Biosimulation Using the Cellworks Computational Omics Biology Model (CBM) Identifies Genomic and Molecular Markers for Decitabine (DAC) Plus Valproic-Acid (VPA) Treatment Response in Patients with Myelodysplastic Syndromes (MDS)

Abstract Background: DNA methyltransferase inhibition (DNMTi) with hypomethylating agents (HMA), azacitidine (AZA) or decitabine (DAC), remains the mainstay of therapy for most high-risk Myelodysplastic syndrome (MDS) patients. However, only 40-50% of MDS patients achieve clinical improvement with DNMTi. Previously, combinations of HMA and histone deacetylase (HDAC) inhibitors have been explored in MDS with varying clinical outcomes. However, the heterogeneity of genomic aberrations in MDS portend widely divergent responses from HDAC inhibition, implying that a predictive clinical decision support tool could select patients most likely to benefit from this combination. We explored the molecular basis of observed clinical response in a group of patients treated with DAC and Valproic-Acid (VPA). Method: 16 MDS patients with known clinical responses to DAC + VPA were selected for study from the Cellworks patient repository. The aberration and copy number variations from individual cases served as input into the Computational Omics Biology Model, a computational multi-omic biology software model largely created using literature sourced from PubMed, to generate a patient-specific protein network map. Disease biomarkers unique to each patient were identified within these maps. The Cellworks Biosimulation Platform has the capacity to biosimulate disease phenotypic behavior and was used to create a patient-specific disease model. Biosimulations were then conducted on each patient-specific disease model to measure the effect of DAC + VPA according to a cell growth score. This score was comprised of a composite of cell proliferation, viability, apoptosis, metastasis, and other cancer hallmarks. Biosimulation of drug response was conducted to identify and predict therapeutic efficacy. Results: In the biosimulation, VPA is a relatively weak HDAC inhibitor, but it also inhibits GSK3B and in turn increases beta-catenin (CTNNB1) levels. Additionally, monosomy 7 associated with loss of CAV1, HIPK2, and TRRAP also causes high CTNNB1, thereby further contributing to drug resistance. Biosimulation correctly identified that 7 of 8 patients with these genomic findings were clinical non-responders (NR) to VPA, indicating that CTNNB1 status is likely to predict treatment failure from the VPA + HMA combination in this disease. Notably, CTNNB1 levels have been reported to foster an immune-evasive tumor microenvironment resistant to CTL activation. By contrast, high levels of c-MYC predict response to VPA + HMA combination. VPA inhibits MYC transcription and thereby reduces MYC-induced downregulation of p21 through CKS1B. Additionally MYC is a transcriptional regulator of DNMT1 which is degraded after hyperacetylation induced by HDAC3 inhibition suggesting that VPA also enhances DNMT1 turnover. One patient analyzed had trisomy 8 resulting in c-MYC over-expression and responded to HMA + VPA. Additionally, other aberrations enhancing c-MYC transcription such as copy number variant (CNV) loss of MXI1, HHEX, FBXW7, SMAD7 or CNV gain of BRD4, BCL7B led to high clinical response to the combination (Table 1). By comparison to the CTNNB1-driven subset, the impact of VPA on CTNNB1 in the MYC-dominant disease network did not negate the benefit of VPA for these patients. Additionally, the inhibition of GSK3B by VPA leading to diminished FBXW7 and less ubiquitin-mediated turnover of c-MYC was not sufficient to overcome the inhibition of MYC transcription and HDAC3i-mediated turnover. Immune activation has become a recognized mechanism of responsiveness to HMA. However, among patients with upregulated CTNNB1, VPA is likely to further decrease response to treatment. By contrast, among MYC-driven cancers that are typically immune-evasive, VPA appears to be a vital mechanism of overcoming MYC-driven immune evasion. Conclusion: Signaling pathway consequences related to CTNNB1 and c-MYC upregulation predict response to DAC + VPA. Although HMA plus HDAC inhibition can be generally beneficial for MDS, variable mechanisms of action among various HDAC inhibitors and unique patient disease characteristics should be considered for optimal treatment selection. Finally, CTNNB1 emerged from the Cellworks biosimulations as a therapeutically relevant target in MDS that determines whether VPA synergizes or antagonizes the effect of other agents in this challenging subtype of MDS. Figure 1 Figure 1. Disclosures Castro: Caris Life Sciences Inc.: Consultancy; Omicure Inc: Consultancy; Cellworks Group Inc.: Current Employment; Exact sciences Inc.: Consultancy; Guardant Health Inc.: Speakers Bureau; Bugworks: Consultancy. Kumar: Cellworks Group Inc.: Current Employment. Grover: Cellworks Group Inc.: Current Employment. Patil: Cellworks Group Inc.: Current Employment. Kapoor: Cellworks Group Inc.: Current Employment. Agrawal: Cellworks Group Inc.: Current Employment. Sauban: Cellworks Group Inc.: Current Employment. Prasad: Cellworks Group Inc.: Current Employment. Basu: Cellworks Group Inc.: Current Employment. Suseela: Cellworks Group Inc.: Current Employment. Kumar: Cellworks Group Inc.: Current Employment. Nair: Cellworks Group Inc.: Current Employment. Kumari: Cellworks Group Inc.: Current Employment. Pampana: Cellworks Group Inc.: Current Employment. Ullal: Cellworks Group Inc.: Current Employment. Azam: Cellworks Group Inc.: Current Employment. Prasad: Cellworks Group Inc.: Current Employment. Amara: Cellworks Group Inc.: Current Employment. Sahu: Cellworks Group Inc.: Current Employment. Raveendaran: Cellworks Group Inc.: Current Employment. Veedu: Cellworks Group Inc.: Current Employment. Mundkur: Cellworks Group Inc: Current Employment. Patel: Cellworks Group Inc.: Current Employment. Christie: Cellworks Group Inc.: Current Employment. Macpherson: Cellworks Group Inc.: Current Employment. Howard: Servier: Consultancy; Cellworks Group Inc.: Consultancy; Sanofi: Consultancy, Other: Speaker fees.

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Induced pluripotent stem cells in the study of a patient‐specific disease model for neurodevelopmental disorder

International Journal of Developmental Neuroscience ◽

10.1016/j.ijdevneu.2012.03.322 ◽

2012 ◽

Vol 30 (8) ◽

pp. 668-668

Keyword(s):

Stem Cells ◽

Induced Pluripotent Stem Cells ◽

Pluripotent Stem Cells ◽

Neurodevelopmental Disorder ◽

Disease Model ◽

Patient Specific ◽

Specific Disease ◽

Induced Pluripotent

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Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma

Neuro-Oncology ◽

10.1093/neuonc/noaa191 ◽

2020 ◽

Author(s):

Jonas Ecker ◽

Venu Thatikonda ◽

Gianluca Sigismondo ◽

Florian Selt ◽

Gintvile Valinciute ◽

...

Keyword(s):

Molecular Interaction ◽

Hdac Inhibitors ◽

Class I ◽

Chromatin Binding ◽

Hdac Inhibition ◽

Primary Tumors ◽

Chip Sequencing ◽

Class I Hdacs ◽

The Impact ◽

Selection Of

Abstract Background The sensitivity of myelocytomatosis oncogene (MYC) amplified medulloblastoma to class I histone deacetylase (HDAC) inhibition has been shown previously; however, understanding the underlying molecular mechanism is crucial for selection of effective HDAC inhibitors for clinical use. The aim of this study was to investigate the direct molecular interaction of MYC and class I HDAC2, and the impact of class I HDAC inhibition on MYC function. Methods Co-immunoprecipitation and mass spectrometry were used to determine the co-localization of MYC and HDAC2. Chromatin immunoprecipitation (ChIP) sequencing and gene expression profiling were used to analyze the co-localization of MYC and HDAC2 on DNA and the impact on transcriptional activity in primary tumors and a MYC amplified cell line treated with the class I HDAC inhibitor entinostat. The effect on MYC was investigated by quantitative real-time PCR, western blot, and immunofluorescence. Results HDAC2 is a cofactor of MYC in MYC amplified medulloblastoma. The MYC-HDAC2 complex is bound to genes defining the MYC-dependent transcriptional profile. Class I HDAC inhibition leads to stabilization and reduced DNA binding of MYC protein, inducing a downregulation of MYC activated genes (MAGs) and upregulation of MYC repressed genes (MRGs). MAGs and MRGs are characterized by opposing biological functions and by distinct enhancer-box distribution. Conclusions Our data elucidate the molecular interaction of MYC and HDAC2 and support a model in which inhibition of class I HDACs directly targets MYC’s transactivating and transrepressing functions.

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Abstract P023: HDAC Inhibition Promotes Cardiogenesis and the Survival of Embryonic Stem Cells Through Proteasome-Dependent Pathway

Circulation Research ◽

10.1161/res.109.suppl_1.ap023 ◽

2011 ◽

Vol 109 (suppl_1) ◽

Author(s):

Ting C Zhao ◽

Hongping Chen ◽

Megan DeNicola ◽

Yu Zhao ◽

Xin Qin ◽

...

Keyword(s):

Cell Death ◽

Sodium Butyrate ◽

Hdac Inhibitors ◽

Embryonic Stem ◽

Embryoid Bodies ◽

Luciferase Assay ◽

Hdac Inhibition ◽

Cardiac Lineage ◽

Proteasome Pathway ◽

The Impact

Objectives: Histone deacetylase (HDAC) inhibition plays a crucial role in mediating cardiogenesis and myocardial protection, whereas HDAC degradation has recently attracted attention in mediating the biological function of HDACs. However, it remains unknown whether HDAC inhibition modulates cardiogenesis and embryonic stem cell (ESC) survival through the proteasome pathway. Methods and Results: Using the well-established mouse CGR8 mouse ESC culture, we evaluated the impact of HDAC inhibition and proteasome pathway on the cell death, viability and apoptosis in ESCs in response to oxidant stress (100μ mol/L hydrogen peroxides). We demonstrated that HDAC inhibitors, both TSA (50 nmol/L) and sodium butyrate (200 μ mol/L) that causes the pronounced reduction of HDAC4 activity, decreased cell death and increased viability of ESCs. HDAC inhibition reduced the cleaved caspase 3, 6, 9, PARP and TUNE-positive ESCs, which were abrogated with MG132 (0.5 μ mol/L), a specific proteasome inhibitor. Furthermore, we employed in vitro “hanging drop” methods to carry out two weeks of embryoid bodies (EB) culture to assess the effect of HDAC inhibition and proteasome pathway on cardiogenesis. HDAC inhibition stimulates the growth of EB, which is associated with faster spontaneous rhythmic contraction. HDAC inhibition increased the up-regulation of GATA4, MEF2, NKX2.5, cardiac actin, and α-SMA mRNA and protein levels that were abrogated by MG132. Immunostaining analysis demonstrates that trichostatin A and sodium butyrate resulted in a significant increase in cardiac lineage commitments that were blocked by the proteasome inhibition. Notably, HDAC inhibitors led to noticeable HDAC4 degradation, which was effectively prevented by MG132. Luciferase assay demonstrates an activation of MEF2 cardiac transcriptional factor by HDAC inhibition, which was repressed by MG132, revealing that the degradation of HDAC4 allows the activation of MEF2. Conclusions: Taken together, our study is the first to demonstrate that HDAC inhibition through proteasome pathway forms a novel signaling to determine the cardiac lineage commitment and elicit the survival pathway, which is dependent on specific HDAC4 degradation and subsequent MEF2 activation of ESCs.

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Dysfunction of autophagy as the pathological mechanism of motor neuron disease based on a patient-specific disease model

Neuroscience Bulletin ◽

10.1007/s12264-015-1541-9 ◽

2015 ◽

Vol 31 (4) ◽

pp. 445-451 ◽

Cited By ~ 8

Author(s):

Dan-Jing Yang ◽

Liang Zhu ◽

Jie Ren ◽

Rong-Jie Ma ◽

Hongwen Zhu ◽

...

Keyword(s):

Motor Neuron ◽

Motor Neuron Disease ◽

Disease Model ◽

Patient Specific ◽

Specific Disease ◽

Pathological Mechanism

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HDAC Inhibitors, FK228 and Valproic Acid, Enhance the Effects of IL-3 or GMCSF on the Generation of Early Megakaryocytic as Well as Erythroid Precursors from Human Hematopoietic Precursors

Blood ◽

10.1182/blood.v112.11.5397.5397 ◽

2008 ◽

Vol 112 (11) ◽

pp. 5397-5397

Author(s):

Kohshi Ohishi ◽

Hyou Ryuu ◽

Kentaro Yamamura ◽

Masahiro Masuya ◽

Yuji Heike ◽

...

Keyword(s):

Valproic Acid ◽

Cell Population ◽

Cultured Cells ◽

Hdac Inhibitors ◽

Hdac Inhibition ◽

Gm Csf ◽

Peripheral Blood Cd34 ◽

Cd34 Cells ◽

Erythroid Precursors ◽

Initial Culture

Abstract We previously reported that HDAC inhibition by FK228 (depsipeptide) stimulates the proliferation of early erythroid precursors in the presence of IL-3. Here, we examined the effects of HDAC inhibition on human megakaryopoiesis. When G-CSF-mobilized peripheral blood CD34+ cells were incubated in serum-free liquid cultures containing SCF+IL-3 for 8–9 days, cultured cells were subdivided into 4 fractions with the expression of CD61 (GPIIIa) and glycophorin A (GPA). In the semisolid cultures containing SCF+TPO+EPO, CD61+GPA− cell population mainly gave rise to megakaryocytic colonies, while both of erythroid and megakaryocytic colonies were formed from CD61+GPA+ cell population. CD61−GPA+ cells exclusively generated erythroid colonies. After CD34+ cells were cultured with IL-3 or SCF+IL-3 for 8–9 days, addition of FK228 (0.4 ng/ml) to the cultures significantly increased the numbers of CD61+GPA− and CD61+GPA+ cells. Nevertheless, differentiation into CD61+CD42b+ more mature megakaryocytic cells was repressed by FK228. As expected, when cultured cells were replated in the secondary cultures containing SCF+TPO for another 7 days, higher number of CD61+CD42b+ mature megakaryocytic cells were developed in the cultures that had contained FK228 during the initial culture period. Stimulatory effects by FK228 on the generation of early megakaryocytic and erythroid precursors were also seen in the presence of GM-CSF. Moreover, we obtained similar findings with pharmacological concentration (100μg/ml) of valproic acid, which is also class I HDAC inhibitor. These data suggest a modulatory role for HDAC in the IL-3- or GM-CSF-mediated megakaryopoiesis and that the combinatory treatment with HDAC inhibitors and IL-3 or GM-CSF would be useful for stimulating early megakaryopoiesis as well as erythropoiesis in clinical settings.

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The impact of paralog genes: detection of copy number variation in spinal muscle atrophy patients

BIOCELL ◽

10.32604/biocell.2018.07016 ◽

2018 ◽

Vol 42 (3) ◽

pp. 87-91 ◽

Cited By ~ 1

Author(s):

Sergio LAURITO ◽

Juan A. CUETO ◽

Jimena PEREZ ◽

Mar韆 ROQU�

Keyword(s):

Copy Number Variation ◽

Muscle Atrophy ◽

Copy Number ◽

Number Variation ◽

The Impact

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Faculty Opinions recommendation of The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1158714.618930 ◽

2009 ◽

Author(s):

Michael Lassner ◽

Antoni Rafalski

Keyword(s):

Gene Expression ◽

Copy Number Variation ◽

Progenitor Cells ◽

Copy Number ◽

Hematopoietic Stem ◽

Stem And Progenitor Cells ◽

Number Variation ◽

The Impact

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Novel Conjugated Quinazolinone-Based Hydroxamic Acids: Design, Synthesis and Biological Evaluation

Medicinal Chemistry ◽

10.2174/1573406416666200420081540 ◽

2020 ◽

Vol 16 ◽

Author(s):

Tran Khac Vu ◽

Nguyen Thi Thanh ◽

Nguyen Van Minh ◽

Nguyen Huong Linh ◽

Nguyen Thi Phương Thao ◽

...

Keyword(s):

Drug Discovery ◽

Cell Lines ◽

Cancer Cell ◽

Hdac Inhibitors ◽

Cancer Cell Lines ◽

Hydroxamic Acids ◽

Biological Evaluation ◽

Hdac Inhibition ◽

Ic50 Value ◽

Mcf 7

Background: Target-based approach to drug discovery currently attracts a great deal of interest from medicinal chemists in anticancer drug discovery and development. Histone deacetylase (HDAC) inhibitors represent an extensive class of targeted anti-cancer agents. Among the most explored structure moieties, hydroxybenzamides and hydroxypropenamides have been demonstrated to have potential HDAC inhibitory effects. Several compounds of these structural classes have been approved for clinical uses to treat different types of cancer, such as vorinostat and belinostat. Aims: This study aims at developing novel HDAC inhibitors bearing conjugated quinazolinone scaffolds with potential cytotoxicity against different cancer cell lines. Method: A series of novel N-hydroxyheptanamides incorporating conjugated 6-hydroxy-2 methylquinazolin-4(3H)- ones (15a-l) was designed, synthesized and evaluated for HDAC inhibitory potency as well as cytotoxicity against three human cancer cell lines, including HepG-2, MCF-7 and SKLu-1. Molecular simulations were finally performed to gain more insight into the structure-activity. relationships. Results: It was found that among novel conjugated quinazolinone-based hydroxamic acids synthesized, compounds 15a, 15c and 15f were the most potent, both in terms of HDAC inhibition and cytotoxicity. Especially, compound 15f displayed up to nearly 4-fold more potent than SAHA (vorinostat) in terms of cytotoxicity against MCF-7 cell line with IC50 value of 1.86 µM, and HDAC inhibition with IC50 value of 6.36 µM. Docking experiments on HDAC2 isozyme showed that these compounds bound to HDAC2 with binding affinities ranging from -10.08 to -14.93 kcal/mol compared to SAHA (-15.84 kcal/mol). It was also found in this research that most of the target compounds seemed to be more cytotoxic toward SKLu-1than MCF-7 and HepG-2. Conclusion: The resesrch results suggest that some hydroxamic acids could emerge for further evaluation and the results are well served as basics for further design of more potent HDAC inhibitors and antitumor agents.

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Uncovering the Diversification of Tissue Engineering on the Emergent Areas of Stem Cells, Nanotechnology and Biomaterials

Current Stem Cell Research & Therapy ◽

10.2174/1574888x15666200103124821 ◽

2020 ◽

Vol 15 (3) ◽

pp. 187-201 ◽

Cited By ~ 1

Author(s):

Sunil K. Dubey ◽

Amit Alexander ◽

Munnangi Sivaram ◽

Mukta Agrawal ◽

Gautam Singhvi ◽

...

Keyword(s):

Tissue Engineering ◽

Stem Cells ◽

Immune System ◽

Clinical Application ◽

Cell Types ◽

Patient Specific ◽

Potential Strategy ◽

Induced Pluripotent ◽

Treat All ◽

The Impact

Damaged or disabled tissue is life-threatening due to the lack of proper treatment. Many conventional transplantation methods like autograft, iso-graft and allograft are in existence for ages, but they are not sufficient to treat all types of tissue or organ damages. Stem cells, with their unique capabilities like self-renewal and differentiate into various cell types, can be a potential strategy for tissue regeneration. However, the challenges like reproducibility, uncontrolled propagation and differentiation, isolation of specific kinds of cell and tumorigenic nature made these stem cells away from clinical application. Today, various types of stem cells like embryonic, fetal or gestational tissue, mesenchymal and induced-pluripotent stem cells are under investigation for their clinical application. Tissue engineering helps in configuring the stem cells to develop into a desired viable tissue, to use them clinically as a substitute for the conventional method. The use of stem cell-derived Extracellular Vesicles (EVs) is being studied to replace the stem cells, which decreases the immunological complications associated with the direct administration of stem cells. Tissue engineering also investigates various biomaterials to use clinically, either to replace the bones or as a scaffold to support the growth of stemcells/ tissue. Depending upon the need, there are various biomaterials like bio-ceramics, natural and synthetic biodegradable polymers to support replacement or regeneration of tissue. Like the other fields of science, tissue engineering is also incorporating the nanotechnology to develop nano-scaffolds to provide and support the growth of stem cells with an environment mimicking the Extracellular matrix (ECM) of the desired tissue. Tissue engineering is also used in the modulation of the immune system by using patient-specific Mesenchymal Stem Cells (MSCs) and by modifying the physical features of scaffolds that may provoke the immune system. This review describes the use of various stem cells, biomaterials and the impact of nanotechnology in regenerative medicine.

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