Progressive Down Regulation of JAK-STAT, Cell Cycle, and ABC Transporter Genes in CD34+/Lin- Cells of Chronic-Phase Chronic Myeloid Leukemia (CP-CML) Patients at Diagnosis Vs. 12 Months of Nilotinib Treatment Vs. Healthy Subjects
Authors: Trojani Alessandra , Pungolino Ester , Rossi Giuseppe , D'adda Mariella , Bossi Luca Emanuele , Baruzzo Giacomo , Di Camillo Barbara , Perego Alessandra , Turrini Mauro , Elena Chiara , Borin Lorenza Maria , Iurlo Alessandra , Malato Simona , Spina Francesco , Latargia Maria Luisa , Spedini Pierangelo , Artale Salvatore , Anghilieri Michela , Carraro Maria Cristina , Bucelli Cristina , De Canal Gabriella , Morra Enrica , Cairoli Roberto 
Published: November 2019

In the PhilosoPhi34 study (EudraCT: 2012-005062-34) on 87 CP-CML patients, we analyzed the gene expression profiling (GEP) of bone marrow (BM) CD34+/lin- cells of 79 patients with chronic-phase chronic myeloid leukemia (CP-CML) patients at diagnosis and after 12 months of nilotinib treatment (Pungolino et al. AM J Hematol. 2018). FISH analyses identified CD34+/lin- Ph+ cells in all 79 CML-CP patients at diagnosis. 78/79 patients achieved at least a complete cytogenetic response after 12 months of nilotinib whereas 1/79 patients relapsed at 12 months. No Ph+ nuclei were detected in 78/79 patients at 12 months.
We have demonstrated that genes involved in the JAK-STAT signaling pathway, the cell cycle, and the ATP-binding cassette (ABC) transporters were significantly over expressed in patients at diagnosis compared to 12 months of nilotinib treatment (Trojani et al, PLoS One. 2019).
In this preliminary study, we isolated BM CD34+/lin- cells from 9 healthy donors (CTRLs). We investigated the gene expression profiling of 79 CP-CML patients at diagnosis vs. the same patients after 12 months of nilotinib treatment (12 months) vs. 9 CTRLs using Affymetrix HTA 2.0. Data was preprocessed and normalized using RMA and ComBat. Selection of differentially expressed genes (DEg) was performed at diagnosis vs. 12 months of nilotinib vs. CTRLs, using Statistical Analysis for Microarrays (SAM) on 3 groups and a Benjamini Hochberg false discovey rate threshold of 5%, followed, for significance comparisons, by a pair-wise SAM test.
We focused on 34 genes of the cell cycle and mitosis, 6 genes belonging to the JAK-STAT signaling pathway, and the ABC transporter gene ABCD3 which were significantly under expressed at diagnosis vs. 12 months of nilotinib vs. CRTLs (Tab.1).
In the cell cycle, we found that ORC2, ORC4, ORC5, MCM6, and HDAC2 (G1 phase) were progressively significantly down regulated at diagnosis vs. 12 months vs. CTRLs. We noticed HDAC2 which showed the high fold changes of 2.89 and 4.29 in the comparison between 12 months vs. CTRLs and between diagnosis vs. CTRLs, respectively. This gene plays a crucial role in CML, as HDAC inhibitors treatment represent an effective strategy to target leukemic stem cells in CP-CML patients receiving tyrosine kinase inhibitors.
CCNA2, CDK7, CDC6, DBF4 (S phase), WEE1, PRKDC, ATM, MDM2, CCNB1 (G2 phase), and TTK, MAD2L1, BUB1, BUB3, ANAPC4, CDC27, SMC3, YWHAE, and YWHAZ (M phase) were progressively down regulated at diagnosis vs. 12 months vs. CTRLs. Among them, SMC3, YWHAE and YWHAZ showed the following high fold changes in the comparison between 12 months vs. CTRLs and between diagnosis vs. CTRLs: 2.31 and 3.15, 2.59 and 3.94, 2.75 and 4.15, respectively. Notably, the proto-oncogene MDM2 which promotes the development of tumors by targeting p53, was progressively up regulated in CTRLs vs. 12 months vs. diagnosis.
In the mitosis, we detected that 10 genes playing a crucial role in mitotic chromosome organization, were progressively under expressed at diagnosis vs. 12 months vs. CTRLs (Tab.1). Notably, CLAPS2, ZW10 and ANLN (hematopoietic cell differentiation) regulate the exit from mitosis. NDC80, SMC4, ZNF207, and NEK2 take part in the mitotic sister chromatid segregation whereas CENPE and SMC2 are mitotic cell cycle check points.
In the JAK-STAT signaling pathway, SOS1, PIK3CA, IL7, JAK2, STAM, and PTPN11 were progressively up regulated in CTRLs vs. 12 months vs. diagnosis (Tab.1).
ABCD3, encoding a protein which pumped drugs out of the cells, was progressively under expressed at diagnosis vs. 12 months vs. CRTLs as shown in Tab.1.
In conclusion, we found progressive gene expression changes in BM CD34+/lin- cells of 79 CP-CML patients at diagnosis vs. 12 months of nilotinib vs. the normal cell counterparts of 9 CTRLs in the cell cycle, JAK-STAT, and the ABC transporter ABCD3. FISH analyses demonstrated that the BM CD34+/lin- cells of 78/79 patients after 12 months of nilotinib were Ph-negative. Despite, our GEP results suggested that BM CD34+/lin- cells after 12 months of nilotinib treatment and the normal cell counterparts differed mostly in the expression of genes regulating the cell cycle and the JAK-STAT signaling pathway.

Disclosures
Rossi: Daiichi-Sankyo: Consultancy; Roche: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Jazz: Membership on an entity's Board of Directors or advisory committees; Astellas: Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria; Mundipharma: Honoraria; BMS: Honoraria; Sandoz: Honoraria. Elena:Novartis: Consultancy; Pfizer: Consultancy. Iurlo:Pfizer: Other: Speaker Honoraria; Incyte: Other: Speaker Honoraria; Novartis: Other: Speaker Honoraria.