Proteomic Profiling of 112 Proteins in Chronic Myeloid Leukemia Patient Samples Using Reverse Phase Proteins Arrays (RPPA) Reveals Distinct Protein Expression Signatures Associated with Advanced Phase Disease and the CD34+ Compartment

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2503-2503 ◽  
Author(s):  
Alfonso Quintás-Cardama ◽  
Yi Hua Qiu ◽  
Sean Post ◽  
Yiqun Zhang ◽  
Chad Creighton ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Stem Cell ◽  
Protein Expression ◽  
Myeloid Leukemia ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Stem Cell Population ◽  
Parp Cleavage ◽  
Adhesion Proteins

Abstract Abstract 2503 Background Having previously shown that protein expression signatures, based on the activation state of cell cycle, apoptosis and signal transduction regulating proteins, existed and were prognostic in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), we extended this to evaluate protein expression patterns in CML. Methodology We have generated RPPA using protein derived from the leukemia-enriched fraction of 40 primary CML samples with the goal of defining comprehensive proteomic expression patterns in CML. Of the 40 patient samples included in this analysis, 25 were in chronic (CP), 5 in accelerated (AP), and 10 in blast phase (BP). Of the latter, 6 were lymphoid BP and 4 myeloid BP. All protein preps were made from fresh cells on the day of collection. Present as controls were 16 CD34+ BM and 9 normal PB lymphocyte samples. Samples are printed as 5 serial 1:2 dilutions in duplicate using an Aushon 2470 Arrayer. Each array has a total of 6912 dots printed. Slides were probed with 112 antibodies (ABs) against apoptosis, cell cycle, signaling (STP), regulating proteins, integrins, and phosphatases among other functional protein groups, including 85 vs. total protein, 22 vs. phospho-specific sites and 5 vs. caspase or PARP cleavage sites. Spot intensities were quantified using MicroVigene software. Data was analysed using R, with loading control and topographical background normalization being utilized. Results We first tested the differences of the protein expression between patients with CP, AP, and BP. To that end, we centered proteins on the median across all samples. An ANOVA analysis revealed 20 proteins (from a total of 112 proteins probed) were differentially expressed across the different phases of CML by using a minimum statistical significance cutoff of p<0.01. The expression of proteins such as HSP90, RB, AIF, PP2A, BCL2, XIAP, SMAD1, SSBP2α, PARP, GAB2, and TRIM24 was low in patients with CML-CP but progressively increased as patients progressed to BP, with samples obtained from patients with CML-AP exhibiting intermediate levels between CP and BP. Conversely, the expression of PKCΔ.p664, AKTpT308, actin, p70S6Kp, Rac1.2.3, PDK1p, MEK, and CDK4 decreased gradually as patients progressed from CP to BP, with samples obtained from patients with CML-AP exhibiting intermediate levels. Notably, downregulation of genes involved in the Ras-MEK-MAPK pathway and upregulation of those encoding cytoskeletal and adhesion proteins (actin, Rac) has been previously reported in gene expression profiles (Radich et al, PNAS 2006). A similar analysis was conducted to investigate differences in protein expression between the CD34+ (23 samples) and CD34- (37 samples) compartments, the former of them putatively containing the CML stem cell population. A t test was used for each protein and those whose expression were significantly (p<0.01) differentially expressed were selected. Forty-two proteins were identified as differentially expressed in CD34+ CML cells, including upregulation in the CD34+ compartment of those involved in the WNT/β-catenin (TCF4, survivin), adhesion proteins (integrin-β3, FAK, SRC), STAT pathway (STAT3, STAT3p705, BclXL), PARP, pPTEN, MYC, pPKCα, mTOR, and PP2A. Conversely, several proteins were downregulated in CD34+ cells: Mdm2, p38, MEK, AKTpT308, NFκB pathway (PKCΔ, NFκB.p65, SHIP1), and proapoptotic proteins (BID, BIM). When segregated according to BCR-ABL1 mutational status, no differences in protein expression were observed between samples carrying the F317L or the T315I mutations versus all other mutations. Similarly, no differences in protein expression were observed between patients carrying unmutated BCR-ABL1 and those carrying a mutant BCR-ABL1 enzyme. Conclusions We have identified by RPPA technology specific subsets of proteins whose expression is associated with CML progression. Likewise, specific proteins appear to be differentially expressed in the CML stem cell compartment. These proteins might represent therapeutic targets. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Cite-Seq Reveals Distinct Patterns and Potential Mechanisms of Relapse in Pediatric AML

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 3458-3458
Author(s):  
Tsz-Kwong Man ◽  
Mohammad Javad Najaf Panah ◽  
Jessica L. Elswood ◽  
Pavel Sumazin ◽  
Michele S. Redell
Keyword(s):  
Protein Expression ◽  
Single Cell ◽  
Actin Polymerization ◽  
Conflicts Of Interest ◽  
Limit Of Detection ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cell Types ◽  
Differentially Expressed ◽  
Pediatric Aml

Abstract Introduction - Acute myeloid leukemia (AML) is an aggressive disease with a relapse rate of approximately 40% in children. Progress in improving cure rates has been slow, in part because AML is very heterogeneous. Molecular studies consistently show that most cases are comprised of distinct subclones that diminish or expand over the course of therapy. Single-cell profiling methods now allow parsing of the leukemic population into subsets based on gene and/or protein expression patterns. We hypothesized that comparing the features of the subsets that are dominant at relapse with those that are dominant at diagnosis would reveal mechanisms of treatment failure. Methods - We profiled diagnosis-relapse pairs from 6 pediatric AML patients by Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq). All patients were treated at Texas Children's Cancer Center and consented to banking of tissue for research. CITE-Seq was performed by Immunai (New York, NY) using a customized panel of 65 oligonucleotide-tagged antibodies, the 10x Genomics Chromium system for single-cell RNA library generation, and the Novaseq 6000 for sequencing. After data cleanup and normalization, clustering by scRNA-seq was done using the Seurat package. Cell-type identification of clusters was facilitated by published healthy bone marrow scRNA-seq datasets (van Galen et al, Cell 2019). Differentially expressed genes (DEGs) and proteins (DEPs) between diagnosis and relapse were determined using Wilcoxin ranked sum tests. Results - We generated single-cell transcriptomes for a total of 28,486 cells from 12 samples, with a mean of 2373 cells and 1416 genes per sample. Samples were integrated with batch effect correction, producing 30 distinct clusters (cell types) in total (Figure 1A). Cell types with expression profiles consistent with lymphocytes and erythroid precursors were identified in multiple patients, whereas AML cell types tended to be specific to individual patients (Figure 1B). For patients TCH1, TCH2 and TCH3, the most abundant cell types at diagnosis were rare at relapse, and cell types that were rare at diagnosis became dominant at relapse. For these 3 cases, we identified DEGs between the dominant diagnosis cell types and dominant relapse cell types. We found 18 genes that were upregulated at relapse in at least 2 of the cases. Several genes related to actin polymerization were enriched (ARPC1B, ACTB, PFN1), possibly reflecting an enhanced capacity for adhesion and migration. Also of note, macrophage migration inhibitory factor (MIF) and its receptor CD74 were upregulated at relapse, suggesting a role in chemoresistance. For patients TCH4, TCH5 and TCH6, the same cell types that were abundant at diagnosis were also abundant at relapse, and few genes were significantly altered between diagnosis and relapse in multiple cases. Only SRGN, which encodes the proteoglycan serglycin, and GAPDH were altered in 2 of these 3 cases, and both were downregulated at relapse. We performed similar comparisons to identify proteins that were differentially expressed between diagnosis and relapse pairs. The number of DEPs between the dominant diagnosis and relapse cell types ranged from 0 (TCH1 and TCH6) to 5 (TCH2). The only protein altered in more than one case was CD7, which was enriched at relapse in TCH2, TCH3 and TCH4. Conclusions - From CITE-Seq profiling of 6 pediatric AML cases we identified two distinct patterns of relapse. For 3 cases, relapse occurred by expansion of a subset that was small but present at diagnosis. Enrichment of genes associated with adhesion and survival signaling suggests that these cells survived because they were well-equipped to take advantage of interactions with the microenvironment. For 3 other cases, the population that was dominant at diagnosis persisted and expanded at relapse with few substantial changes in gene or protein expression profiles. This pattern suggests that these AML cells were a priori equipped to survive chemotherapy, even though bulk disease levels were transiently reduced below the limit of detection. Most profiled proteins did not change substantially between diagnosis and relapse. An exception is CD7, which was enriched at relapse in 50% of our cases and represents a potential therapeutic target. Analysis of more cases will refine these relapse patterns, reveal potential mechanisms of chemoresistance and inform the development of novel therapies. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Differentially Expressed Protein Patterns in Chronic Lymphocytic Leukemia (CLL) after Thymosin beta4 (Tb4) and Lenalidomide (Len) Treatment: Two-Dimensional Gel Electrophoresis (2DE) Analysis

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1729-1729
Author(s):  
Sabrina Bossio ◽  
Laura De Stefano ◽  
Mariavaleria Pellicanò ◽  
Angela Palummo ◽  
Francesca Storino ◽  
...  
Keyword(s):  
Protein Expression ◽  
Silver Nitrate ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Protein Patterns ◽  
Maldi Tof ◽  
Silver Nitrate Staining ◽  
Normal Controls

Abstract Proteomic approaches are commonly secondary to genetic studies but are essential in the multi-disciplinary field of hematological research. As opposed to mRNA microarray data, proteomics provides a better understanding of which proteins are actually expressed, although the identification of specific proteins remains challenging (Unwin et al Blood Rev 2014; Boyd J Proteomics 2010). In neoplastic hematology such as CLL, protein studies have contributed to the elucidation of disease mechanisms, defined prognostic or therapeutic biomarkers (Boyd J Proteomics 2010). In this study we used proteomics and 2DE analysis to evaluate differential protein expression patterns after treatment with Len. Len can improve immune dysfunction in CLL by repairing F-actin polymerization and signaling at the immunological synapse (Ramsay et al 2008 J Clin Invest). Our previous data obtained from MALDI-TOF analysis identified Tβ4, a G-actin sequestering protein involved in the regeneration of injured tissues and cell migration, as a downregulated protein in CLL patients, also confirmed by an independent GEP analysis comparing B-cell from CLL cases (n=80) and normal controls (n=6), supported by Tβ4 mRNA down-regulation in CLL (3604±1244 vs 5715±1004, respectively; mean±SD; p=0.001). Here, we investigated whether purified B-CLL cells respond differently to the chemoattractant SDF1a and whether different protein expression patterns can be identified after exogenous Tβ4 and Len treatment using 2DE analysis. Highly purified B-CLL lymphocytes were isolated from untreated Binet stage A CLL patients prospectively enrolled from diagnosis (O-CLL1 protocol, clinicaltrial.gov identifier NCT00917540) and healthy controls. Tb4 was identified by MALDI TOF using 100 patient samples. Next, cells were pre-treated with Len (5uM) and then treated with Tb4 (100nM) for 30min. Cells were plated in transwells using 5.0 um pores with SDF1a as chemoattractant for migration assays. Protein was extracted from CLL cell pellets by RIPA buffer and quantified. Sample preparation and 2DE was performed as described by Scielzo et al (J Clin Inves, 2005). Protein samples (100 ug) were applied to 7-cm IPG strips, pH 3-11NL (Amersham Biosciences), respectively, by in-gel rehydration. Isoelectric focusing was performed with a Protean i12 IEF system (Biorad). Strips were equilibrated and loaded onto 9-16% gradient acrylamide SDS-PAGE gels for the second dimension separation. Silver nitrate staining (Sinha P et al Proteomic, 2001) was used to visualize proteins and images were digitally acquired (ChemiDoc MP, Biorad) and spots were analyzed using PDQuest basic 2D Gel Analysis Software (Biorad). CLL samples with the lowest Tβ4 expression (n=12) also had higher F-actin levels as evaluated by FC analysis than normal controls. B-CLL strongly responded to the migratory stimulus SDF-1a, which was further increased (by 20%) in presence of Len treatment, likely due to an alteration in actin remodeling and changes in the expression of unknown proteins. Purified CD19+CD5+ leukemic cells were lysed and proteins resolved on 2DE and visualized by silver nitrate staining. The protein profile analysis on silver-stained gels showed a number of protein spots ranging from 18 to 60kDa that were differentially expressed with respect to untreated cells. Our preliminary qualitative analysis suggests that there are groups of proteins with a lower expression in the presence of Tβ4 or Len, which are more strongly inhibited following exposure to their combination. Conversely, an opposite pattern of protein expression was observed whereby an additive effect on protein expression was observed by combined exposure to Tβ4 and Len. This approach allowed us to identify an altered protein expression pattern after treatment with Len and Tβ4, and may be useful to identify changes in expression profiles of CLL proteins, which may translate into functional differences in the malignant clone. Disclosures No relevant conflicts of interest to declare.

Comparative Transcriptome Analysis of Different Subsets of CD34+ Normal and Chronic Myeloid Leukemia Cells Identifies Novel Perturbations in the CML Stem Cell Population.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 35-35 ◽  
Author(s):  
Yun Zhao ◽  
Allen Delaney ◽  
Marco A. Marra ◽  
Xiaoyan Jiang ◽  
Allen C. Eaves ◽  
...  
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Chronic Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Chronic Phase ◽  
K562 Cells ◽  
Differentially Expressed ◽  
Stem Cell Population ◽  
Cell Populations ◽  
Beta Catenin

Abstract Chronic myeloid leukemia (CML) arises from a hematopoietic stem cell that acquires a BCR-ABL fusion gene. During the chronic phase of the disease, this cell produces an expanding multi-lineage clone that usually comes to dominate all terminal stages of myelopoiesis. However, eventually, further mutations are acquired which cause progression to a rapidly fatal acute leukemia. To obtain new insights into the molecular perturbations that cause CML stem cells to initiate chronic phase disease, we generated Long Serial Analysis of Gene Expression (LongSAGE) libraries (∼200,000 tags/library) from extracts of highly purified lin−CD34+CD45RA−CD36−CD71−CD7−CD38+ and lin−CD34+CD45RA−CD36−CD71−CD7−CD38− normal bone marrow (BM) and G-CSF-mobilized peripheral blood (G-mPB) cells as well as cells from 3 chronic phase CML patients with predominantly Ph+/BCR-ABL+ cells in both of these very primitive cell subsets. Long term culture-initiating cell (LTC-IC) and direct colony-forming cell (CFC) assays performed on an aliquot of each of these cell populations showed the frequency of LTC-IC were 4 to 130-fold higher in the 34+38− cells than in the matching 34+38+ cells with the opposite trend for the CFCs. Comparison of the tags present in the pooled CML and pooled normal BM and G-mPB libraries revealed many differentially expressed genes. Real-time RT-PCR analysis of lin−CD34+ cells from 14 chronic phase CML patients and 3 normal BMs confirmed the differential expression of 14 candidate transcripts identified by SAGE (changes ranging from 3-fold lower to 80-fold higher in the CML cells, p<0.05). The altered levels of expression of 5 of these genes (i.e., beta-catenin, MLLT3, IL1R1, LY6E and GAS2) were highly correlated with the relative levels of BCR-ABL transcripts in the same cells (r ≥0.6). 5 of the 14 genes (IL1R1, vWF, SOX4, SELL and RHOB) were found to be differentially expressed in the 3-day post-transduction progeny of CD34+ cord blood cells exposed to a BCR/ABL-IRES-GFP vs a control GFP- lentivirus preparation (n=2). 3 (GAS2, DUSP1 and TP53BP2) were upregulated (5 to 11-fold) in imatinib-treated K562 cells (as compared to untreated K562 cells) but their expression remained unchanged in similarly treated KG1 cells (a primitive BCR-ABL-negative human AML cell line) providing further evidence that their deregulated expression is secondary to the kinase activity of p210BCR-ABL. In addition, from a comparison of the meta-library for the 34+38− CML cells with the meta-libraries for both the normal 34+38− and 34+38+ cells, the meta-library for the 34+38+ CML cells and most publicly accessible SAGE data, we were able to identify 65 novel tags in the 34+38− CML cells. 32 of these unique tags were located within conserved genomic regions and >2 kb away from known transcripts, and of these 32, 3 were confirmed to represent novel transcripts using a PCR approach. These results illustrate the potential of SAGE to reveal novel as well as known components in the transcriptomes of rare normal and cancer stem cell populations. Investigation of their roles in primitive human cells transduced with BCR-ABL and BCR-ABL+ cell lines indicates the utility of these models for further delineation of the complex effects of BCR-ABL expression in chronic phase CML stem cells.

Proteomic Profiling of 128 Proteins In 194 Acute Lymphocytic Leukemia (ALL) Patients Using Reverse Phase Proteins Arrays (RPPA) Reveals Recurrent Proteins Expression Signatures with Prognostic Implications

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3230-3230
Author(s):  
Steven M. Kornblau ◽  
Yi Hua Qiu ◽  
Nianxiang Zhang ◽  
Kevin R Coombes ◽  
Susan O'Brien ◽  
...  
Keyword(s):  
Cell Cycle ◽  
T Cell ◽  
Protein Expression ◽  
Conflicts Of Interest ◽  
Pearson Correlation ◽  
Expression Patterns ◽  
High Expression ◽  
Parp Cleavage ◽  
Outcome Analysis ◽  
Remission Duration

Abstract Abstract 3230 Background. Having previously shown that protein expression signatures (ProExpSig), based on the activation state of cell cycle, apoptosis and signal transduction (STP) regulating proteins, existed and were prognostic in AML, we extended this to evaluate protein expression patterns in ALL. Methodology. We have generated RPPA using protein derived from the leukemia-enriched fraction of 283 primary ALL samples from 216 cases with the goal of providing comprehensive proteomic based classification of ALL. Included are 253 samples from 194 newly diagnosed ALL patients (179 Marrow (BM), 95 blood (PB) samples, 41 with concurrent PB and BM specimens), and 14 relapse (REL) samples from these same cases. Phenotypes included 163 pre-B, 22 T-Cell and 9 Burkitt's cases. There were 42 PH1+ cases but only the 28 treated with TKIs were included for outcome analysis. All protein preps were made from fresh cells on the day of collection as we previously observed that protein expression changes dramatically in ALLs cells with cryopreservation. Present as controls were 16 CD34+ BM and 9 normal PB lymphocyte samples. Samples are printed as 5 serial 1:2 dilutions in duplicate using an Aushon 2470 Arrayer. Each array has a total of 6912 dots printed. Slides were probed with 128 antibodies (ABs) against apoptosis, cell cycle, signaling (STP), regulating proteins, integrins, phosphatases etc including 90 vs. total protein, 33 vs. phos-specific sites and 5 vs. caspase or PARP cleavage sites. Spot intensities were quantified using MicroVigene software. Data was analysed using R, with loading control and topographical background normalization being utilized. Results. Proteins were clustered using absolute Pearson correlation and Ward linkage. Based on the Gap statistic there appeared to be 15 constellations of protein with correlated expression. Many formed expected associations e.g., cleaved caspases, phosphorylated STATs, activated STPs. Based on the combination of expression of these 15 constellations, 7 distinct ProExpSig were defined containing between 18 and 37 cases. Phenotype was highly unbalanced with T cell and Burkitt's cases significantly overrepresented and B cell underrepresented in Signature 3 (O/E 5.7,4.2 and .3) and T cell ALL underrepresented in signatures 2, 4,5 and 6 (O/E .47, .76, .4 and .28). PH+ disease was strongly associated with signatures 5 (18 of 22) and 2 (11 of 375 cases). The PH+ dominated Sig5 was characterized by high expression of Myc, ARC, Survivin as well as high levels of activated STPs and Stats. The Ph+ cases in Sig 2 and 5 differed in that Sig5 had high expression of phospho PKCα, GAB2 and Stat 3 and 6, while Sig 2 had higher expression of proteins in the mTOR and TSC2 axis Almost all t(4:11) cases (9 of 11) were in Sig6, which was characterized by high levels of expression of most proteins excluding those that were highly expressed in the PH+ cases. Cases with Burkitt's were characterized by high expression of cyclins D1 and D3, pRB and by high levels of cleaved caspases. The WBC was markedly higher in Sig 3 and 6. The vast majority n=174) achieved remission with 9 primary refractory and 10 induction deaths occurring, so a signature predicting primary resistance was not observed. It was readily evident that there was a group of favorable signatures (1,2, 4 and 7) and another distinctly unfavorable group of signatures (3, 5, and 6). The favorable group had superior remission duration (median 172 vs. 96 weeks, p= 0.35), event free survival (median 132 vs. 72 weeks, p=0.03) and overall survival (median 180 vs. 93 weeks, P=0.04) compared to the unfavorable signatures. Conclusions. ALL is characterized by 7 distinct protein expression signatures which form a favorable and an unfavorable prognostic group. The adverse ProExpSig are associated with significantly shorter remission duration and survival. Differences within these ProExpSig can be used to direct the rational application of various targeted therapies to those patients most likely to benefit from them thereby improving outcome. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Comprehensive Comparison of Amnion Stromal Cells and Chorion Stromal Cells by RNA-Seq

2021 ◽  
Vol 22 (4) ◽  
pp. 1901
Author(s):  
Brielle Jones ◽  
Chaoyang Li ◽  
Min Sung Park ◽  
Anne Lerch ◽  
Vimal Jacob ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stromal Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Principal Component ◽  
Differentially Expressed ◽  
Inflammatory Factor ◽  
Next Generation Sequencing Technology ◽  
Angiogenic Potential ◽  
Anti Inflammatory

Mesenchymal stromal cells derived from the fetal placenta, composed of an amnion membrane, chorion membrane, and umbilical cord, have emerged as promising sources for regenerative medicine. Here, we used next-generation sequencing technology to comprehensively compare amniotic stromal cells (ASCs) with chorionic stromal cells (CSCs) at the molecular and signaling levels. Principal component analysis showed a clear dichotomy of gene expression profiles between ASCs and CSCs. Unsupervised hierarchical clustering confirmed that the biological repeats of ASCs and CSCs were able to respectively group together. Supervised analysis identified differentially expressed genes, such as LMO3, HOXA11, and HOXA13, and differentially expressed isoforms, such as CXCL6 and HGF. Gene Ontology (GO) analysis showed that the GO terms of the extracellular matrix, angiogenesis, and cell adhesion were significantly enriched in CSCs. We further explored the factors associated with inflammation and angiogenesis using a multiplex assay. In comparison with ASCs, CSCs secreted higher levels of angiogenic factors, including angiogenin, VEGFA, HGF, and bFGF. The results of a tube formation assay proved that CSCs exhibited a strong angiogenic function. However, ASCs secreted two-fold more of an anti-inflammatory factor, TSG-6, than CSCs. In conclusion, our study demonstrated the differential gene expression patterns between ASCs and CSCs. CSCs have superior angiogenic potential, whereas ASCs exhibit increased anti-inflammatory properties.

Regional variations in ABC transporter expression along the mouse intestinal tract

2004 ◽  
Vol 17 (1) ◽  
pp. 11-20 ◽  
Author(s):  
David M. Mutch ◽  
Pascale Anderle ◽  
Muriel Fiaux ◽  
Robert Mansourian ◽  
Karine Vidal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abc Transporter ◽  
Expression Profile ◽  
Abc Transporters ◽  
Intestinal Tract ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Assessment Model ◽  
Differentially Expressed ◽  
Distal Intestine

The ATP-binding cassette (ABC) family of proteins comprise a group of membrane transporters involved in the transport of a wide variety of compounds, such as xenobiotics, vitamins, lipids, amino acids, and carbohydrates. Determining their regional expression patterns along the intestinal tract will further characterize their transport functions in the gut. The mRNA expression levels of murine ABC transporters in the duodenum, jejunum, ileum, and colon were examined using the Affymetrix MuU74v2 GeneChip set. Eight ABC transporters (Abcb2, Abcb3, Abcb9, Abcc3, Abcc6, Abcd1, Abcg5, and Abcg8) displayed significant differential gene expression along the intestinal tract, as determined by two statistical models (a global error assessment model and a classic ANOVA, both with a P < 0.01). Concordance with semiquantitative real-time PCR was high. Analyzing the promoters of the differentially expressed ABC transporters did not identify common transcriptional motifs between family members or with other genes; however, the expression profile for Abcb9 was highly correlated with fibulin-1, and both genes share a common complex promoter model involving the NFκB, zinc binding protein factor (ZBPF), GC-box factors SP1/GC (SP1F), and early growth response factor (EGRF) transcription binding motifs. The cellular location of another of the differentially expressed ABC transporters, Abcc3, was examined by immunohistochemistry. Staining revealed that the protein is consistently expressed in the basolateral compartment of enterocytes along the anterior-posterior axis of the intestine. Furthermore, the intensity of the staining pattern is concordant with the expression profile. This agrees with previous findings in which the mRNA, protein, and transport function of Abcc3 were increased in the rat distal intestine. These data reveal regional differences in gene expression profiles along the intestinal tract and demonstrate that a complete understanding of intestinal ABC transporter function can only be achieved by examining the physiologically distinct regions of the gut.

scholarly journals A Branching Process to Characterize the Dynamics of Stem Cell Differentiation

2015 ◽  
Author(s):  
david miguez
Keyword(s):  
Mathematical Model ◽  
Cell Cycle ◽  
Stem Cell ◽  
Cycle Length ◽  
Branching Process ◽  
Stem Cell Differentiation ◽  
Stem Cell Population ◽  
Mathematical Framework ◽  
Average Cell ◽  
Cell Cycle Length

The understanding of the regulatory processes that orchestrate stem cell maintenance is a cornerstone in developmental biology. Here, we present a mathematical model based on a branching process formalism that predicts average rates of proliferative and differentiative divisions in a given stem cell population. In the context of vertebrate spinal neurogenesis, the model predicts complex non-monotonic variations in the rates of pp, pd and dd modes of division as well as in cell cycle length, in agreement with experimental results. Moreover, the model shows that the differentiation probability follows a binomial distribution, allowing us to develop equations to predict the rates of each mode of division. A phenomenological simulation of the developing spinal cord informed with the average cell cycle length and division rates predicted by the mathematical model reproduces the correct dynamics of proliferation and differentiation in terms of average numbers of progenitors and differentiated cells. Overall, the present mathematical framework represents a powerful tool to unveil the changes in the rate and mode of division of a given stem cell pool by simply quantifying numbers of cells at different times.

scholarly journals Is gene expression among women with rheumatoid arthritis dysregulated during a postpartum flare?

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Matthew Wright ◽  
Mette K. Smed ◽  
J. Lee Nelson ◽  
Jørn Olsen ◽  
Merete L. Hetland ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Disease Activity ◽  
Activity Index ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Time Frame ◽  
Differentially Expressed ◽  
Healthy Women ◽  
Immune Related Genes

Abstract Background To evaluate our hypotheses that, when rheumatoid arthritis (RA) flares postpartum, gene expression patterns are altered compared to (a) healthy women, (b) RA women whose disease activity is low or in remission postpartum, and (c) pre-pregnancy expression profiles. Methods Twelve women with RA and five healthy women were included in this pilot study. RA disease activity and postpartum flare were assessed using the Clinical Disease Activity Index (CDAI). Total RNA from frozen whole blood was used for RNA sequencing. Differential gene expression within the same women (within-group) over time, i.e., postpartum vs. third trimester (T3) or pre-pregnancy (T0), were examined, using a significance threshold of q < 0.05 and fold-change ≥ 2. Results Nine of the women with RA experienced a flare postpartum (RAFlare), while three had low disease activity or were in remission (RANoFlare) during that time frame. Numerous immune-related genes were differentially expressed postpartum (vs. T3) during a flare. Fold-changes in expression from T3 to postpartum were mostly comparable between the RAFlare and healthy groups. At 3 months postpartum, compared to healthy women, several genes were significantly differentially expressed only among the RAFlare women, and not among the RANoFlare women. Some of these genes were among those whose “normal” expression was significantly modulated postpartum, and the postpartum expression patterns were significantly altered during the RA flare. There were also some genes that were significantly differentially expressed in RAFlare compared to both healthy and RANoFlare women, even though their expression was not significantly modulated postpartum. Furthermore, while postpartum expression profiles were similar to those at pre-pregnancy among healthy women, significant differences were found between those time points among the RAFlare women. Conclusions The large majority of gene expression changes between T3 and 3 months postpartum among RA women who flared postpartum reflected normal postpartum changes also seen among healthy women. Nonetheless, during a postpartum flare, a set of immune-related genes showed dysregulated expression compared to healthy women and women with RA whose disease activity was low or in remission during the same time frame, while other genes demonstrated significant differences in expression compared to RA pre-pregnancy levels.

scholarly journals Comparative Transcriptome Analysis Suggests Key Roles for 5-Hydroxytryptamlne Receptors in Control of Goose Egg Production

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 455 ◽  
Author(s):  
Qingyuan Ouyang ◽  
Shenqiang Hu ◽  
Guosong Wang ◽  
Jiwei Hu ◽  
Jiaman Zhang ◽  
...  
Keyword(s):  
Egg Production ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Production Performance ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Anser Anser

To date, research on poultry egg production performance has only been conducted within inter or intra-breed groups, while those combining both inter- and intra-breed groups are lacking. Egg production performance is known to differ markedly between Sichuan white goose (Anser cygnoides) and Landes goose (Anser anser). In order to understand the mechanism of egg production performance in geese, we undertook this study. Here, 18 ovarian stromal samples from both Sichuan white goose and Landes goose at the age of 145 days (3 individuals before egg production initiation for each breed) and 730 days (3 high- and low egg production individuals during non-laying periods for each breed) were collected to reveal the genome-wide expression profiles of ovarian mRNAs and lncRNAs between these two geese breeds at different physiological stages. Briefly, 58, 347, 797, 777, and 881 differentially expressed genes (DEGs) and 56, 24, 154, 105, and 224 differentially expressed long non-coding RNAs (DElncRNAs) were found in LLD vs. HLD (low egg production Landes goose vs. high egg production Landes goose), LSC vs. HSC (low egg production Sichuan White goose vs. high egg production Sichuan white goose), YLD vs. YSC (young Landes goose vs. young Sichuan white goose), HLD vs. HSC (high egg production Landes goose vs. high egg production Sichuan white goose), and LLD vs. LSC (low egg production Landes goose vs. low egg production Sichuan white goose) groups, respectively. Functional enrichment analysis of these DEGs and DElncRNAs suggest that the “neuroactive ligand–receptor interaction pathway” is crucial for egg production, and particularly, members of the 5-hydroxytryptamine receptor (HTR) family affect egg production by regulating ovarian metabolic function. Furthermore, the big differences in the secondary structures among HTR1F and HTR1B, HTR2B, and HTR7 may lead to their different expression patterns in goose ovaries of both inter- and intra-breed groups. These results provide novel insights into the mechanisms regulating poultry egg production performance.

171 THE EFFECT OF TRICHOSTATIN A ON THE DEVELOPMENT AND THE GLOBAL GENE EXPRESSION PATTERNS IN MOUSE EMBRYOS DEVELOPING IN VITRO

2008 ◽  
Vol 20 (1) ◽  
pp. 165
Author(s):  
X. S. Cui ◽  
X. Y. Li ◽  
T. Kim ◽  
N.-H. Kim
Keyword(s):  
Gene Expression ◽  
Trichostatin A ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Mouse Embryos ◽  
Differentially Expressed ◽  
Gene Expression Patterns ◽  
Cell Stage

Trichostatin A (TSA) is an inhibitor of histone deacetylase and is able to alter gene expression patterns by interfering with the removal of acetyl groups from histones. The aim of this study was to determine the effect of TSA treatment on the development and gene expression patterns of mouse zygotes developing in vitro. The addition of 100 nm TSA to the culture medium did not affect the cleavage of mouse embryos (TSA treatment, 148/150 (99%) v. control, 107/107 (100%)); however, embryos that were treated with TSA arrested at the 2-cell stage (145/148, 98%). We estimated the number of nuclei in control and TSA-treated embryos by propidium iodide staining, taking into account the presence of any cells with two or more nuclei. At 62–63 h post-hCG stimulation, control zygotes had developed to the 4-cell stage and exhibited one nucleus in each blastomere, indicative of normal development. In contrast, we observed tetraploid nuclei in at least one blastomere in 20.8% (11/53) of the embryos that had been treated with TSA. At 28–29 h post-hCG stimulation (metaphase of the 1-cell stage), there was no difference in the mitotic index (as determined by analyzing the microtubule configuration) in the TSA group compared to the control group. At the 2-cell stage, however, we did not observe mitotic spindles and metaphase chromatin in embryos in the TSA treatment group compared to the controls. Interestingly, when embryos were cultured in TSA-free medium from 35 h post-hCG stimulation (S- or early G2-phase of the 2-cell stage) onward, almost all of them (47/50) developed to the blastocyst stage. In contrast, when embryos were cultured in TSA-free medium from 42 h post-hCG stimulation (middle G2-phase of the 2-cell stage) onward, they did not develop to the 4-cell stage. We used Illumina microarray technology to analyze the gene expression profiles in control and TSA-treated late 2-cell-stage embryos. Applied Biosystems Expression System software was used to extract assay signals and assay signal-to-noise ratio values from the microarray images. Our data showed that 897 genes were significantly (P < 0.05; 2-sample t-test) up- or down-regulated by TSA treatment compared to controls. Analysis using the PANTHER classification system (https://panther.appliedbiosystems.com) revealed that the 575 genes that were differentially expressed in the TSA group compared to the control were classified as being associated with putative biological processes or molecular function. Overall, in terms of putative biological processes, more nucleoside, nucleotide, and nucleic acid metabolism, protein metabolism and modification, signal transduction, developmental process, and cell cycle genes were differentially expressed between the TSA and control groups. In terms of putative molecular function, more nucleic acid-binding transcription factor and transferase genes were differentially expressed between the groups. The results collectively suggest that inhibition of histone acetylation in mouse embryos affects gene expression profiles at the time of zygotic genome activation, and this subsequently affects further development.

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