Wide-transcriptome analysis and cellularity of bone marrow CD34+/lin- cells of patients with chronic-phase chronic myeloid leukemia at diagnosis vs. 12 months of first-line nilotinib treatment

Trojani, Alessandra; Pungolino, Ester; Rossi, Giuseppe; D’Adda, Mariella; Lodola, Milena; Camillo, Barbara Di; Perego, Alessandra; Turrini, Mauro; Orlandi, Ester; Borin, Lorenza; Iurlo, Alessandra; Malato, Simona; Spina, Francesco; Latargia, Maria Luisa; Lanza, Francesco; Artale, Salvatore; Anghilieri, Michela; Carraro, Maria Cristina; Canal, Gabriella De; Morra, Enrica; Cairoli, Roberto

doi:10.3233/cbm-170209

Cited by 3 publications

(9 citation statements)

References 44 publications

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“…The methods were described in http://dx.doi.org/10.17504/protocols.io.yncfvaw, and showed in our previous study [18].…”

Section: Methodsmentioning

confidence: 99%

“…Standard FISH tests were performed on isolated BM CD34+/lin- cells for 87 patients at diagnosis and for 80/87 patients after 3, 6 and 12 months of nilotinib treatment. For each patient, a small sample of selected CD34+/lin- cells (containing at least 10 3 cells fixed in Carnoy’s solution) was analyzed by FISH using standard method [18]. Samples were co-hybridized to XL BCR/ABL1 plus Translocation/Dual Fusion Probe (MetaSystems, Milan, Italy) on ThermoBrite Statspin Model (Leica Biosystems, US).…”

Section: Methodsmentioning

confidence: 99%

“…Each available interphase nucleus was read even in sub-optimal specimens. FISH analyses were performed as described by Trojani et al [18], and in http://dx.doi.org/10.17504/protocols.io.yncfvaw.…”

Section: Methodsmentioning

confidence: 99%

“…Selected BM CD34+/lin- cells of 80 CP-CML patients were resuspended in 50 μl of RNAlater (Thermo Fisher Scientific, Milano, Italy) and stored at -20°C until RNA extraction was performed as previously described [18].…”

Section: Methodsmentioning

confidence: 99%

“…Total RNA was isolated from the BM CD34+/lin- cells stored in RNAlater using MagMAX 96 Total RNA Isolation Kit (Thermo Fisher Scientific) [18], according to the manufacturer’s instructions. The quality and the yield of the extracted RNA were measured using Nanodrop (Thermo Fisher Scientific) (see http://dx.doi.org/10.17504/protocols.io.yncfvaw).…”

Section: Methodsmentioning

confidence: 99%

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Nilotinib interferes with cell cycle, ABC transporters and JAK-STAT signaling pathway in CD34+/lin- cells of patients with chronic phase chronic myeloid leukemia after 12 months of treatment

et al. 2019

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Chronic myeloid leukemia (CML) is characterized by the constitutive tyrosine kinase activity of the oncoprotein BCR-ABL1 in myeloid progenitor cells that activates multiple signal transduction pathways leading to the leukemic phenotype. The tyrosine-kinase inhibitor (TKI) nilotinib inhibits the tyrosine kinase activity of BCR-ABL1 in CML patients. Despite the success of nilotinib treatment in patients with chronic-phase (CP) CML, a population of Philadelphia-positive (Ph+) quiescent stem cells escapes the drug activity and can lead to drug resistance. The molecular mechanism by which these quiescent cells remain insensitive is poorly understood. The aim of this study was to compare the gene expression profiling (GEP) of bone marrow (BM) CD34+/lin- cells from CP-CML patients at diagnosis and after 12 months of nilotinib treatment by microarray, in order to identify gene expression changes and the dysregulation of pathways due to nilotinib action. We selected BM CD34+/lin- cells from 78 CP-CML patients at diagnosis and after 12 months of first-line nilotinib therapy and microarray analysis was performed. GEP bioinformatic analyses identified 2,959 differently expressed probes and functional clustering determined some significantly enriched pathways between diagnosis and 12 months of nilotinib treatment. Among these pathways, we observed the under expression of 26 genes encoding proteins belonging to the cell cycle after 12 months of nilotinib treatment which led to the up-regulation of chromosome replication, cell proliferation, DNA replication, and DNA damage checkpoint at diagnosis. We demonstrated the under expression of the ATP-binding cassette (ABC) transporters ABCC4 , ABCC5 , and ABCD3 encoding proteins which pumped drugs out of the cells after 12 months of nilotinib. Moreover, GEP data demonstrated the deregulation of genes involved in the JAK-STAT signaling pathway. The down-regulation of JAK2 , IL7 , STAM , PIK3CA , PTPN11 , RAF1 , and SOS1 key genes after 12 months of nilotinib could demonstrate the up-regulation of cell cycle, proliferation and differentiation via MAPK and PI3K-AKT signaling pathways at diagnosis.

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“…The methods were described in http://dx.doi.org/10.17504/protocols.io.yncfvaw, and showed in our previous study [18].…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Nilotinib interferes with cell cycle, ABC transporters and JAK-STAT signaling pathway in CD34+/lin- cells of patients with chronic phase chronic myeloid leukemia after 12 months of treatment

et al. 2019

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Nilotinib induced bone marrow CD34+/lin–Ph+ cells early clearance in newly diagnosed CP‐chronic myeloid leukemia

et al. 2018

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Occurrence of L1M Elements in Chromosomal Rearrangements Associated to Chronic Myeloid Leukemia (CML): Insights from Patient-Specific Breakpoints Characterization

L’Abbate

Moretti

Pungolino

et al. 2023

Genes

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Chronic myeloid leukemia (CML) is a rare myeloproliferative disorder caused by the reciprocal translocation t(9;22)(q34;q11) in hematopoietic stem cells (HSCs). This chromosomal translocation results in the formation of an extra-short chromosome 22, called a Philadelphia chromosome (Ph), containing the BCR-ABL1 fusion gene responsible for the expression of a constitutively active tyrosine kinase that causes uncontrolled growth and replication of leukemic cells. Mechanisms behind the formation of this chromosomal rearrangement are not well known, even if, as observed in tumors, repetitive DNA may be involved as core elements in chromosomal rearrangements. We have participated in the explorative investigations of the PhilosoPhi34 study to evaluate residual Ph+ cells in patients with negative FISH analysis on CD34+/lin- cells with gDNA qPCR. Using targeted next-generation deep sequencing strategies, we analyzed the genomic region around the t(9;22) translocations of 82 CML patients and one CML cell line and assessed the relevance of interspersed repeat elements at breakpoints (BP). We found a statistically higher presence of LINE elements, in particular belonging to the subfamily L1M, in BP cluster regions of both chromosome 22 and 9 compared to the whole human genome. These data suggest that L1M elements could be potential drivers of t(9;22) translocation leading to the generation of the BCR-ABL1 chimeric gene and the expression of the active BCR-ABL1-controlled tyrosine kinase chimeric protein responsible for CML.

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Wide-transcriptome analysis and cellularity of bone marrow CD34+/lin- cells of patients with chronic-phase chronic myeloid leukemia at diagnosis vs. 12 months of first-line nilotinib treatment

Abstract: We undertook a gene expression profiling (GEP) study of selected bone marrow (BM) CD34+/lin- cells of chronic-phase CML patients at diagnosis and after 12 months of TKI nilotinib to investigate molecular signatures characterizing both conditions.

Cited by 3 publications

References 44 publications

Nilotinib interferes with cell cycle, ABC transporters and JAK-STAT signaling pathway in CD34+/lin- cells of patients with chronic phase chronic myeloid leukemia after 12 months of treatment

Nilotinib interferes with cell cycle, ABC transporters and JAK-STAT signaling pathway in CD34+/lin- cells of patients with chronic phase chronic myeloid leukemia after 12 months of treatment

Nilotinib induced bone marrow CD34+/lin–Ph+ cells early clearance in newly diagnosed CP‐chronic myeloid leukemia

Occurrence of L1M Elements in Chromosomal Rearrangements Associated to Chronic Myeloid Leukemia (CML): Insights from Patient-Specific Breakpoints Characterization

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