scholarly journals 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

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Abdul Waheed Khan ◽  
Antonella Minelli ◽  
Annalisa Frattini ◽  
Giuseppe Montalbano ◽  
Alessia Bogni ◽  
...  

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.

2018 ◽  
Vol 184 (6) ◽  
pp. 974-981 ◽  
Author(s):  
Roberto Valli ◽  
Antonella Minelli ◽  
Marta Galbiati ◽  
Giovanna D'Amico ◽  
Annalisa Frattini ◽  
...  

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4501-4501
Author(s):  
Antonio Roberto L. Araújo ◽  
Ana Silvia G. Lima ◽  
Rodrigo A. Panepucci ◽  
Eduardo M. Rego

Abstract The p73 protein is a p53 homolog and acts on cell cycle and apoptosis regulation. Resistance to apoptosis is a common feature of Acute Myeloid Leukemia (AML), but mutations on the genes p53 and p73 are rare. It is translated in two distinct isoforms: TAp73 and ΔNp73. The later does not possess the N-terminal transactivation domain and exerts a dominant negative action over TAp73 and p53 functions. Theoretically an aberrant high expression of ΔNp73 may lead to a block of p53 and TAp73, thus conferring a proliferative advantage to the leukemic cells. In order to evaluate this issue, we proposed to: Compare the gene expression levels of TAp73 and ΔNp73 isoforms in the bone marrow from de novo AML patients and normal individuals; Correlate these expression patterns with the presence of the rearrangements PML-RARα, AML1-ETO and CBFβ-MHY11, (previously determined by RT-PCR according the BIOMED-1 protocol). From 137 AML patients whose samples were evaluated by Real Time PCR, 78 harbored the genetic rearrangements (referred to as RP group): PML-RARα (n = 30), AML1-ETO (n = 16) or CBFβ-MHY11 (n = 32), whereas in the 59 remaining samples these rearrangements were not detected (RN group). Additionally, CD34+ cell samples of 22 normal bone marrow donors were also evaluated. Sample input was normalized by GAPDH expression and the relative expression was calculated using the cell line k562 as reference sample. The mean expression of TAp73 and ΔNp73 was significantly lower on normal CD34+ cell compared to leukemic samples [(TAp73: mean (m) = 0.0162 ± standard deviation = 0.004 vs m = 0.623 ± 0.0845, p = 0,0047); (ΔNp73: m = 0.277 ± 0.09 vs m = 8.09 ± 1.34, p = 0,0215)]. A higher expression of TAp73 and ΔNp73 was observed on RN compared to RP samples [(TAp73: m = 0.992 ± 0.171 vs m = 0.344 ± 0.055, p < 0,0001); (ΔNp73: m = 12.44 ± 2.434 vs m = 4.80 ± 1.382, p = 0,0046)]. There was no difference in the expression of TAp73 between PML-RARα positive samples (m = 0.391 ± 0.095) and the remaining leukemic samples (m = 0.688 ± 0.104, p = 0,1476). However, the expression levels of ΔNp73 were significantly lower in the PML-RARα positive samples (m = 2.656 ± 0.370 vs m = 9.62 ± 1.69, p = 0,0317). No significant difference was observed in ΔNp73 and TAp73 expression between PML-RARα positive samples and the remaining samples with gene rearrengements (TAp73: m = 0.391 ± 0.095 vs m = 0.3144 ± 0.0671, p = 0,4990; ΔNp73: m = 2.656 ± 0.37 vs m = 6.153 ± 2.221, p = 0,2205). When compared to AML1-ETO and CBFβ-MHY11, the RN samples had a higher expression level of TAp73 (m = 0.3144 ± 0.0672 vs m = 0.992 ± 0.1717, p = 0.001), while there was no significant difference on the expression levels of ΔNp73 (m = 6.15 ± 2.22 vs m = 12.44 ± 2.43, p = 0.0642). These findings suggest that both p73 isoforms pathways are involved in the leukemogenic process. Moreover, the lower expression of ΔNp73 in the group with gene rearrangements may contribute to its better prognosis. The distinct pattern of ΔNp73 isoforms expression in AML with PML-RARα rearrangements suggests that it may be associated to a distinct response to apoptotic stimuli and to treatment outcome.


2012 ◽  
Vol 157 (4) ◽  
pp. 503-505 ◽  
Author(s):  
Barbara Pressato ◽  
Roberto Valli ◽  
Cristina Marletta ◽  
Lydia Mare ◽  
Giuseppe Montalbano ◽  
...  

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4189-4189
Author(s):  
Davendra Sohal ◽  
Andrew Yeatts ◽  
Joanna Opalinska ◽  
Li Zhou ◽  
Perry Pahanish ◽  
...  

Abstract While microarray analysis of global gene expression yields enormous amounts of data, there are concerns about standardization and validity of findings. Consequently, we wanted to determine the variability in gene expression studies of human bone marrow in the literature and study the factors that account for these differences. We also wanted to determine if certain genes were consistently and differentially enriched in human bone marrow stem cells. A total of 64 individual datasets were collected from gene expression omnimbus (GEO) database for our analysis (2001–2006). Most of the datasets had been used as controls in studies of hematological malignancies. 13 datasets were hybridized to the Affymetrix U95 chip, 38 analyzed by the Affymetrix human U133A chip and 13 by the U133 plus 2.0 platform. RNA for these studies was derived from purified normal CD34+ cells in 48 cases and from unsorted normal bone marrow mononuclear cells in 16 cases. To merge data from different platforms, we converted individual probe Sequence_ids to RefSeq gene IDs and analyzed them by SAS (SAS Institute, Cary, NC) and Arrayassist software package (Stratagene©). A total of 23686 unique gene IDs were obtained for analysis after the data were normalized, and a KNN algorithm was used to fill the gaps in the data. Our results reveal that there is marked variability in gene expression patterns in this cohort. The data sets clustered together primarily on the basis of the laboratory that performed the assays. (Hierarchical clustering based on average Euclidean distances). Clustering was further defined by the type of chip/platform used for the analysis. Interestingly, the similarity between CD34+ sorted and ununsorted whole BM samples was greater than interplatform similarity between the same phenotypes of cells examined. Notwithstanding the variability in gene expression, there were a novel set of genes that were differentially enriched in all 64 samples. These genes included transcription factors (Kruppel like factor 6), translational proteins (eukaryotic translation initiation factor 4A, isoform 1, ribosomal proteins) and other proteins not previously implicated in hematopoeisis (guanine nucleotide binding protein (GNAS), Calnexin, HLA associated proteins, dUTP pryophosphatase etc.) Mouse homologues of several of these proteins were found to be overexpressed in a previous well respected study of mouse hematopoeitic stem cells (Ramalho-Santos et al, Science2002;298(5593)). To further validate these findings, we performed gene expression array analysis on primary bone marrow cells using a completely different platform (Nimblegen 37K arrays) and demonstrated enrichment of majority of these genes. Thus, we provide a blueprint for conducting similar meta-analysis across various microarray platforms and our findings disclose tremendous platform and lab dependant differences in microarray gene expression patterns. In spite of this variability, data mining of discrete datasets can be a useful tool for gene discovery. Finally, we are in the process of constructing a publicly searchable database of normal human bone marrow gene expression which may serve as a source of controls for gene expression studies of hematopoeitic malignancies by various investigators.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1700-1700
Author(s):  
Masayuki Shiseki ◽  
Mayuko Ishii ◽  
Mari Ohwashi ◽  
Kentaro Yoshinaga ◽  
Naoki Mori ◽  
...  

Abstract The PLCG1 gene encodes phospholipase C g isoform, which is involved in diverse physiological and pathological cellular processes through catalyzing the hydrolysis of phosphatidylinositol 4,5-bisphosphate to produce the second messenger molecules inositol 1,4,5-trisphosphate and diacylglycerole. Until now, roles of phospholipase C g 1 in hematopoiesis have been shown in animal models. Plcg1 deficient mouse lacks erythropoiesis and die in early embryonic stage. In zebrafish model, it was demonstrated that phospholipase C g 1 is required in granulocyte maturation. Physiological and/or pathological role of phospholipase C g 1 in human hematopoiesis has not been elucidated. In human, the PLCG1 gene is located on long arm of chromosome 20. Deletion of long arm of chromosome 20 (del(20q)) is commonly observed in myelodysplastic syndromes (MDS). Previously, we determined the common deleted region (CDR) of del(20q) in MDS, and the PLCG1 gene is located within the CDR. Reduced expression of genes located in the CDR due to haploinsufficiency may play role in molecular pathogenesis of MDS. Therefore, we analyzed PLCG1 expression in bone marrow mononuclear cells in MDS patients with or without del(20q), and investigated its clinical significance in the present study. Mononuclear cells separated from bone marrow samples taken at the time of diagnosis with written informed consent from patients were used. To analyze PLCG1 expression, quantitative RT-PCR was performed. Total RNA was extracted from mononuclear cells and subjected to cDNA synthesis. Real-time RT-PCR was carried out using cDNA as template by the TaqMan probe method (Applied Biosystems) with co-amplification of the endogenous control gene, human GAPDH (Applied Biosystems) were performed. The human PLCG1 primer-probe set was from Applied Biosystems. A total of 109 MDS patients, 65 males and 44 females with median age of 69 years (range: 22-91 years), with (n=20) or without (n=89) del(20q), were included in the present study. They were classified as RCUD (n=11), RCMD (n=55), RARS (n=11), RAEB-1 (n=16), and RAEB-2 (n=16) according to WHO classification. They were categorized in four IPSS risk groups, low risk (n=21), intermediate-1 risk (n=52), intermediate-2 risk (n=20), and high risk (n=6). Relative PLCG1 expression level was significantly reduced in MDS patients with del(20q) compared to control subjects (n=20) (P=0.011). Median values of relative PLCG1 expression level in MDS patients with del(20q) and control subjects were 0.94 and 1.96. In addition, relative expression level of PLCG1 in whole MDS cohort significantly lower than that in control subjects (P=0.046). Expression patterns of PLCG1 among, were not different. Median values of relative PLCG1 expression level in five WHO-subtypes, RCUD, RCMD, RARS, RAEB-1, and RAEB-2 were 1.50, 1.55, 1.29, 1.13, and 1.12, respectively, but no statistically difference was observed. WHO-subtypes with high blast counts (RAEB-1 and RAEB-2) showed trend in association with reduced PLCG1 expression compared with those with low blast counts (RCUD, RCMD, and RARS) (median value: 1.01 vs. 1.54, P =0.11). To investigate prognostic implication of PLCG1 expression in MDS, we analyzed impact of PLCG1 expression on overall survival (OS). Based on PLCG1 expression level, 109 patients were divided into four groups, high (Q1), intermediate (Q2, Q3), and low (Q4) quartiles. Kaplan-Meier analysis demonstrated that the lowest quartile (Q4) showed significantly worse survival compared with remaining quartiles (Q1-Q3) (P =0.0015). The estimated 5-year OS rates in Q1-3 group and Q4 group were 63.2% and 29.7%, respectively. Percentage of patients with WHO-subtypes with high blast count (RAEB-1 and RAEB-2) was significantly higher in Q4 than other quartiles (46.9% vs 22.1%, P =0.019 by Fisher's exact test). The present study demonstrated that reduced PLCG1 expression is associated with inferior clinical outcome, indicating that PLCG1 expression could be a useful prognostic marker in MDS. Association between reduced PLCG1 expression and WHO-subtypes with high blasts counts, suggesting that PLCG1 dysfunction play a role in disease progression. Disclosures No relevant conflicts of interest to declare.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3008-3008 ◽  
Author(s):  
Yeo-Kyeoung Kim ◽  
Je-Jung Lee ◽  
Yu-Ra Lee ◽  
Il-Kwon Lee ◽  
Hee-Nam Kim ◽  
...  

Abstract An internal tandem duplication of the FLT3 gene (FLT3/ITD) has been detected in approximately 20–30% of patients with acute myeloid leukemia (AML). These are frequently associated with poor outcome in AML patients, but it is still a matter of debate whether the FLT3/ITD mutations play a role in the prognosis of AML patients independently or not. We investigated the presence of FLT3/ITD mutation in 165 patients with de novo AML, except acute promyelocytic leukemia (APL), to evaluate its clinical and prognostic significance. The FLT3/ITD mutations were studied on bone marrow samples at diagnosis using PCR assay. Of the patients, 58 patients (35.2%) demonstrated the aberrant FLT3/ITD mutations. The patients with FLT3/ITD had significantly higher WBC counts at presentation compared with patients without FLT3/ITD (52.9 ± 66.9 ×109/L vs. 32.4 ± 41.8 ×109/L, p < 0.05). However, there was no statistically significant difference in age, gender, hemoglobin level, platelet count, percentage of peripheral or bone marrow blasts, or the presence of molecular abnormalities between the patients with FLT3/ITD and the patients without FLT3/ITD. To analyze the response to or outcome of therapy, we evaluated 118 patients who received intensive induction chemotherapy. In univariate analysis, there was no significant difference in complete response rate (p = 0.21), in median duration of overall survival (13.9±3.8 ms. vs. 16.5±0 ms., p = 0.07), or in median duration of leukemic-free survival (LFS) (9.8±3.5 ms. vs. 34.6±17.9 ms., p = 0.09) between the patients with FLT3/ITD and the patients without FLT3/ITD. However, the presence of FLT3/ITD was associated with lower LFS in the patients with a cytogenetically intermediate-risk group (p < 0.05). Furthermore, in multivariate analysis, FLT3/ITD mutations were an independent prognostic factor in LFS in AML patients with normal karyotype (p < 0.05). In conclusion, this study demonstrates that the presence of FLT3/ITD mutations is a significantly poor prognostic factor for leukemic free survival in non-APL patients with a cytogenetically intermediate-risk group, especially normal karyotype.


2019 ◽  
Vol 30 (5) ◽  
pp. 585-592 ◽  
Author(s):  
Nicola Montemurro ◽  
Paolo Perrini ◽  
Vittoriano Mangini ◽  
Massimo Galli ◽  
Andrea Papini

OBJECTIVEOdontoid process fractures are very common in both young and geriatric patients. The axial trabecular architecture of the dens appears to be crucial for physiological and biomechanical function of the C1–2 joint. The aim of this study is to demonstrate the presence of a Y-shaped trabecular structure of the dens on axial CT and to describe its anatomical and biomechanical implications.METHODSFifty-four C2 odontoid processes in healthy subjects were prospectively examined for the presence of a Y-shaped trabecular structure at the odontocentral synchondrosis level with a dental cone beam CT scan. Length, width, and axial area of the odontoid process were measured in all subjects. In addition, measurements of the one-third right anterior area of the Y-shaped structure were taken.RESULTSThe Y-shaped trabecular structure was found in 79.6% of cases. Length and width of the odontoid process were 13.5 ± 0.6 mm and 11.2 ± 0.9 mm, respectively. The mean area of the odontoid process at the odontocentral synchondrosis was 93.5 ± 4.3 mm2, whereas the mean one-third right anterior area of the odontoid process at the same level was 29.3 ± 2.5 mm2. The mean area of the odontoid process and its length and width were similar in men and women (p > 0.05). No significant difference was found in the mean area of the odontoid process in people older than 65 years (94 ± 4.2 mm2) compared to people younger than 65 years (93.3 ± 4.4 mm2; p > 0.05).CONCLUSIONSThe authors identified a new anatomical entity, named the Y-shaped trabecular structure of the odontoid process, on axial CT scans. This structure appears to be the result of bone transformation induced by the elevated dynamic loading at the C1–2 level. The presence of the Y-shaped structure provides new insights into biomechanical responses of C2 under physiological loading and traumatic conditions.


Author(s):  
Qinglin Meng ◽  
Mengqi Liu ◽  
Weiwei Deng ◽  
Ke Chen ◽  
Botao Wang ◽  
...  

Background: Calcium-suppressed (CaSupp) technique involving spectral-based images has been used to observe bone marrow edema by removing calcium components from the image. Objective: This study aimed to evaluate the knee articular cartilage using the CaSupp technique in dual-layer detector computed tomography (DLCT). Methods: Twenty-eight healthy participants and two patients with osteoarthritis were enrolled, who underwent DLCT and magnetic resonance imaging (MRI) examination. CaSupp images were reconstructed from spectral-based images using a calcium suppression algorithm and were overlaid conventional CT images for visual evaluation. The morphology of the knee cartilage was evaluated, and the thickness of the articular cartilage was measured on sagittal proton density– weighted and CaSupp images in the patellofemoral compartment. Results: No abnormal signal or density, cartilage defect, and subjacent bone ulceration were observed in the lateral and medial femorotibial compartments and the patellofemoral compartment on MRI images and CaSupp images for the 48 normal knee joints. CaSupp images could clearly identify cartilage thinning, defect, subjacent bone marrow edema, and edema of the infrapatellar fat pad in the same way as MRI images in the three knee joints with osteoarthritis. A significant difference was found in the mean thickness of the patellar cartilage between MRI images and CaSupp images, while the femoral cartilage presented no significant difference in thickness between MRI images and CaSupp images over all 48 knee joints. Conclusion: The present study demonstrated that CaSupp images could effectively be used to perform the visual and quantitative assessment of knee cartilage.


2021 ◽  
pp. 039139882110255
Author(s):  
Sara Anajafi ◽  
Azam Ranjbar ◽  
Monireh Torabi-Rahvar ◽  
Naser Ahmadbeigi

Background: Sufficient blood vessel formation in bioengineered tissues is essential in order to keep the viability of the organs. Impaired development of blood vasculatures results in failure of the implanted tissue. The cellular source which is seeded in the scaffold is one of the crucial factors involved in tissue engineering methods. Materials and methods: Considering the notable competence of Bone Marrow derived Mesenchymal Stem Cell aggregates for tissue engineering purposes, in this study BM-aggregates and expanded BM-MSCs were applied without any inductive agent or co-cultured cells, in order to investigate their own angiogenesis potency in vivo. BM-aggregates and BM-MSC were seeded in Poly-L Lactic acid (PLLA) scaffold and implanted in the peritoneal cavity of mice. Result: Immunohistochemistry results indicated that there was a significant difference ( p < 0.050) in CD31+ cells between PLLA scaffolds contained cultured BM-MSC; PLLA scaffolds contained BM-aggregates and empty PLLA. According to morphological evidence, obvious connections with recipient vasculature and acceptable integration with surroundings were established in MSC and aggregate-seeded scaffolds. Conclusion: Our findings revealed cultured BM-MSC and BM-aggregates, capacity in order to develop numerous connections between PLLA scaffold and recipient’s vasculature which is crucial to the survival of tissues, and considerable tendency to develop constructs containing CD31+ endothelial cells which can contribute in vessel’s tube formation.


2021 ◽  
pp. 1-5
Author(s):  
Mahdi Ramezani ◽  
Alireza Komaki ◽  
Mohammad Mahdi Eftekharian ◽  
Mehrdokht Mazdeh ◽  
Soudeh Ghafouri-Fard

Migraine is a common disorder which is placed among the top ten reasons of years lived with disability. Cytokines are among the molecules that contribute in the pathophysiology of migraine. In the current study, we evaluated expression levels of IL-6 coding gene in the peripheral blood of 120 migraine patients (54 migraine without aura and 66 migraine with aura patients) and 40 healthy subjects. No significant difference was detected in expression of IL-6 between total migraine patients and healthy controls (Posterior beta = 0.253, P value = 0.199). The interaction effect between gender and group was significant (Posterior beta =-1.274, P value = 0.011), therefore, we conducted subgroup analysis within gender group. Such analysis revealed that while expression of this gene is not different between male patients and male controls (Posterior beta =-0.371, P value > 0.999), it was significantly over-expressed in female patients compared with female controls (Posterior beta = 0.86, P= 0.002). Expression of IL-6 was significantly higher in patients with aura compared with controls (Posterior beta = 0.63, adjusted P value = 0.019). However, expression of this cytokine coding gene was not different between patients without aura and healthy subjects (Posterior beta = 0.193, adjusted P value = 0.281). Therefore, IL-6 might be involved in the pathophysiology of migraine among females and migraine with aura among both sexes.


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