Microarray expression studies on bone marrow of patients with Shwachman-Diamond syndrome in relation to deletion of the long arm of chromosome 20, other chromosome anomalies or normal karyotype

Abdul Waheed Khan, Antonella Minelli, Annalisa Frattini, Giuseppe Montalbano, Alessia Bogni, Marco Fabbri, Giovanni Porta, Francesco Acquati, Rita Maria Pinto, Elena Bergami, Rossella Mura, Anna Pegoraro, Simone Cesaro, Marco Cipolli, Marco Zecca, Cesare Danesino, Franco Locatelli, Emanuela Maserati, Francesco Pasquali, Roberto Valli

Research output: Contribution to journalArticle

Abstract

Background: Clonal chromosome changes are often found in the bone marrow (BM) of patients with Shwachman-Diamond syndrome (SDS). The most frequent ones include an isochromosome of the long arm of chromosome 7, i (7)(q10), and an interstitial deletion of the long arm of chromosome 20, del (20)(q). These two imbalances are mechanisms of somatic genetic rescue. The literature offers few expression studies on SDS. Results: We report the expression analysis of bone marrow (BM) cells of patients with SDS in relation to normal karyotype or to the presence of clonal chromosome anomalies: del (20)(q) (five cases), i (7)(q10) (one case), and other anomalies (two cases). The study was performed using the microarray technique considering the whole transcriptome (WT) and three gene subsets selected as relevant in BM functions. The expression patterns of nine healthy controls and SDS patients with or without chromosome anomalies in the bone marrow showed clear differences. Conclusions: There is a significant difference between gene expression in the BM of SDS patients and healthy subjects, both at the WT level and in the selected gene sets. The deletion del (20)(q), with the EIF6 gene consistently lost, even in patients with the smallest losses of material, changes the transcription pattern: a low proportion of abnormal cells led to a pattern similar to SDS patients without acquired anomalies, whereas a high proportion yields a pattern similar to healthy subjects. Hence, the benign prognostic value of del (20)(q). The case of i (7)(q10) showed a transcription pattern similar to healthy subjects, paralleling the positive prognostic role of this anomaly as well.

Original languageEnglish
Article number1
JournalMolecular Cytogenetics
Volume13
Issue number1
DOIs
Publication statusPublished - Jan 2 2020

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Chromosomes, Human, Pair 20
Diamond
Microarrays
Chromosomes
Karyotype
Bone
Bone Marrow
Healthy Volunteers
Genes
Transcription
Transcriptome
Isochromosomes
Chromosomes, Human, Pair 7
Set theory
Gene expression
Bone Marrow Cells
Shwachman syndrome
Cells
Gene Expression

Keywords

  • Clonal chromosome anomalies in bone marrow
  • EIF6 gene
  • Expression analysis
  • Risk of MDS/AML
  • Shwachman-diamond syndrome
  • Somatic genetic rescue

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Biochemistry, medical

Cite this

Microarray expression studies on bone marrow of patients with Shwachman-Diamond syndrome in relation to deletion of the long arm of chromosome 20, other chromosome anomalies or normal karyotype. / Khan, Abdul Waheed; Minelli, Antonella; Frattini, Annalisa; Montalbano, Giuseppe; Bogni, Alessia; Fabbri, Marco; Porta, Giovanni; Acquati, Francesco; Pinto, Rita Maria; Bergami, Elena; Mura, Rossella; Pegoraro, Anna; Cesaro, Simone; Cipolli, Marco; Zecca, Marco; Danesino, Cesare; Locatelli, Franco; Maserati, Emanuela; Pasquali, Francesco; Valli, Roberto.

In: Molecular Cytogenetics, Vol. 13, No. 1, 1, 02.01.2020.

Research output: Contribution to journalArticle

Khan, Abdul Waheed ; Minelli, Antonella ; Frattini, Annalisa ; Montalbano, Giuseppe ; Bogni, Alessia ; Fabbri, Marco ; Porta, Giovanni ; Acquati, Francesco ; Pinto, Rita Maria ; Bergami, Elena ; Mura, Rossella ; Pegoraro, Anna ; Cesaro, Simone ; Cipolli, Marco ; Zecca, Marco ; Danesino, Cesare ; Locatelli, Franco ; Maserati, Emanuela ; Pasquali, Francesco ; Valli, Roberto. / Microarray expression studies on bone marrow of patients with Shwachman-Diamond syndrome in relation to deletion of the long arm of chromosome 20, other chromosome anomalies or normal karyotype. In: Molecular Cytogenetics. 2020 ; Vol. 13, No. 1.
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abstract = "Background: Clonal chromosome changes are often found in the bone marrow (BM) of patients with Shwachman-Diamond syndrome (SDS). The most frequent ones include an isochromosome of the long arm of chromosome 7, i (7)(q10), and an interstitial deletion of the long arm of chromosome 20, del (20)(q). These two imbalances are mechanisms of somatic genetic rescue. The literature offers few expression studies on SDS. Results: We report the expression analysis of bone marrow (BM) cells of patients with SDS in relation to normal karyotype or to the presence of clonal chromosome anomalies: del (20)(q) (five cases), i (7)(q10) (one case), and other anomalies (two cases). The study was performed using the microarray technique considering the whole transcriptome (WT) and three gene subsets selected as relevant in BM functions. The expression patterns of nine healthy controls and SDS patients with or without chromosome anomalies in the bone marrow showed clear differences. Conclusions: There is a significant difference between gene expression in the BM of SDS patients and healthy subjects, both at the WT level and in the selected gene sets. The deletion del (20)(q), with the EIF6 gene consistently lost, even in patients with the smallest losses of material, changes the transcription pattern: a low proportion of abnormal cells led to a pattern similar to SDS patients without acquired anomalies, whereas a high proportion yields a pattern similar to healthy subjects. Hence, the benign prognostic value of del (20)(q). The case of i (7)(q10) showed a transcription pattern similar to healthy subjects, paralleling the positive prognostic role of this anomaly as well.",
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T1 - Microarray expression studies on bone marrow of patients with Shwachman-Diamond syndrome in relation to deletion of the long arm of chromosome 20, other chromosome anomalies or normal karyotype

AU - Khan, Abdul Waheed

AU - Minelli, Antonella

AU - Frattini, Annalisa

AU - Montalbano, Giuseppe

AU - Bogni, Alessia

AU - Fabbri, Marco

AU - Porta, Giovanni

AU - Acquati, Francesco

AU - Pinto, Rita Maria

AU - Bergami, Elena

AU - Mura, Rossella

AU - Pegoraro, Anna

AU - Cesaro, Simone

AU - Cipolli, Marco

AU - Zecca, Marco

AU - Danesino, Cesare

AU - Locatelli, Franco

AU - Maserati, Emanuela

AU - Pasquali, Francesco

AU - Valli, Roberto

PY - 2020/1/2

Y1 - 2020/1/2

N2 - Background: Clonal chromosome changes are often found in the bone marrow (BM) of patients with Shwachman-Diamond syndrome (SDS). The most frequent ones include an isochromosome of the long arm of chromosome 7, i (7)(q10), and an interstitial deletion of the long arm of chromosome 20, del (20)(q). These two imbalances are mechanisms of somatic genetic rescue. The literature offers few expression studies on SDS. Results: We report the expression analysis of bone marrow (BM) cells of patients with SDS in relation to normal karyotype or to the presence of clonal chromosome anomalies: del (20)(q) (five cases), i (7)(q10) (one case), and other anomalies (two cases). The study was performed using the microarray technique considering the whole transcriptome (WT) and three gene subsets selected as relevant in BM functions. The expression patterns of nine healthy controls and SDS patients with or without chromosome anomalies in the bone marrow showed clear differences. Conclusions: There is a significant difference between gene expression in the BM of SDS patients and healthy subjects, both at the WT level and in the selected gene sets. The deletion del (20)(q), with the EIF6 gene consistently lost, even in patients with the smallest losses of material, changes the transcription pattern: a low proportion of abnormal cells led to a pattern similar to SDS patients without acquired anomalies, whereas a high proportion yields a pattern similar to healthy subjects. Hence, the benign prognostic value of del (20)(q). The case of i (7)(q10) showed a transcription pattern similar to healthy subjects, paralleling the positive prognostic role of this anomaly as well.

AB - Background: Clonal chromosome changes are often found in the bone marrow (BM) of patients with Shwachman-Diamond syndrome (SDS). The most frequent ones include an isochromosome of the long arm of chromosome 7, i (7)(q10), and an interstitial deletion of the long arm of chromosome 20, del (20)(q). These two imbalances are mechanisms of somatic genetic rescue. The literature offers few expression studies on SDS. Results: We report the expression analysis of bone marrow (BM) cells of patients with SDS in relation to normal karyotype or to the presence of clonal chromosome anomalies: del (20)(q) (five cases), i (7)(q10) (one case), and other anomalies (two cases). The study was performed using the microarray technique considering the whole transcriptome (WT) and three gene subsets selected as relevant in BM functions. The expression patterns of nine healthy controls and SDS patients with or without chromosome anomalies in the bone marrow showed clear differences. Conclusions: There is a significant difference between gene expression in the BM of SDS patients and healthy subjects, both at the WT level and in the selected gene sets. The deletion del (20)(q), with the EIF6 gene consistently lost, even in patients with the smallest losses of material, changes the transcription pattern: a low proportion of abnormal cells led to a pattern similar to SDS patients without acquired anomalies, whereas a high proportion yields a pattern similar to healthy subjects. Hence, the benign prognostic value of del (20)(q). The case of i (7)(q10) showed a transcription pattern similar to healthy subjects, paralleling the positive prognostic role of this anomaly as well.

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KW - EIF6 gene

KW - Expression analysis

KW - Risk of MDS/AML

KW - Shwachman-diamond syndrome

KW - Somatic genetic rescue

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