scholarly journals Gene expression rearrangements denoting changes in the biological state

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Augusto Gonzalez ◽  
Joan Nieves ◽  
Dario A. Leon ◽  
Maria Luisa Bringas Vega ◽  
Pedro Valdes Sosa

AbstractIn many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may be the result of a selective pressure, as in the Long Term Evolution Experiment with E. Coli populations, or the progression to Alzheimer disease in aged brains, or the progression from a normal tissue to the cancer state. The first two cases seem to belong to a class of transitions, where the initial and final states are relatively close to each other, and the distribution function for the differential expressions is short ranged, with a tail of only a few dozens of strongly varying genes. In the latter case, cancer, the initial and final states are far apart and separated by a low-fitness barrier. The distribution function shows a very heavy tail, with thousands of silenced and over-expressed genes. We characterize the biological states by means of their principal component representations, and the expression distribution functions by their maximal and minimal differential expression values and the exponents of the Pareto laws describing the tails.

2015 ◽  
Author(s):  
Caroline B. Turner ◽  
Zachary D. Blount ◽  
Daniel H. Mitchell ◽  
Richard E. Lenski

Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following evolution of a novel function in the long-term evolution experiment (LTEE) withEscherichia coli. A characteristic feature ofE. coliis its inability to consume citrate aerobically. However, that ability evolved in one of the LTEE populations. In this population, citrate-utilizing bacteria (Cit+) coexisted stably with another clade of bacteria that lacked the capacity to utilize citrate (Cit−). This coexistence was shaped by the evolution of a cross-feeding relationship in which Cit+cells released the dicarboxylic acids succinate, fumarate, and malate into the medium, and Cit−cells evolved improved growth on these carbon sources, as did the Cit+cells. Thus, the evolution of citrate consumption led to a flask-based ecosystem that went from a single limiting resource, glucose, to one with five resources either shared or partitioned between two coexisting clades. Our findings show how evolutionary novelties can change environmental conditions, thereby facilitating diversity and altering both the structure of an ecosystem and the evolutionary trajectories of coexisting organisms.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 105-105
Author(s):  
Jennifer Tsai ◽  
Kelsey R. Logas ◽  
Lauren D. Van Wassenhove ◽  
Beruh Dejene ◽  
Che-Hong Chen ◽  
...  

HSC loss in FA is due to failure to resolve DNA inter-strand crosslinks (ICL), which can be induced by reactive aldehydes, radiation, or other clastogenic agents. Aldehyde exposure may occur through environmental sources, e.g. ingestion, absorption, and inhalation, or endogenously as a byproduct of cellular metabolism. The ALDH2*2 genotype, a dominant-negative point mutation in the aldehyde dehydrogenase 2 (ALDH2) gene, causes the "Asian flushing syndrome" when ethanol (EtOH) is ingested, due to decreased metabolism of small aldehydes, particularly acetaldehyde. ALDH2*2 is a disease modifier in FA, causing more rapid bone marrow failure and earlier leukemia onset in doubly affected children. Similarly, mice experimentally doubly knocked out for FANCD2 and ALDH2 demonstrate increased HSC loss, which is accelerated by EtOH exposure. To reduce aldehyde exposure, we developed a small molecule ALDH activator, Alda-1, which increases the enzymatic activity of both wild type (WT) and mutant ALDH2. We hypothesized that DNA damage and HSC loss in FA would be prevented by reduction of the aldehyde load. To test the effects of Alda-1 mediated ALDH2 activation, we generated a novel murine FA model with FANCD2 KO and knock-in of the ALDH2*2 mutation into the murine locus. The FANCD2-/- ALDH2*1/*2 genetic model and parental controls were then tested after exogenous aldehydic challenge and/or therapeutic intervention with Alda-1. Increased aldehydic load was experimentally induced by EtOH administration 10 mg/kg/day IP, while Alda-1 10 ug/kg/day was continuously administered via osmotic pump. For each of these conditions, marrow was analyzed for HSC and progenitor cell (HSPC) number, HSC gene expression, and function. The importance of the altered aldehyde metabolism due to ALDH2*2 genotype was demonstrated by progressive loss of HSPC in ALDH2*2/*2 and FANCD2-/- ALDH2*1/*2 mice, e.g., 5-fold and 2-fold decline in long-term HSC (LT-HSC), respectively, by 36 weeks. Experimental EtOH challenge to increase the aldehyde load precipitously decreased HSC numbers of all genotypes. After 5 weeks of EtOH challenge, LT-HSC decreased 35-fold in FANCD2-/- ALDH2*1/*2, 12.5-fold in FANCD2-/-ALDH2*1/*1, and 10.5-fold in WT mice. Long-term Alda-1 treatment to decrease aldehydic load rescued FA mice from HSC loss. After 7 months of Alda-1 treatment, LT-HSC numbers in FANCD2-/-ALDH2*1/*2 and FANCD2-/-ALDH2*1/*1 were approximately 10-fold higher than untreated controls. There were no clinically observed adverse effects. Aldehyde exposure and Alda-1 treatment altered gene expression of HSC. Principal component analysis and clustering of HSC gene expression showed that the first principal component representing 40% of the variation in gene expression could be attributed to increased aldehydic load, either genetically (ALDH2*2 genotype) or environmentally (EtOH administration) induced, while Alda-1 treatment obviated these effects. HSC from Alda-1 treated mice clustered with those from control WT mice. To test whether Alda-1 improved HSC function as well as phenotypic number, engraftment potential was assessed with competitive repopulation assays of sorted HSC from congenic untreated donors vs short-term (3 weeks) Alda-1 treated donors. HSC from Alda-1 treated mice had 2-4 fold greater granulocyte repopulating capacity than those from the untreated donors. Our results demonstrate that Alda-1 treatment rescues HSC from aldehyde induced loss, whether from genetic variation (FANCD2- and/or ALDH2*2) or experimental challenge (EtOH administration). Furthermore, Alda-1 treatment prevents the abnormal HSC gene expression induced by increased aldehydic load. HSC function is improved by Alda-1 with greater repopulating capacity observed even after short-term treatment. These preclinical experiments provide compelling proof-of-concept that sustained activation of ALDH2 can prevent HSC loss in FA. Potential applications include long-term administration to prevent the development of marrow failure or leukemia, and HSC expansion to increase the number of cells available for gene therapy with autologous HSC. Our results suggest that a clinical trial of ALDH2 activation in FA patients to prevent marrow failure is warranted. Disclosures Van Wassenhove: U.S. Patent Office: Patents & Royalties: patent pending - submitted for ALDH2 activators to expand hematopoietic stem cells. Chen:Foresee Pharmaceuticals: Patents & Royalties: patents licensed to Foresee related to compounds that activate aldehyde dehydrogenase 2 (ALDH2) and correct the dysfunction in ALDH2*2; U.S. Patent Office: Patents & Royalties: patent pending - submitted for aldehyde dehydrogenase 2 (ALDH2) activators to expand hematopoietic stem cells. Mochly-Rosen:Foresee Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Patents & Royalties: patents licensed to Foresee related to compounds that activate aldehyde dehydrogenase 2 (ALDH2) and correct the dysfunction in ALDH2*2; U.S. Patent Office: Patents & Royalties: patent pending - submitted for aldehyde dehydrogenase 2 (ALDH2) activators to expand hematopoietic stem cells. Weinberg:U.S. Patent Office: Patents & Royalties: patent pending - submitted for aldehyde dehydrogenase 2 (ALDH2) activators to expand hematopoietic stem cells.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2695-2695
Author(s):  
Silvia Bresolin ◽  
Luca Trentin ◽  
Geertruy Kronnie ◽  
Laura Sainati ◽  
Marco Zecca ◽  
...  

Abstract Myelodysplatic syndromes (MDS) are rare malignant haematopoietic stem cell disorders in children. They have the propensity to transform into acute myeloid leukemia and, for this reason they can be considered as a pre-leukemia condition. In this study we analyzed the gene expression profile (GEP) of a large cohort of pediatric patients: 14 MDS [6 refractory cytopenias (RC), 6 refractory anemias with excess blasts (RAEB) and 2 refractory anemias with excess blasts in transformation (RAEB-t)], 50 de-novo acute myeloid leukemia (AML) and 6 normal bone marrow (BM) aspirates. Furthermore, in 5 cases, samples were available for analysis both at diagnosis and at time of secondary AML progression. Gene expression analysis was performed on the Affymetrix HG U133 Plus 2.0 oligonucleotide microarrays using Partek software packages and the leukemia classifier version 7(LCver7). Statistical analyses were performed to determine the correlation between the gene expression signature and MDS subtype. Unsupervised hierarchical clustering analysis separated the majority of MDS cases from the diagnostic AML samples and placed the normal BM specimens into the MDS cluster. Remarkably, all the MDS cases that evolved into an AML within one year, except one, clustered together inside the diagnostic AML group. Performing principal component analysis (PCA) we observed that MDS samples were clustered between the group of normal BM and AML samples. Moreover the RC samples were located proximal to the cluster of normal BM samples while RAEB and RAEB-t specimens were nearest to the AML samples cluster (Fig 1). Further, we classified the MDS samples using the LCver7 classifier, an algorithm developed inside the MILE (Microarray Innovation In LEukemia) study that gives an overall cross-validation accuracy of >95% for distinct sub-classes of pediatric and adult leukemias using gene expression profiles. The 14 MDS samples had 57.2 % and 42.8 % AML and non AML-like signatures, respectively. The Fisher exact test showed that there was a statistical concordance (p=0.008) between the FAB classification and the gene expression signature. In fact, 83% of RC patients had a non AML-like signature whereas only 17% had an AML-like signature. On the contrary 85% of the RAEB and RAEB-t patients had an AML-like signature. In conclusion, the results of unsupervised analysis not only demonstrated that gene expression technology is able to distinguish between MDS, AML and normal BM samples but, in addition, GEP can identify an AML-like signature in samples at diagnosis of MDS, with a higher risk of AML-evolution, allowing to identify a group of patients that could be eligible for a more intensive treatment. Fig.1. Principal component analysis (PCA) of MDS, AML and normal BM samples. Red: MDS samples, Blue: de novo AML, Green: secondary AML, Violet: normal BM. RC samples are placed closer to the normal BM specimens. The three MDS patients that will evolve into secondary AML are included into the green ellipsoids. Fig.1. Principal component analysis (PCA) of MDS, AML and normal BM samples. Red: MDS samples, Blue: de novo AML, Green: secondary AML, Violet: normal BM. RC samples are placed closer to the normal BM specimens. The three MDS patients that will evolve into secondary AML are included into the green ellipsoids.


2020 ◽  
Vol 295 (35) ◽  
pp. 12355-12367
Author(s):  
Josh McQuail ◽  
Amy Switzer ◽  
Lynn Burchell ◽  
Sivaramesh Wigneshweraraj

The initial adaptive responses to nutrient depletion in bacteria often occur at the level of gene expression. Hfq is an RNA-binding protein present in diverse bacterial lineages that contributes to many different aspects of RNA metabolism during gene expression. Using photoactivated localization microscopy and single-molecule tracking, we demonstrate that Hfq forms a distinct and reversible focus-like structure in Escherichia coli specifically experiencing long-term nitrogen starvation. Using the ability of T7 phage to replicate in nitrogen-starved bacteria as a biological probe of E. coli cell function during nitrogen starvation, we demonstrate that Hfq foci have a role in the adaptive response of E. coli to long-term nitrogen starvation. We further show that Hfq foci formation does not depend on gene expression once nitrogen starvation has set in and occurs indepen-dently of the transcription factor N-regulatory protein C, which activates the initial adaptive response to N starvation in E. coli. These results serve as a paradigm to demonstrate that bacterial adaptation to long-term nutrient starvation can be spatiotemporally coordinated and can occur independently of de novo gene expression during starvation.


2020 ◽  
Author(s):  
Yasser Perera ◽  
Augusto Gonzalez ◽  
Rolando Perez

AbstractProstate cancer is a highly heterogeneous disease and the second more common tumor in males. Molecular and genetic profiles are currently used to identify subtypes and to guide therapeutic intervention. However, roughly 26% of primary prostate cancers of both good and poor prognosis is driven by unknown molecular lesions. Thus, ongoing research aims at providing better prognostic biomarkers and causal molecular alterations to intervene. Here, we use Principal Component Analysis (PCA) and custom RNAseq-data normalization to identify a gene expression signature which segregates primary PRAD from normal tissues. This Core-Expression Signature (PRAD-CES) includes 33 genes and accounts for 39% of data complexity along what we call the PC1-cancer axis. The PRAD-CES is populated by protein-coding (AMACR, TP63, HPN) and RNA-genes (PCA3, ARLN1) sparsely found in previous studies, others with validated/predicted roles as biomarkers (HOXC6, TDRD1, DLX1), and/or cancer drivers (PCA3, ARLN1, PCAT-14). Of note, the PRAD-CES also comprises six over-expressed LncRNAs with no previous association with Pca biology. Overall, the PCA allows us to capture roughly 3/4 of data complexity in the first eight PCs, whereas PC1, PC2 and PC3 altogether comprise 57% of such variability. Finally, GO enrichment analysis and PCs correlation with major PRAD clinical features (i.e. Gleason Score, AR Score, TMPRSS2-ERG fusions and Tumor Cellularity) suggest that PC2 and PC3 gene signatures might describe more aggressive and inflammation-prone transitional forms of PRAD with infiltrating immunosystem. The list of surfaced genes may entails putative novel prognostic biomarkers and/or molecular alterations to intervene.


2020 ◽  
Author(s):  
Briana G. Nixon ◽  
Fengshen Kuo ◽  
Ming Liu ◽  
Kristelle Capistrano ◽  
Mytrang Do ◽  
...  

SummaryTumor progression is associated with overstimulation of cytotoxic T lymphocytes (CTLs), resulting in a dysfunctional state of exhaustion. How T cell exhaustion is elicited in the tumor remains poorly understood. Here we show that tumor-associated macrophages (TAMs) present cancer cell antigen and induce CTL exhaustion through a gene expression program dependent on the transcription factor interferon regulatory factor-8 (IRF8). In a transgenic model of murine breast cancer, CTL priming was supported by IRF8-dependent dendritic cells; yet, CTL exhaustion required TAM expression of IRF8, and its ablation suppressed tumor growth. An analysis of the highly immune-infiltrated human renal cell carcinoma tumors revealed abundant TAMs that expressed IRF8 and were enriched for an IRF8 gene expression signature. The IRF8 signature co-segregated with T cell exhaustion markers and was negatively associated with long-term patient survival. Thus, CTL exhaustion is promoted by TAMs via IRF8, and this crosstalk may be disrupted in TAM-targeted therapies.


2016 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Philip J. Hatcher ◽  
Anna G. Green ◽  
Barry L. Williams ◽  
Debora S. Marks ◽  
...  

AbstractBacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that are fast evolving in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. We identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to fine-tune protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to the long sweep of its evolution in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.Competing Interests StatementWe, the authors, declare that we have no conflicts of interest.


2019 ◽  
Vol 20 (7) ◽  
pp. 1581 ◽  
Author(s):  
Lucie Janeckova ◽  
Klara Kostovcikova ◽  
Jiri Svec ◽  
Monika Stastna ◽  
Hynek Strnad ◽  
...  

Commensal microbiota contribute to gut homeostasis by inducing transcription of mucosal genes. Analysis of the impact of various microbiota on intestinal tissue provides an important insight into the function of this organ. We used cDNA microarrays to determine the gene expression signature of mucosa isolated from the small intestine and colon of germ-free (GF) mice and animals monoassociated with two E. coli strains. The results were compared to the expression data obtained in conventionally reared (CR) mice. In addition, we analyzed gene expression in colon organoids derived from CR, GF, and monoassociated animals. The analysis revealed that the complete absence of intestinal microbiota mainly affected the mucosal immune system, which was not restored upon monoassociation. The most important expression changes observed in the colon mucosa indicated alterations in adipose tissue and lipid metabolism. In the comparison of differentially expressed genes in the mucosa or organoids obtained from GF and CR mice, only six genes were common for both types of samples. The results show that the increased expression of the angiopoietin-like 4 (Angptl4) gene encoding a secreted regulator of lipid metabolism indicates the GF status.


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