Programming cell growth into different cluster shapes using diffusible signals

Advances in genetic engineering technologies have allowed the construction of artificial genetic circuits, which have been used to generate spatial patterns of differential gene expression. However, the question of how cells can be programmed, and how complex the rules need to be, to achieve a desired tissue morphology has received less attention. Here, we address these questions by developing a mathematical model to study how cells can collectively grow into clusters with different structural morphologies by secreting diffusible signals that can influence cellular growth rates. We formulate how growth regulators can be used to control the formation of cellular protrusions and how the range of achievable structures scales with the number of distinct signals. We show that a single growth inhibitor is insufficient for the formation of multiple protrusions but may be achieved with multiple growth inhibitors, and that other types of signals can regulate the shape of protrusion tips. These examples illustrate how our approach could potentially be used to guide the design of regulatory circuits for achieving a desired target structure.

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Programming cell growth into different cluster shapes using diffusible signals

10.1101/2020.08.29.273607 ◽

2020 ◽

Author(s):

Yipei Guo ◽

Mor Nitzan ◽

Michael P. Brenner

Keyword(s):

Growth Regulators ◽

Growth Inhibitor ◽

Spatial Arrangement ◽

Cell Types ◽

Growth Inhibitors ◽

Genetic Circuits ◽

Regulatory Circuits ◽

Differential Gene ◽

Different Shapes ◽

Different Cell Types

Recent advances in genetic engineering technologies has made it possible to construct artificial genetic circuits and use them to control how cells respond to their surroundings. This has been used to generate spatial patterns of differential gene expression. In addition to the spatial arrangement of different cell types, another important aspect of spatial structure lies in the overall shape of the group of cells. However, the question of how cells can be programmed, and how complex the rules need to be, to achieve a desired tissue morphology has received less attention. In this paper, we attempt to address these questions by developing a mathematical model to study how cells can use diffusion-mediated local rules to grow into clusters with different shapes. Within our model, cells are allowed to secrete diffusible chemicals which can either directly regulate the growth rate of cells (‘growth regulator’), or indirectly affect growth by changing the secretion rate or the effect of other growth regulators. We find that (1) a single growth inhibitor can be used to grow a rod-like structure, (2) multiple growth regulators are required to grow multiple protrusions, and (3) the length and shape of each protrusion can be controlled using growth-threshold regulators. Based on these regulatory schemes, we also postulate how the range of achievable structures scales with the number of signals: (A) the maximum possible number of protrusions increases exponentially with the number of growth inhibitors involved, and (B) to control the growth of each set of protrusions, it is necessary to have an independent threshold regulator. Together, these experimentally-testable findings illustrate how our approach can be used to guide the design of regulatory circuits for achieving a desired target structure.

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Effects of Static Magnetic Field on Cell Growth, Viability, and Differential Gene Expression in Salmonella

Foodborne Pathogens and Disease ◽

10.1089/fpd.2008.0244 ◽

2009 ◽

Vol 6 (5) ◽

pp. 547-552 ◽

Cited By ~ 24

Author(s):

Alya El May ◽

Sarra Snoussi ◽

Najla Ben Miloud ◽

Imed Maatouk ◽

Hafedh Abdelmelek ◽

...

Keyword(s):

Gene Expression ◽

Magnetic Field ◽

Cell Growth ◽

Differential Gene Expression ◽

Static Magnetic Field ◽

Differential Gene

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Cellular Growth Arrest and Efflux Pumps Are Associated With Antibiotic Persisters in Streptococcus pyogenes Induced in Biofilm-Like Environments

Frontiers in Microbiology ◽

10.3389/fmicb.2021.716628 ◽

2021 ◽

Vol 12 ◽

Author(s):

Caroline Lopes Martini ◽

Amada Zambrana Coronado ◽

Maria Celeste Nunes Melo ◽

Clarice Neffa Gobbi ◽

Úrsula Santos Lopez ◽

...

Keyword(s):

Gene Expression ◽

Cell Growth ◽

Streptococcus Pyogenes ◽

Protein Biosynthesis ◽

Efflux Pumps ◽

Resistance Mechanisms ◽

Cellular Growth ◽

Abiotic Surfaces ◽

Invasive Infections ◽

Group A

Streptococcus pyogenes (group A Streptococcus-GAS) is an important pathogen for humans. GAS has been associated with severe and invasive diseases. Despite the fact that these bacteria remain universally susceptible to penicillin, therapeutic failures have been reported in some GAS infections. Many hypotheses have been proposed to explain these antibiotic-unresponsive infections; however, none of them have fully elucidated this phenomenon. In this study, we show that GAS strains have the ability to form antimicrobial persisters when inoculated on abiotic surfaces to form a film of bacterial agglomerates (biofilm-like environment). Our data suggest that efflux pumps were possibly involved in this phenomenon. In fact, gene expression assays by real-time qRT-PCR showed upregulation of some genes associated with efflux pumps in persisters arising in the presence of penicillin. Phenotypic reversion assay and whole-genome sequencing indicated that this event was due to non-inherited resistance mechanisms. The persister cells showed downregulation of genes associated with protein biosynthesis and cell growth, as demonstrated by gene expression assays. Moreover, the proteomic analysis revealed that susceptible cells express higher levels of ribosome proteins. It is remarkable that previous studies have reported the recovery of S. pyogenes viable cells from tissue biopsies of patients presented with GAS invasive infections and submitted to therapy with antibiotics. The persistence phenomenon described herein brings new insights into the origin of therapeutic failures in S. pyogenes infections. Multifactorial mechanisms involving protein synthesis inhibition, cell growth impairment and efflux pumps seem to play roles in the formation of antimicrobial persisters in S. pyogenes.

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Differential Gene Expression Patterns and Interaction Networks in BCR/ABL Positive and Negative Adult Acute Lymphoblastic Leukemias.

Blood ◽

10.1182/blood.v108.11.1836.1836 ◽

2006 ◽

Vol 108 (11) ◽

pp. 1836-1836

Author(s):

Dejan Juric ◽

Norman J. Lacayo ◽

Meghan C. Ramsey ◽

Janis Racevskis ◽

Peter H. Wiernik ◽

...

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Expression Profiles ◽

Lymphoblastic Leukemia ◽

Expression Patterns ◽

Cellular Growth ◽

Interaction Networks ◽

Pcr Analysis ◽

Interaction Patterns ◽

Differential Gene

Abstract BCR/ABL is associated with an unfavorable prognosis in adults with acute lymphoblastic leukemia (ALL). We used DNA microarrays to identify gene expression profiles and molecular interaction networks related to BCR/ABL status and clinical outcome in a set of 54 adult ALL specimens from the MRC UKALL XII/ECOG E2993 intergroup study (21 p185BCR/ABL- and 16 p210BCR/ABL-positive and 17 BCR/ABL negative). In order to avoid biases associated with commonly used sample amplification procedures, we have implemented an indirect two-step labeling protocol based on signal amplification by use of dendrimer technology. Using a two-class, non-parametric t-test and a false discovery rate cutoff of 5%, we identified 271 genes (including GAB1, CIITA, XBP1, CD83, SERPINB9, PTP4A3, NOV, LOX, CTNND1, BAALC and RAB21) as differentially expressed in BCR/ABL positive ALL compared with BCR/ABL negative ALL. They separate these two classes of adult ALL with an overall accuracy of 93% and are enriched for three highly relevant biological functions: Cellular Growth and Proliferation (57 genes, p = 0.004–0.044), Cell Death (49 genes, p = 0.0007–0.049), and Hematological System Development and Function (40 genes, p = 0.00004–0.049). Network analysis demonstrated complex interaction patterns of these genes, and identified FYN and IL15 as the hubs of the top-scoring network. We confirmed these findings by both qRT-PCR analysis of the initial set of samples and by cross-platform validation in an independent cohort of 128 adult ALL specimens. In addition, within the BCR/ABL positive subgroup, we identified 14 clones found to be over-expressed (TSPAN16, ADAMTSL4) or under-expressed (PILRB, STS-1, SPRY1) in p185BCR-ABL- relative to p210BCR-ABL-ALL. In a nearest-centroid classification, these clones correctly predict the BCR/ABL subtype with a cross-validated prediction accuracy of 95%. No differential gene expression was detected among Rho family GTPases and their known interaction partners. Finally, we constructed a gene expression- and interaction-based outcome predictor consisting of 27 genes (including GRB2, GAB1, GLI1, IRS1, RUNX2 and SPP1), which strongly correlated with overall survival in BCR/ABL positive adult ALL (p=0.0001), independently of other clinical parameters such as age (p=0.25) and white blood cell count at presentation (p = 0.003). These findings may be useful for developing novel therapeutic targets and prognostic markers in adult ALL.

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ORNITHINE DECARBOXYLASE GENE EXPRESSION IN HUMAN LUNG ADENOCARCINOMA CELL (A549) TREATED WITH POMEGRANATE JUICE

Jurnal Teknologi ◽

10.11113/jt.v77.6746 ◽

2015 ◽

Vol 77 (25) ◽

Author(s):

Radiah Abdul Ghani ◽

Nik Nurasyikin Nik Abdul Malek ◽

Najwa Farhah Md. Yusof ◽

Elyna Fatini Jamil

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Cell Growth ◽

Ornithine Decarboxylase ◽

Quantitative Polymerase Chain Reaction ◽

A549 Cells ◽

Cellular Growth ◽

Pomegranate Juice ◽

Trypan Blue Exclusion ◽

Cancer Management

The polyamine biosynthesis pathway plays a significant role in cell growth, both normal and malignant. As polyamines are crucial in cellular growth and differentiation, they are linked to the development of cancer, with higher polyamine level observed in cancerous cells than in healthy cells. Accordingly, suppressing the polyamine pathway has been found to disrupt tumour development. Chemoprevention is considered a more feasible option in cancer management than chemotherapy, with a focus on natural chemopreventive agent. Pomegranate is known to inhibit several progression of lung cancer, although prior studies on the chemopreventive effect of pomegranate on lung cancer did not explore into polyamine pathway. Hence, this study investigated the effect of pomegranate juice on the polyamine pathway, by focusing on the biosynthesis involving ornithine decarboxylase (ODC), the rate limiting enzyme in the pathway. Quantitative polymerase chain reaction (qPCR) was applied to quantify the changes in ODC gene expression in A549 cells treated with pomegranate. The inhibition of growth was determined using Trypan Blue exclusion and the changes in intracellular polyamine in pomegranate treated cells was observed using High Performance Liquid Chromatography (HPLC). It was found that there was inhibition of A549 cell growth and reduced in intracellular polyamine content in pomegranate treated cells. The ODC expression was significantly inhibited compared to untreated cells, with a 48-fold difference. While this finding supports the hypothesis, there is much yet to be elucidated regarding its exact mechanism.

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Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis

Genes ◽

10.3390/genes11080884 ◽

2020 ◽

Vol 11 (8) ◽

pp. 884

Author(s):

Dominique J. Wiener ◽

Kátia R. Groch ◽

Magdalena A.T. Brunner ◽

Tosso Leeb ◽

Vidhya Jagannathan ◽

...

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Transcriptome Profiling ◽

Structure And Function ◽

Hair Follicles ◽

Cellular Growth ◽

Genes Encoding ◽

Interfollicular Epidermis ◽

Differential Gene ◽

And Function

The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were evaluated. Transcriptome profiling revealed that late anagen follicles expressed mainly keratins and telogen follicles expressed GSN and KRT15. The interfollicular epidermis expressed predominately genes encoding for proteins associated with differentiation. All sample groups express genes encoding for proteins involved in cellular growth and signal transduction. The expression pattern of skin-associated genes in dogs is similar to humans. Differences in expression compared to mice and humans include BMP2 expression mainly in telogen and high KRT17 expression in the interfollicular epidermis of dogs. Our data provide the basis for the investigation of the structure and function of canine skin or skin disease and support the use of dogs as a model for human cutaneous disease by assigning gene expression to specific tissue states.

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Generating complex patterns of gene expression without regulatory circuits

10.1101/2020.11.25.398248 ◽

2020 ◽

Author(s):

Sahil B. Shah ◽

Alexis M. Hill ◽

Claus O. Wilke ◽

Adam J. Hockenberry

Keyword(s):

Gene Expression ◽

Genome Engineering ◽

Expression Patterns ◽

Fine Tuning ◽

Genetic Circuits ◽

Viral Genomes ◽

Regulatory Circuits ◽

Degradation Rates ◽

Changes Over Time ◽

Genetic Constructs

AbstractSynthetic biology has successfully advanced our ability to design complex, time-varying genetic circuits executing precisely specified gene expression patterns. However, such circuits usually require regulatory genes whose only purpose is to regulate the expression of other genes. When designing very small genetic constructs, such as viral genomes, we may want to avoid introducing such auxiliary gene products. To this end, here we demonstrate that varying only the placement and strengths of promoters, terminators, and RNase cleavage sites in a computational model of a bacteriophage genome is sufficient to achieve solutions to a variety of basic expression patterns. We discover these solutions by computationally evolving genomes to reproduce desired target expression patterns. Our approach shows non-trivial patterns can be evolved, including patterns in which the relative ordering of genes by abundance changes over time. We find that some patterns are easier to evolve than others, and different genomes that express comparable expression patterns may differ in their genetic architecture. Our work opens up a novel avenue to genome engineering via fine-tuning the balance of gene expression and gene degradation rates.

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Same same but different: Cluster architecture variation in five ‘Pinot Noir’ clonal selection lines correlates with differential expression of three transcription factors and further growth related genes

10.1101/2020.03.17.993907 ◽

2020 ◽

Author(s):

Robert Richter ◽

Susanne Rossmann ◽

Doreen Gabriel ◽

Reinhard Töpfer ◽

Klaus Theres ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Differential Gene Expression ◽

Fungal Infections ◽

Clonal Selection ◽

Pinot Noir ◽

Cellular Growth ◽

Wine Production ◽

Cluster Architecture ◽

Differential Gene

AbstractGrapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid losses caused by fungal infections. Grapevine cultivars with loose cluster architecture enable to reduce protective chemical treatments due to their enhanced resilience against fungal infections such as Botrytis cinerea induced grey mold. A recent study identified transcription factor gene VvGRF4 as determinant of inflorescence structure in exemplary samples of loose and compact quasi-isogenic ‘Pinot Noir’ clones. Here, we extended the analysis to 12 differently clustered ‘Pinot Noir’ clones originating from five different clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons in demonstrative vineyards. Two phenotypically contrasting clones were grown at all three locations and served for standardization of downstream analyses. Differential gene expression data were correlated to the phenotypic variation of cluster architecture sub-traits. A consistent differential gene expression of VvGRF4 in relation to loose clusters was verified over the different environments and in the extended set of ‘Pinot Noir’ clones. In addition, 14 more genes with consistent expression differences between loosely and compactly clustered clones independent from season and location were identified. These genes show annotations related to cellular growth, cell wall extension, cell division and auxin metabolism. They include two more transcription factor genes.

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