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Genetic alterations in indolent GI T-cell LPD
Next-generation sequencing analysis
Targeted sequencing of 20 ITLPD biopsies from ten patients and seven matched normal samples (cases 1, 2, 4, 7-10) revealed 36 genetic variants, including 29 nonsyn- onymous single nucleotide variants, one small indel, and six structural variants. The average on-target coverage was 1059x (range 809x - 1639x). Twenty-three of the 36 alter- ations were predicted to be pathogenic based on the pub- lished literature or prediction algorithms; the remaining 13 mutations were classified as variants of uncertain signifi- cance (Online Supplementary Table S2).
The genetic alterations and their expected functional consequences are summarized in Table 3. Pathogenic or
potentially pathogenic changes were identified in eight of ten (80%) ITLPD. Three of four (75%) CD4+ cases and the CD4+/CD8+ and CD4-/CD8- cases harbored alterations of JAK-STAT signaling pathway genes. STAT3 SH2 domain hotspot mutations (D661Y and S614R) were noted in three cases and one case each had a SOCS1 deletion and a STAT3-JAK2 rearrangement. Of note, conventional cyto- genetic analysis had previously revealed a balanced translocation t(9;17)(p24;q21) in the latter case, the break- points corresponding to the JAK2 and STAT3 loci, and JAK2 rearrangement was confirmed by FISH analysis. Concomitant mutations in epigenetic modifier genes (TET2, DNMT3A, and KMT2D) were observed in four
Table 3. Genetic alterations in gastrointestinal indolent T-cell lymphoproliferative disorders.
Phenotype
CD4+
CD4+
CD4+
CD4+
CD4+/CD8+
CD4-/CD8-
CD8+
CD8+
CD8+
CD8+
7.9
0 2.2 6.4
0
0.5 7.4
11.5
11.7†
0
0
0
3.9
6.1
0 4.3 6.4
14
10.8
Genetic alterations
STAT3 (c.1981G>T, p. D661Y) TET2 (c.2457T>G, p. Y819*)
STAT3 (c.1981G>T, p. D661Y) TET2 (c.2457T>G, p. Y819*)
STAT3-JAK2 rearrangement TNFAIP3 (c.857T>G, p.L286*) STAT3-JAK2 rearrangement TNFAIP3 (c.857T>G, p.L286*) STAT3-JAK2 rearrangement TNFAIP3 (c.857T>G, p.L286*)
SOCS1 deletion
KMT2D (c.13105_13108del, p.L4369fs) KMT2D (c.13105_13108del, p.L4369fs) DIS3 (c.1115T>C, p.L372P) KMT2D (c.13105_13108del, p.L4369fs) DIS3 (c.1115T>C, p.L372P) MAPK1 (c.965A>T, p.E322V) TP53 (c.743G>A, p.R248Q) POLE (c.4090C>T, p.R1364C) KMT2D (c.13105_13108del, p.L4369fs) DIS3 (c.1115T>C, p.L372P) MAPK1 (c.965A>T, p.E322V) TP53 (c.743G>A, p.R248Q) POLE (c.4090C>T, p.R1364C) TET2 (c.2725C>T, p.Q909*) SMAD4 (c.404G>A, p.R135Q) SF3B1 (c.2584G>A, p.E862K)
STAT3 (c.1842C>G, p.S614R) DNMT3A (c.2116G>T, p.G706W) CDKN2A (c.322G>A, p.D108N)
STAT3 (c.1840A>C, p.S614R) KMT2D (c.9415C>G, p.P3139A)
IL2-RHOH rearrangement‡
IL2-RHOH rearrangement‡
IL2-RHOH rearrangement‡
IL2 3’ UTR deletion‡, IL2-TNIP3 rearrangement‡ MCM5 (c.2080A>T, p.I694F)
IL2 3’ UTR deletion‡, IL2-TNIP3 rearrangement‡ MCM5 (c.2080A>T, p.I694F)
IL2 3’ UTR deletion‡, IL2-TNIP3 rearrangement‡ MCM5 (c.2080A>T, p.I694F)
None identified
None identified
Case
1
2
3
4
Time point
(years following diagnosis)
2.5
Predicted functional consequence
Activation of JAK-STAT pathway Altered DNA methylation Activation of JAK-STAT pathway Altered DNA methylation
Activation of JAK-STAT pathway Activation of NF-kB pathway Activation of JAK-STAT pathway Activation of NF-kB pathway Activation of JAK-STAT pathway Activation of NF-kB pathway
Activation of JAK-STAT pathway
Altered histone modification
Altered histone modification Altered RNA processing and decay Altered histone modification Altered RNA processing and decay Activation of RAS-RAF-MAPK pathway DNA repair/cell cycle dysregulation Altered DNA repair and replication Altered histone modification Altered RNA processing and decay Activation of RAS-RAF-MAPK pathway DNA repair/ cell cycle dysregulation Altered DNA repair and replication Altered DNA methylation Activation of TGF-β pathway Altered RNA splicing
Activation of JAK-STAT pathway Altered DNA methylation Cell cycle checkpoint (G1-to-S) dysregulation
Activation of JAK-STAT pathway
Altered histone modification
Unknown Unknown Unknown
Unknown
Cell cycle dysregulation Unknown
Cell cycle dysregulation Unknown
Cell cycle dysregulation
5
6
7
8
9 NA
10 NA
NA: not applicable. †Large cell transformation. ‡Confirmed by breakpoint-specific polymerase chain reaction and Sanger sequencing.
haematologica | 2020; 105(7)
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