, AGG ACC CTG CAG GAC ACAC; exon 21 forward, CAC CTC AGG TTC TGG CAGC and reverse, ACT GGG AGG AAG TGA GAC AGG; and exon 22 forward, GAG TTG ATG CCT AGG TTT GGC and reverse GAG CCT GGT CCC AGC ATAG. Exons in NOTCH1, FBXW7, PHF6, phosphatase and tensin homolog (PTEN), JAK1 and interleukin (IL)-7R were also amplified as previously reported (11)(12)(13)(14)(15) Cytogenetic and molecular analyses. Conventional cytogenetic analysis was performed at the time of diagnosis, using unstimulated short-term cultures, according to the recommendations of the International System for Human Cytogenetic Nomenclature (16).…”

New Challenges in Targeting Signaling Pathways in Acute Lymphoblastic Leukemia by NGS Approaches: An Update

“…Oncogenic activating mutations in epigenetic modifiers (i.e., IDH1/2 , EZH2 , and DNMT3A ) and inactivating mutations in chromatin modifiers (i.e., KDM6A , CREBBP , EP300 , and SMARCB1 ) have been observed in ALL [ 24 , 93 ]. Acquired somatic lesions of chromatin structure modifiers and epigenetic regulators correspond to non-synonymous single nucleotide substitutions, frameshift, and nonsense changes [ 90 , 91 , 92 , 94 ]. Some of these genes such as CREBBP , EED , EZH2 , KDM6A , PHF6 , and SUZ12 harbor deletions in ALL cases [ 11 , 27 ].…”