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Luo Q, Maity AK, Teschendorff AE. Distance covariance entropy reveals primed states and bifurcation dynamics in single-cell RNA-Seq data. iScience 2022; 25:105709. [PMID: 36578319 PMCID: PMC9791356 DOI: 10.1016/j.isci.2022.105709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/08/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Cell-fate transitions are fundamental to development and differentiation. Studying them with single-cell omic data is important to advance our understanding of the cell-fate commitment process, yet this remains challenging. Here we present a computational method called DICE, which analyzes the entropy of expression covariation patterns and which is applicable to static and dynamically changing cell populations. Using only single-cell RNA-Seq data, DICE is able to predict multipotent primed states and their regulatory factors, which we subsequently validate with single-cell epigenomic data. DICE reveals that primed states are often defined by epigenetic regulators or pioneer factors alongside lineage-specific transcription factors. In developmental time course single-cell RNA-Seq datasets, DICE can pinpoint the timing of bifurcations more precisely than lineage-trajectory inference algorithms or competing variance-based methods. In summary, by studying the dynamic changes of expression covariation entropy, DICE can help elucidate primed states and bifurcation dynamics without the need for single-cell epigenomic data.
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Affiliation(s)
- Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Alok K. Maity
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China,Corresponding author
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2
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Chakraborty S, Shapiro LC, de Oliveira S, Rivera-Pena B, Verma A, Shastri A. Therapeutic targeting of the inflammasome in myeloid malignancies. Blood Cancer J 2021; 11:152. [PMID: 34521810 PMCID: PMC8440507 DOI: 10.1038/s41408-021-00547-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 12/16/2022] Open
Abstract
Even though genetic perturbations and mutations are important for the development of myeloid malignancies, the effects of an inflammatory microenvironment are a critical modulator of carcinogenesis. Activation of the innate immune system through various ligands and signaling pathways is an important driver of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). The DAMPs, or alarmins, which activate the inflammasome pathway via the TLR4/NLR signaling cascade causes the lytic cell death of hematopoietic stem and progenitor cells (HSPCs), ineffective hematopoiesis, and β-catenin-induced proliferation of cancer cells, leading to the development of MDS/AML phenotype. It is also associated with other myeloid malignancies and involved in the pathogenesis of associated cytopenias. Ongoing research suggests the interplay of inflammasome mediators with immune modulators and transcription factors to have a significant role in the development of myeloid diseases, and possibly therapy resistance. This review discusses the role and importance of inflammasomes and immune pathways in myeloid malignancies, particularly MDS/AML, to better understand the disease pathophysiology and decipher the scope of therapeutic interventions.
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Affiliation(s)
- Samarpana Chakraborty
- Division of Hemato-Oncology, Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Lauren C Shapiro
- Division of Hemato-Oncology, Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Montefiore Medical Center, Bronx, NY, 10461, USA
| | - Sofia de Oliveira
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Medicine (Hepatology), Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Bianca Rivera-Pena
- Division of Hemato-Oncology, Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Amit Verma
- Division of Hemato-Oncology, Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Montefiore Medical Center, Bronx, NY, 10461, USA
| | - Aditi Shastri
- Division of Hemato-Oncology, Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Montefiore Medical Center, Bronx, NY, 10461, USA.
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Bokes P, King JR. Limit-cycle oscillatory coexpression of cross-inhibitory transcription factors: a model mechanism for lineage promiscuity. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2019; 36:113-137. [PMID: 30869799 DOI: 10.1093/imammb/dqy003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/29/2018] [Indexed: 12/12/2022]
Abstract
Lineage switches are genetic regulatory motifs that govern and maintain the commitment of a developing cell to a particular cell fate. A canonical example of a lineage switch is the pair of transcription factors PU.1 and GATA-1, of which the former is affiliated with the myeloid and the latter with the erythroid lineage within the haematopoietic system. On a molecular level, PU.1 and GATA-1 positively regulate themselves and antagonize each other via direct protein-protein interactions. Here we use mathematical modelling to identify a novel type of dynamic behaviour that can be supported by such a regulatory architecture. Guided by the specifics of the PU.1-GATA-1 interaction, we formulate, using the law of mass action, a system of differential equations for the key molecular concentrations. After a series of systematic approximations, the system is reduced to a simpler one, which is tractable to phase-plane and linearization methods. The reduced system formally resembles, and generalizes, a well-known model for competitive species from mathematical ecology. However, in addition to the qualitative regimes exhibited by a pair of competitive species (exclusivity, bistable exclusivity, stable-node coexpression) it also allows for oscillatory limit-cycle coexpression. A key outcome of the model is that, in the context of cell-fate choice, such oscillations could be harnessed by a differentiating cell to prime alternately for opposite outcomes; a bifurcation-theory approach is adopted to characterize this possibility.
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Affiliation(s)
- Pavol Bokes
- Department of Applied Mathematics and Statistics, Comenius University, Bratislava, Slovakia
| | - John R King
- School of Mathematical Sciences and SBRC Nottingham, University of Nottingham, Nottingham, United Kingdom
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Nené NR, Rivington J, Zaikin A. Sensitivity of asymmetric rate-dependent critical systems to initial conditions: Insights into cellular decision making. Phys Rev E 2018; 98:022317. [PMID: 30253525 DOI: 10.1103/physreve.98.022317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 11/07/2022]
Abstract
The work reported here aims to address the effects of time-dependent parameters and stochasticity on decision making in biological systems. We achieve this by extending previous studies that resorted to simple bifurcation normal forms, although in the present case we focus primarily on the issue of the system's sensitivity to initial conditions in the presence of two different noise distributions, Gaussian and Lévy. In addition, we also assess the impact of two-way sweeping at different rates through the critical region of a canonical Pitchfork bifurcation with a constant external asymmetry. The parallel with decision making in biocircuits is performed on this simple system since it is equivalent in its available states and dynamics to more complex genetic circuits published previously. Overall we verify that rate-dependent effects, previously reported as being important features of bifurcating systems, are specific to particular initial conditions. Processing of each starting state, which for the normal form underlying this study is akin to a classification task, is affected by the balance between sweeping speed through critical regions and the type of fluctuations added. For the heavy-tailed noise, two-way dynamic bifurcations are more efficient in processing the external signals, here understood to be jointly represented by the critical parameter profile and the external asymmetry amplitude, when compared to the system relying on escape dynamics. This is particular to the case when the system starts at an attractor not favored by the asymmetry and, in conjunction, when the sweeping amplitude is large.
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Affiliation(s)
- Nuno R Nené
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, United Kingdom.,Institute for Women's Health, University College London, Gower Street, WC1E 6BT London, United Kingdom
| | - James Rivington
- Department of Mathematics, University College London, Gower Street, WC1E 6BT London, United Kingdom
| | - Alexey Zaikin
- Institute for Women's Health, University College London, Gower Street, WC1E 6BT London, United Kingdom.,Department of Mathematics, University College London, Gower Street, WC1E 6BT London, United Kingdom.,Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
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A Regulated Double-Negative Feedback Decodes the Temporal Gradient of Input Stimulation in a Cell Signaling Network. PLoS One 2016; 11:e0162153. [PMID: 27584002 PMCID: PMC5008701 DOI: 10.1371/journal.pone.0162153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 08/18/2016] [Indexed: 11/23/2022] Open
Abstract
Revealing the hidden mechanism of how cells sense and react to environmental signals has been a central question in cell biology. We focused on the rate of increase of stimulation, or temporal gradient, known to cause different responses of cells. We have investigated all possible three-node enzymatic networks and identified a network motif that robustly generates a transient or sustained response by acute or gradual stimulation, respectively. We also found that a regulated double-negative feedback within the motif is essential for the temporal gradient-sensitive switching. Our analysis highlights the essential structure and mechanism enabling cells to properly respond to dynamic environmental changes.
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Nouri M, Deezagi A, Ebrahimi M. Reprogramming of human peripheral blood monocytes to erythroid lineage by blocking of the PU-1 gene expression. Ann Hematol 2016; 95:549-56. [PMID: 26758270 DOI: 10.1007/s00277-015-2583-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/23/2015] [Indexed: 11/26/2022]
Abstract
In hematopoietic system development, PU.1 and GATA-1 as lineage-specific transcription factors (TF) are expressed in common myeloid progenitors. The cross antagonism between them ascertains gene expression programs of monocytic and erythroid cells, respectively. This concept in transdifferentiation approaches has not been well considered yet, especially in intralineage conversion systems. To demonstrate whether PU.1 suppression induces monocyte lineage conversion into red blood cells, a combination of three PU.1-specific siRNAs was implemented to knock down PU.1 gene expression and generate the balance in favor of GATA-1 expression to induce erythroid differentiation. For this purpose, monocytes were isolated from human peripheral blood and transfected by PU.1 siRNAs. In transfected monocytes, the rate of PU.1 expression in mRNA level was significantly decreased until 0.38 ± 0.118 when compared to untreated monocytes at 72 h (p value ≤0.05) which resulted in significant overexpression of GATA1 of 16.1 ± 0.343-fold compared to the untreated group (p value ≤0.01). Subsequently, overexpression of hemoglobin (α 13.26 ± 1.34-fold; p value≤0.0001) and β-globin (37.55 ± 16.56-fold; p value≤0.0001) was observed when compared to control groups. The results of western immunoblotting confirm those findings too. While, reduced expression of monocyte, CD14 gene, was observed in qRT-PCR and flow cytometry results. Our results suggest that manipulating the ratio of the two TFs in bifurcation differentiation pathways via applying siRNA technology can possibly change the cells' fate as a safe way for therapeutics application.
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Affiliation(s)
- Masoumeh Nouri
- Department of Molecular Medicine and Biochemistry, National Institute of Genetic Engineering and Biotechnology Km. 17, Karaj-Tehran freeway Pajouhesh Blvd., P.O.Box 14155-6343, Tehran, Iran
| | - Abdolkhalegh Deezagi
- Department of Molecular Medicine and Biochemistry, National Institute of Genetic Engineering and Biotechnology Km. 17, Karaj-Tehran freeway Pajouhesh Blvd., P.O.Box 14155-6343, Tehran, Iran.
| | - Marzieh Ebrahimi
- Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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Ashwin P, Zaikin A. Pattern selection: the importance of "how you get there". Biophys J 2015; 108:1307-1308. [PMID: 25809241 DOI: 10.1016/j.bpj.2015.01.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/16/2015] [Indexed: 12/01/2022] Open
Affiliation(s)
- Peter Ashwin
- Centre for Systems, Dynamics and Control, University of Exeter, Exeter, United Kingdom
| | - Alexey Zaikin
- Institute for Women's Heaalth, University College London, London, United Kingdom; Department of Mathematics, University College London, London, United Kingdom; Lobachevsky State University of Nizhniy Novgorod, Nizhniy Novgorod, Russia.
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Rabajante JF, Babierra AL. Branching and oscillations in the epigenetic landscape of cell-fate determination. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:240-249. [DOI: 10.1016/j.pbiomolbio.2015.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 01/05/2015] [Accepted: 01/18/2015] [Indexed: 12/15/2022]
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Affiliation(s)
- Ramit Mehr
- Computational Immunology Lab, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan , Israel
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