by Keyword: Transcription factor

Astro, V, Ramirez-Calderon, G, Pennucci, R, Caroli, J, Saera-Vila, A, Cardona-Londono, K, Forastieri, C, Fiacco, E, Maksoud, F, Alowaysi, M, Sogne, E, Falqui, A, Gonzalez, F, Montserrat, N, Battaglioli, E, Mattevi, A, Adamo, A, (2022). Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism Iscience 25, 104665

The histone demethylase KDM1A is a multi- faceted regulator of vital developmental processes, including mesodermal and cardiac tube formation during gastrulation. However, it is unknown whether the fine-tuning of KDM1A splicing isoforms, already shown to regulate neuronal maturation, is crucial for the specification and maintenance of cell identity during cardiogenesis. Here, we discovered a temporal modulation of ubKDM1A and KDM1A+2a during human and mice fetal cardiac development and evaluated their impact on the regulation of cardiac differentiation. We revealed a severely impaired cardiac differentiation in KDM1A(-/-) hESCs that can be rescued by re-expressing ubKDM1A or catalytically impaired ubKDM1A-K661A, but not by KDM1A+2a or KDM1A+2a-K661A. Conversely, KDM1A+2a(-/-) hESCs give rise to functional cardiac cells, displaying increased beating amplitude and frequency and enhanced expression of critical cardiogenic markers. Our findings prove the existence of a divergent scaffolding role of KDM1A splice variants, independent of their enzymatic activity, during hESC differentiation into cardiac cells.

JTD Keywords: Bhlh transcription factor, Corest, Differentiation, Dna, Embryonic stem-cells, Heart, Lsd1, Phosphorylation, Proteins, Swirm domain

Aydin, Onur, Passaro, Austin P., Raman, Ritu, Spellicy, Samantha E., Weinberg, Robert P., Kamm, Roger D., Sample, Matthew, Truskey, George A., Zartman, Jeremiah, Dar, Roy D., Palacios, Sebastian, Wang, Jason, Tordoff, Jesse, Montserrat, Nuria, Bashir, Rashid, Saif, MTaher A., Weiss, Ron, (2022). Principles for the design of multicellular engineered living systems Apl Bioengineering 6, 010903

Remarkable progress in bioengineering over the past two decades has enabled the formulation of fundamental design principles for a variety of medical and non-medical applications. These advancements have laid the foundation for building multicellular engineered living systems (M-CELS) from biological parts, forming functional modules integrated into living machines. These cognizant design principles for living systems encompass novel genetic circuit manipulation, self-assembly, cell–cell/matrix communication, and artificial tissues/organs enabled through systems biology, bioinformatics, computational biology, genetic engineering, and microfluidics. Here, we introduce design principles and a blueprint for forward production of robust and standardized M-CELS, which may undergo variable reiterations through the classic design-build-test-debug cycle. This Review provides practical and theoretical frameworks to forward-design, control, and optimize novel M-CELS. Potential applications include biopharmaceuticals, bioreactor factories, biofuels, environmental bioremediation, cellular computing, biohybrid digital technology, and experimental investigations into mechanisms of multicellular organisms normally hidden inside the “black box” of living cells.

JTD Keywords: cell-fate specification, endothelial-cells, escherichia-coli, extracellular-matrix, gene-expression noise, nuclear hormone-receptors, pluripotent stem-cells, primitive endoderm, transcription factors, Artificial tissues, Assembly cells, Biological parts, Biological systems, Bioremediation, Blood-brain-barrier, Cell engineering, Cell/matrix communication, Design principles, Environmental technology, Functional modules, Fundamental design, Genetic circuits, Genetic engineering, Living machines, Living systems, Medical applications, Molecular biology, Synthetic biology

Zañudo JGT, Mao P, Alcon C, Kowalski K, Johnson GN, Xu G, Baselga J, Scaltriti M, Letai A, Montero J, Albert R, Wagle N, (2021). Cell line-specific network models of er breast cancer identify potential pi3kainhibitor resistance mechanisms and drug combinations Cancer Research 81, 4603-4617

Durable control of invasive solid tumors necessitates identifying therapeutic resistance mechanisms and effective drug combinations. In this work, we used a network-based mathematical model to identify sensitivity regulators and drug combinations for the PI3Ka inhibitor alpelisib in estrogen receptor positive (ER) PIK3CAmutant breast cancer. The model-predicted efficacious combination of alpelisib and BH3 mimetics, for example, MCL1 inhibitors, was experimentally validated in ER breast cancer cell lines. Consistent with the model, FOXO3 downregulation reduced sensitivity to alpelisib, revealing a novel potential resistance mechanism. Cell line-specific sensitivity to combinations of alpelisib and BH3 mimetics depended on which BCL2 family members were highly expressed. On the basis of these results, newly developed cell line-specific network models were able to recapitulate the observed differential response to alpelisib and BH3 mimetics. This approach illustrates how network-based mathematical models can contribute to overcoming the challenge of cancer drug resistance.

JTD Keywords: activation, akt, feedback, foxo, leads, p27(kip1), phosphorylation, reveals, transcription factors, Dependent kinase inhibitor

Watt, AC, Cejas, P, DeCristo, MJ, Metzger, O, Lam, EYN, Qiu, XT, BrinJones, H, Kesten, N, Coulson, R, Font-Tello, A, Lim, K, Vadhi, R, Daniels, VW, Montero, J, Taing, L, Meyer, CA, Gilan, O, Bell, CC, Korthauer, KD, Giambartolomei, C, Pasaniuc, B, Seo, JH, Freedman, ML, Ma, CT, Ellis, MJ, Krop, I, Winer, E, Letai, A, Brown, M, Dawson, MA, Long, HW, Zhao, JJ, Goel, S, (2021). CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity Nature Cancer 2, 34-+

Goel and colleagues show that CDK4/6 inhibition induces global chromatin changes mediated by AP-1 factors, which mediate key biological and clinical effects in breast cancer. Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) were designed to induce cancer cell cycle arrest. Recent studies have suggested that these agents also exert other effects, influencing cancer cell immunogenicity, apoptotic responses and differentiation. Using cell-based and mouse models of breast cancer together with clinical specimens, we show that CDK4/6 inhibitors induce remodeling of cancer cell chromatin characterized by widespread enhancer activation, and that this explains many of these effects. The newly activated enhancers include classical super-enhancers that drive luminal differentiation and apoptotic evasion, as well as a set of enhancers overlying endogenous retroviral elements that are enriched for proximity to interferon-driven genes. Mechanistically, CDK4/6 inhibition increases the level of several activator protein-1 transcription factor proteins, which are in turn implicated in the activity of many of the new enhancers. Our findings offer insights into CDK4/6 pathway biology and should inform the future development of CDK4/6 inhibitors.

JTD Keywords: Abemaciclib, Androgen receptor, Animal experiment, Animal model, Animal tissue, Apoptosis, Article, Breast cancer, C-jun, Cancer cell, Carcinoembryonic antigen related cell adhesion molecule 1, Caspase 3, Cell cycle arrest, Cells, Chromatin, Chromatin immunoprecipitation, Controlled study, Cyclin dependent kinase 4, Cyclin dependent kinase 6, Dna damage, Epidermal growth factor receptor 2, Estrogen receptor, Female, Flow cytometry, Fulvestrant, Hla drb1 antigen, Human, Human cell, Immunoblotting, Immunogenicity, Immunoprecipitation, Interferon, Luciferase assay, Mcf-7 cell line, Mda-mb-231 cell line, Microarray analysis, Morphogenesis, Mouse, Nonhuman, Palbociclib, Protein, Protein expression, Rb, Resistance, Rna polymerase ii, Rna sequence, Selective-inhibition, Senescence, Short tandem repeat, Signal transduction, Tamoxifen, Transcription elongation, Transcription factor, Transcription factor ap 1, Transcriptome, Tumor biopsy, Tumor differentiation, Tumor spheroid, Tumor xenograft, Vinculin, Whole exome sequencing

Torrents, Eduard, (2014). Ribonucleotide reductases: Essential Enzymes for bacterial life Frontiers in Cellular and Infection Microbiology , 4, 1-9

Ribonucleotide reductase (RNR) is a key enzyme that mediates the synthesis of deoxyribonucleotides, the DNA precursors, for DNA synthesis in every living cell. This enzyme converts ribonucleotides to deoxyribonucleotides, the building blocks for DNA replication, and repair. Clearly, RNR enzymes have contributed to the appearance of genetic material that exists today, being essential for the evolution of all organisms on Earth. The strict control of RNR activity and dNTP pool sizes is important, as pool imbalances increase mutation rates, replication anomalies, and genome instability. Thus, RNR activity should be finely regulated allosterically and at the transcriptional level. In this review we examine the distribution, the evolution, and the genetic regulation of bacterial RNRs. Moreover, this enzyme can be considered an ideal target for anti-proliferative compounds designed to inhibit cell replication in eukaryotic cells (cancer cells), parasites, viruses, and bacteria.

JTD Keywords: Anaerobiosis, Transcription Factors, Evolution, Gene regulation, Ribonucleotide reductase, DNA Synthesis, NrdR,nrd

Pairo, E., Marco, S., Perera, A., (2010). A subspace method for the detection of transcription factor binding sites BIOINFORMATICS 2010. Proceedings of the First International Conference on Bioinformatics BIOINFORMATICS 2010. First International Conference on Bioinformatics (ed. Fred, A., Filipe, J., Gamboa, H.), INSTICC Press (Valencia, Spain) , 102-107

Transcription Factor binding sites are short and degenerate sequences, located mostly at the promoter of the gene, where some proteins bind in order to regulate transcription. Locating these sequences is an important issue, and many experimental and computational methods have been developed. Algorithms to search binding sites are usually based on Position Specific Scoring Matrices (PSSM), where each position is treated independently. Mapping symbolical DNA to numerical sequences, a detector has been built with a Principal Component Analysis of the numerical sequences, taking into account covariances between positions. When a treatment of missing values is incorporated the Q-residuals detector, based on PCA, performs better than a PSSM algorithm. The performance on the detector depends on the estimation of missing values and the percentage of missing values considered in the model.

JTD Keywords: Binding sites, BPCA, Missing values, Numerical DNA, Principal components analysis, Transcription factors

Pairo, E., Marco, S., Perera, A., (2009). A preliminary study on the detection of transcription factor binding sites Biosignals 2009: Proceedings of the International Conference on Bio-Inspired Systems and Signal Processing 2nd International Conference on Bio-Inspired Systems and Signal Processing (ed. Encarnacao, P., Veloso, A.), Insticc-Inst Syst Technologies Information Control & Communication (Oporto, Portugal) , 506-509

Transcription starts when multiple proteins, known as transcription factors recognize and bind to transcription start site in DNA sequences. Since mutation in transcription factor binding sites are known to underlie diseases it remains a major challenge to identify these binding sites. Conversion from symbolic DNA to numerical sequences and genome data make it possible to construct a detector based on a numerical analysis of DNA binding sites. A subspace model for the TFBS is built. TFBS will show a very small distance to this particular subspace. Using this distance binding sites are distinguished from random sequences and from genome data.

JTD Keywords: Transcription factors, Binding sites, Principal components analysis