scholarly journals Gene Expression Profiling Reveals Progesterone-Mediated Cell Cycle and Immunoregulatory Roles of Hoxa-10 in the Preimplantation Uterus

2003 ◽  
Vol 17 (4) ◽  
pp. 610-627 ◽  
Author(s):  
Mylene W. M. Yao ◽  
Hyunjung Lim ◽  
Daniel J. Schust ◽  
Sung E. Choe ◽  
Anna Farago ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Pregnancy Loss ◽  
Stromal Cell ◽  
Recurrent Pregnancy Loss ◽  
Kinase Inhibitor ◽  
Cyclin Dependent Kinase Inhibitor ◽  
Local Immunosuppression

Abstract Human infertility and recurrent pregnancy loss caused by implantation defects are poorly understood. Hoxa-10-deficient female mice have severe infertility and recurrent pregnancy loss due to defective uterine implantation. Gene expression profiling experiments reveal that Hoxa-10 is an important regulator of two critical events in implantation: stromal cell proliferation and local immunosuppression. At the time of implantation, Hoxa-10 mediates the progesterone-stimulated proliferation of uterine stromal cells. Hoxa-10 mutants express a stromal cell proliferation defect that is accompanied by quantitative or spatial alterations in the expression of two cyclin-dependent kinase inhibitor genes, p57 and p15. Hoxa-10 deficiencyFS also leads to a severe local immunological disturbance, characterized by a polyclonal proliferation of T cells, that occurs in place of the normal progesterone-mediated immunosuppression in the periimplantation uterus.

scholarly journals Identification of novel regulators of hematopoietic stem cell development through refinement of stem cell localization and expression profiling

Blood ◽  
2009 ◽  
Vol 114 (21) ◽  
pp. 4645-4653 ◽  
Author(s):  
Maria I. Mascarenhas ◽  
Aimée Parker ◽  
Elaine Dzierzak ◽  
Katrin Ottersbach
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Expression Profiling ◽  
Gene Expression Analysis ◽  
Kinase Inhibitor ◽  
Cyclin Dependent Kinase ◽  
Hematopoietic Stem ◽  
Cyclin Dependent Kinase Inhibitor ◽  
Cell Localization ◽  
Before And After

Abstract The first adult-repopulating hematopoietic stem cells (HSCs) are detected starting at day 10.5 of gestation in the aorta-gonads-mesonephros (AGM) region of the mouse embryo. Despite the importance of the AGM in initiating HSC production, very little is currently known about the regulators that control HSC emergence in this region. We have therefore further defined the location of HSCs in the AGM and incorporated this information into a spatial and temporal comparative gene expression analysis of the AGM. The comparisons included gene expression profiling (1) in the newly identified HSC-containing region compared with the region devoid of HSCs, (2) before and after HSC emergence in the AGM microenvironment, and (3) on populations enriched for HSCs and their putative precursors. Two genes found to be up-regulated at the time and place where HSCs are first detected, the cyclin-dependent kinase inhibitor p57Kip2/Cdkn1c and the insulin-like growth factor 2, were chosen for further analysis. We demonstrate here that they play a novel role in AGM hematopoiesis. Interestingly, many genes involved in the development of the tissues surrounding the dorsal aorta are also up-regulated during HSC emergence, suggesting that the regulation of HSC generation occurs in coordination with the development of other organs.

Global gene expression profiling in early-stage polycystic kidney disease in the Han:SPRD Cy rat identifies a role for RXR signaling

2011 ◽  
Vol 300 (1) ◽  
pp. F177-F188 ◽  
Author(s):  
Masanori Kugita ◽  
Kazuhiro Nishii ◽  
Miwa Morita ◽  
Daisuke Yoshihara ◽  
Hiroe Kowa-Sugiyama ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Kidney Disease ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Early Stage ◽  
Global Gene Expression ◽  
Rt Pcr ◽  
Polycystic Kidney ◽  
Global Gene Expression Profiling

Han:SPRD Cy is a spontaneous rat model of polycystic kidney disease (PKD) caused by a missense mutation in Pkdr1. Cystogenesis in this model is not clearly understood. In the current study, we performed global gene expression profiling in early-stage PKD cyst development in Cy/Cy kidneys and normal (+/+) kidneys at 3 and 7 days of postnatal age. Expression profiles were determined by microarray analysis, followed by validation with real-time RT-PCR. Genes were selected with over 1.5-fold expression changes compared with age-matched +/+ kidneys for canonical pathway analysis. We found nine pathways in common between 3- and 7-day Cy/Cy kidneys. Three significantly changed pathways were designated “Vitamin D Receptor (VDR)/Retinoid X Receptor (RXR) Activation,” “LPS/IL-1-Mediated Inhibition of RXR Function,” and “Liver X Receptor (LXR)/RXR Activation.” These results suggest that RXR-mediated signaling is significantly altered in developing kidneys with mutated Pkdr1. In gene ontology analysis, the functions of these RXR-related genes were found to be involved in regulating cell proliferation and organ morphogenesis. With real-time RT-PCR analysis, the upregulation of Ptx2, Alox15b, OSP, and PCNA, major markers of cell proliferation associated with the RXR pathway, were confirmed in 3- and 7-day Cy/Cy kidneys compared with 3-day +/+ kidneys. The increased RXR protein was observed in both the nucleus and cytoplasm of cystic epithelial cells in early-stage Cy/Cy kidneys, and the RXR-positive cells were strongly positive for PCNA staining. Taken together, cell proliferation and organ morphogenesis signals transduced by RXR-mediated pathways may have important roles for cystogenesis in early-stage PKD in this Pkdr1-mutated Cy rat.

Gene Expression Profiling of Isolated Mesenchymal and Osteoblastic Cells Exhibits a Different Pattern of Expression in Multiple Myeloma Patients as Compared to Healthy Subjects: Potential Relationship with the Presence of Bone Lesions.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3513-3513
Author(s):  
Nicola Giuliani ◽  
Katia Todoerti ◽  
Gina Lisignoli ◽  
Sara Tagliaferri ◽  
Luca Agnelli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Cell Proliferation ◽  
Osteogenic Differentiation ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Differentially Expressed ◽  
Bone Lesions ◽  
Bone Status ◽  
Probe Set

Abstract Gene expression alterations occurring in the bone microenvironment cells and their potential relationships with the occurrence of bone lesions in multiple myeloma (MM) patients have never been investigated. In this study, we have isolated both mesenchymal (MSC) and osteoblastic (OB) cells, without in vitro differentiation, from bone biopsies obtained by iliac crest of 24 MM patients, 7 MGUS subjects and 8 healthy donors (N) who underwent orthopedics surgery. Bone status was evaluated in all MM patients by total X rays scan and MRI for the spine. Firstly, we evaluated cell proliferation in relationship with growth substrate (bone and glass) and cell phenotype by flow cytometry and immunohistochemistry. We found that both MSC and OB cells have higher cell doubling rate in MM patients as compared to N. Higher expression of alkaline phosphatase and Runx2 was observed in OB as compared to MSC cells in both N and MM patients without osteolytic lesions, but not in osteolytic ones. We performed a gene expression profiling analysis of isolated MSC and OB cells using GeneChip® Affymetrix HG-U133A oligonucleotide arrays. An unsupervised analysis of the most variable genes across the dataset generated a hierarchical clustering with the two major branches containing respectively MSC and OB samples. A multiclass analysis of N, MGUS and MM patients identified 33 differentially expressed probe-set (specific for 27 genes) in MSC cells, and 19 differentially expressed probe-set (13 genes) in OB, and the identified transcripts mainly characterized N versus MM and MGUS samples. A supervised analysis between N and MM samples identified 65 probes (56 genes: 17 up-regulated and 39 down-regulated) differentially expressed in MSC and 35 probes (29 genes, 12 up-regulated and 17 down-regulated) in OB. Notably, genes encoding the Homeobox class proteins, such as HOXB2-6-7, were up-regulated in both MSC and OB of MM patients as compared to N. As regards the bone status, a total of 60 probe-sets (3 up-regulated and 57 down-regulated genes) were found differentially expressed in MSC from osteolytic vs. non-osteolytic MM patients, whereas MGUS-MSC exhibited an intermediate transcriptional profile between osteolytic and non-osteolytic MM patients. A distinct pattern of gene expression profiling was also observed in MSC versus OB when osteolytic and non-osteolytic MM patients were compared (26 vs. 94 differentially expressed probe-sets, respectively), including transcription factors related to MSC osteogenic differentiation belonging to Runx2 pathway (HEY1) or Wnt and BMP signaling On the other hand, few genes were found differentially expressed in OB cells in relationship with the presence of bone lesions. In conclusion, we identified a distinctive transcriptional fingerprint in isolated MSC and OB cells of MM patients as compared to N subjects, which mainly correlated with cell proliferation. Moreover, a different gene expression profile was observed in MSC cells of MM patients according to the presence/absence of bone lesions, highlighting the critical role of the block of the osteogenic differentiation.

Tumor genomic analysis for biomarker identification in a phase I trial of the Wee 1 inhibitor adavosertib (AZD1775).

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 3624-3624
Author(s):  
Abdul Rafeh Naqash ◽  
Arjun Mittra ◽  
Geraldine Helen O'Sullivan Coyne ◽  
Li Chen ◽  
Biswajit Das ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Kinase Inhibitor ◽  
Genomic Analysis ◽  
M Cell ◽  
Cyclin E1 ◽  
Potential Biomarker ◽  
Duration Of Response ◽  
Tumor Biopsies

3624 Background: Adavosertib, a first-in-class Wee1 kinase inhibitor, abrogates G2/M cell cycle arrest causing premature mitosis and DNA replication stress, yielding enhanced DNA damage. Here we report on potential biomarkers of response from tumor genomic analysis in patients (pts) with solid tumors treated with adavosertib. Methods: Adavosertib was administered once daily on days 1-5 and 8-12 of a 21-day cycle. RECIST 1.1 was used to evaluate clinical response. Paired tumor biopsies were obtained for RNASeq gene expression profiling (GEP) and for whole-exome sequencing (WES) to evaluate gene mutation and copy number amplification (CNA). Fold change (FC) was calculated to define gene overexpression. To identify the frequency of CNA and mRNA overexpression for the genomic biomarkers of interest, cBioPortal analysis using TCGA and MSK-IMPACT datasets was performed. Differential GEP analysis of tumor and paired normal tissue was performed using the gene expression profiling interactive analysis (GEPIA) interface (Tang et al. 2017). Results: Out of 35 pts evaluable for response, 6 (17%) had partial response (PR; 4 ovarian carcinoma [OVC], 2 endometrial carcinoma [EC]). The median duration of response was 5.2 months (range 4.0-23.1). Eighteen pts (51.4%) had stable disease. Genomic analysis of tumor biopsies was available for 9 pts; 7 of these pts were evaluable for response, and 3 had PR (2 OVC, 1 EC). WES revealed TP53 mutations in 6 pts (66.6%; 3 pts with PR, 2 with progressive disease,1 not evaluable). On WES, tumor Cyclin E1 ( CCNE1) CNA was present in 1 of 3 PR pts while tumors from all 3 PR samples showed relatively high CCNE1 expression by RNAseq (FC = 4.07). In the MSK-IMPACT 2017 dataset, CCNE1 CNA was identified in 1.8% of pts (194 of 10336); of which, OVC (10.3%) and EC (8.7%) had the highest incidence of CCNE1 CNAs. In separate tumor-specific (OVC, EC) TCGA datasets having CCNE1 overexpression and/or CNA, overlap in CCNE1 overexpression with CCNE1 CNA was 35.5% (OVC) and 25.2% (EC). Compared to normal ovarian/ endometrial tissues, GEPIA analysis revealed significantly higher CCNE1 mRNA expression in OVC (FC = 3.5) and EC (FC = 3.8). Conclusions: CCNE1alterations (overexpression and/or CNA) tend to be enriched in OVC and EC with a limited fraction showing both overexpression and CNA. Tumor genomic analysis of additional OVC and EC pts treated with adavosertib is required to determine whether CCNE1 mRNA overexpression, regardless of CCNE1 CNA, is a potential biomarker of response to this drug in these tumor types. Funded by NCI contract No. HHSN261200800001E. Clinical trial information: NCT01748825 .

Characterization of Mesenchymal Stromal Cells (MSCs) Derived From Acute Myeloid Leukemia (AML) Bone Marrow

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2558-2558
Author(s):  
Soumit K. Basu ◽  
Xin Zhao ◽  
Sylvia Chien ◽  
Min Fang ◽  
Vivian Oehler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Stromal Cell ◽  
Collagen Type ◽  
Β1 Integrin ◽  
Normal Bone Marrow ◽  
Bone Marrow Mscs ◽  
Normal Bone

Abstract Abstract 2558 INTRODUCTION Recent evidence has implicated the bone marrow microenvironment directly in the pathogenesis of preleukemic bone marrow disorders (Raaijmakers MHGP et al, Nature 2010) with potential to transform to AML. Moreover, the bone marrow microenvironment is critical to AML survival (Garrido et al 2001, Meads et al 2008). We sought to investigate aspects of the bone marrow microenvironment which may contribute to the pathogenesis and persistence of AML by direct analysis of primary bone marrow MSCs isolated from AML patients in comparison with primary bone marrow MSCs from normal subjects. Our analyses included (1) a comparison of cytokine elaboration between normal and AML bone marrow MSCs (2) immunophenotyping of normal and AML bone marrow MSCs (3) characterisation of binding by AML cells to their autologous stroma and (4) gene expression profiling of normal and AML bone marrow MSCs and (5) cytogenetic analysis AML bone marrow MSCs. METHODS We have been able to derive confluent cultures of mesenchymal stromal cells from 80% of AML patient marrow samples. Fresh or cryopreserved bone marrow samples were plated in non-hematopoietic expansion media (Miltenyi) under reduced oxygen conditions. After 48 hours of culture, nonadherent cells are removed, and over a period of 1–2 weeks, cultures of spindle shaped cells are derived, that can be sustained in culture for up to 5 passages. Similar cultures were derived from normal bone marrow. Gene expression profiling of bone marrow MSCs was performed by whole genome analysis using Illumina's BeadChip microarray platform. Samples included mRNAs isolated from confluent cultures of AML bone marrow MSCs, normal bone marrow MSCs, and the normal bone marrow stromal cell lines HS27a and HS5. RESULTS Comparison of cytokine elaboration showed a statistically significant (p = 0.037) 5-fold decrease in stromal MCP-1 production by AML bone marrow MSCs compared with normal bone marrow MSCs (327 ± 169 vs. 1669 ± 570 pg/mL, mean ± SE). Normal and AML MSCs showed no statistically significant differences in the production of G-CSF, GM-CSF, M-CSF, IL6, IL12, SCF, TNFα, MCP1 and SDF1β. Like their normal counterparts, AML bone marrow MSCs strongly express CD90, CD29 (β1 integrin), CD73, CD105, CD146, and CD44. The normal bone marrow derived stromal cell lines HS27a and HS5 demonstrated moderate expression of CD324/E-cadherin (28.4% and 37.9% respectively). E-cadherin expression proved highly variable among normal bone marrow MSCs (1.9%-54.9%) and similarly variable in AML bone marrow MSCs (7.8%–56.5%). AML binding to autologous MSCs primarily dependent on β1 integrin, L-selectin and VCAM-1. In contrast, prior data (Basu et al., ASH 2010 Abstract 2756) demonstrated AML binding to the normal bone marrow stromal cell line HS27a as primarily dependent on β1 integrin, CXCR4, and E-cadherin. Gene expression profiling demonstrated no significant differences between 6 AML and 5 normal bone marrow MSCs. AML bone marrow MSCs, as expected, demonstrated marked differences from AML bone marrow mononuclear cells, expressing higher levels of connective tissue growth factor (128 fold), tropomyosin 1 (84.4 fold), collagen type 1 α1 (194 fold), collagen type 1 α2 (137 fold), collagen type 4 α1 (128 fold), collagen type 5 α1 (119 fold), transgelin (111 fold), cadherin 11 (21 fold), biglycan (137 fold), IGF binding protein 6 (18 fold), and procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 (74 fold). In our cytogenetic analyses of MSCs to date, bone marrow MSCs derived from one of the complex karyotype AML patients demonstrated normal cytogenetics. In contrast, bone marrow MSCs derived from a second AML patient shared a common t(2;11) translocation present in the AML cells but demonstrated an abnormal clone with del(4q) which lacked the t(6;9) also present in the AML cells [i.e.-MSC karyotype: t(2;11), del(4q); AML karyotype: t(2;11), t(6;9)]. These results suggest that in some patients AML cells and their autologous MSCs may share the same clonal origin, while in other cases, the MSCs may have a distinct origin. CONCLUSION AML and normal bone marrow MSCs demonstrate only subtle differences, providing an explanation of the ability of AML bone marrow MSCs to support normal hematopoiesis after leukemic debulking (e.g. via induction chemotherapy or allogeneic stem cell transplant). Disclosures: No relevant conflicts of interest to declare.

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