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Chauhan BK, Medsinge A, Scanga HL, Chu CT, Nischal KK. Transcriptome from opaque cornea of Fanconi anemia patient uncovers fibrosis and two connected players. Mol Genet Metab Rep 2021; 26:100712. [PMID: 33552906 PMCID: PMC7846932 DOI: 10.1016/j.ymgmr.2021.100712] [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: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 11/28/2022] Open
Abstract
Congenital corneal opacities (CCO) are a group of blinding corneal disorders, where the underlying molecular mechanisms are poorly understood. Phenotyping through specialized imaging and histopathology analysis, together with assessment of key transcriptomic changes (including glycosaminoglycan metabolic enzymes) in cornea(s) with CCO from a case of Fanconi anemia is the approach taken in this study to identify causal mechanisms. Based on our findings, we propose a novel mechanism and two key players contributing to CCO.
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Affiliation(s)
- Bharesh K Chauhan
- UPMC Eye Center, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.,Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Anagha Medsinge
- UPMC Eye Center, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Hannah L Scanga
- UPMC Eye Center, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Charleen T Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ken K Nischal
- UPMC Eye Center, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.,Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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2
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Zipporah E B, Patra B, Govarthanan K, Yadav R, Mohan S, Shyamsunder P, Verma RS. Defective cell proliferation is an attribute of overexpressed Notch1 receptor and impaired autophagy in Fanconi Anemia. Genomics 2020; 112:4628-4639. [PMID: 32800766 DOI: 10.1016/j.ygeno.2020.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/01/2020] [Accepted: 08/07/2020] [Indexed: 01/22/2023]
Abstract
Fanconi Anemia (FA) is an inherited bone marrow failure syndrome caused by mutation in FA pathway proteins, involved in Interstrand Cross Link (ICL) repair. FA cells exhibit in vitro proliferation arrest due to accumulated DNA damage, hence understanding the rescue mechanism that renders proliferation advantage is required. Gene expression profiling performed in FA patients Peripheral Blood Mononuclear Cells (PBMCs) revealed a wide array of dysregulated biological processes. Functional enrichment and gene clustering analysis showed crippled autophagy process and escalated Notch signalling pathway in FA clinical samples and cell lines. Notch pathway mediators overexpression were reverted in FANCA mutant cells when treated with Rapamycin, an autophagy inducer. Additionally, Rapamycin stabilized cell viability after treatment with the DNA damaging agent, MitomycinC (MMC) and enhanced cell proliferation genes expression in FANCA mutant cells. Inherently FANCA mutant cells express impaired autophagy; thus activation of autophagy channelizes Notch signalling cascade and sustains cell viability.
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Affiliation(s)
- Binita Zipporah E
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Bamadeb Patra
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Kavitha Govarthanan
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Rajesh Yadav
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Sheila Mohan
- Apollo Speciality hospital, 320 Padma complex, Anna Salai, Chennai 600 035, India; Registry for Fanconi Anemia in India (REFAIN), India
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 119077, Singapore
| | - Rama Shanker Verma
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India.
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Degan P, Cappelli E, Longobardi M, Pulliero A, Cuccarolo P, Dufour C, Ravera S, Calzia D, Izzotti A. A Global MicroRNA Profile in Fanconi Anemia: A Pilot Study. Metab Syndr Relat Disord 2018; 17:53-59. [PMID: 30376422 DOI: 10.1089/met.2018.0085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Fanconi anemia (FA) is a complex tumor-prone disease defined by an entangled genotype and phenotype. Despite enormous efforts in the last 20 years, a comprehensive and integrated view of the disease is still missing. The aim of this pilot study was to establish whether a global microRNA (miRNA) analysis approach could be helpful in defining aspects in FA phenotype, which might deserve future attention with the perspective to develop miRNA-based therapies. METHODS miRNA array were employed to characterize the global miRNA (miRNoma) profile of FA RNA samples with respect to normal samples. RESULTS We report and compare miRNA profile from two FA established cell lines and three FA patients. This analysis reveals that 36 and 64 miRNAs, respectively, are found differentially expressed (>2-fold variation and P < 0.05) in the samples from FA cell lines and FA patients. Overlap of these data results in 24 miRNAs as shared in the two sample populations. Available bioinformatics methods were used to predict target genes for the differentially expressed miRNAs and to perform pathway enrichment analysis. CONCLUSIONS Seven pathway results associated with the FA phenotype. It is interesting to note that some of these pathways were previously unrelated to FA phenotype. It might be important to focus on these pathways not previously emerged as dysfunctional in FA to better define the pathophysiological context of this disease. This is the first report of a global miRNA analysis in FA.
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Affiliation(s)
- Paolo Degan
- 1 Mutagenesis and Preventive Oncology, Ospedale Policlinico San Martino, Genova, Italy
| | | | | | - Alessandra Pulliero
- 3 Department of Health Sciences, School of Medicine, University of Genoa, Genova, Italy
| | - Paola Cuccarolo
- 1 Mutagenesis and Preventive Oncology, Ospedale Policlinico San Martino, Genova, Italy
| | - Carlo Dufour
- 2 Hematology, Istituto Giannina Gaslini, Genova, Italy
| | - Silvia Ravera
- 4 Department of Pharmacy, Biochemistry Laboratory, University of Genova, Genova, Italy
| | - Daniela Calzia
- 4 Department of Pharmacy, Biochemistry Laboratory, University of Genova, Genova, Italy
| | - Alberto Izzotti
- 1 Mutagenesis and Preventive Oncology, Ospedale Policlinico San Martino, Genova, Italy.,3 Department of Health Sciences, School of Medicine, University of Genoa, Genova, Italy
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Zipporah E B, Govarthanan K, Shyamsunder P, Verma RS. Expression Profiling of Differentially Regulated Genes in Fanconi Anemia. Methods Mol Biol 2018; 1783:243-258. [PMID: 29767366 DOI: 10.1007/978-1-4939-7834-2_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gene expression analysis mainly helps to study gene quantification methods by using various downstream detection approaches like imaging, amplification, probe hybridization, or sequencing. With respect to DNA, which is less static, mRNA levels vary over time, between cell types under divergent conditions. Gene expression analysis is principally focused on determination of mRNA levels transcribed from DNA. DNA microarrays are one of the robust and powerful tools to detect changes in multiple transcripts in larger cohorts in parallel. The basic principle of DNA microarray hybridization is complementary base pairing of single-stranded nucleic-acid sequences. On a microarray platform (also called a chip), known sequences called targets are attached at fixed locations (spots) to a solid surface such as glass using robotic spotting. Since a large number of samples (variables) are used in a typical hybridization experiment, which often leads to impreciseness for example, target mRNA transcribed from the same source should be identical every time. In such cases, developing an optimized protocol for microarray platform to study the expression profiling of differentially regulated genes is a challenging task. Thus genome-wide expression array analysis yields data about candidate genes that may be involved in disease acquisition progression, and helps in better understanding the pathophysiology of the disease. In this chapter we describe in detail the microarray technique, a well-accepted method for understanding the development and progression of Fanconi anemia (FA), a genetic disorder which is characterized by progressive bone marrow failure and a predisposition to cancer.
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Affiliation(s)
- Binita Zipporah E
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Kavitha Govarthanan
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | | | - Rama S Verma
- Stem Cell and Molecular Biology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India.
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Shyamsunder P, Esner M, Barvalia M, Wu YJ, Loja T, Boon HB, Lleonart ME, Verma RS, Krejci L, Lyakhovich A. Impaired mitophagy in Fanconi anemia is dependent on mitochondrial fission. Oncotarget 2016; 7:58065-58074. [PMID: 27517150 PMCID: PMC5295412 DOI: 10.18632/oncotarget.11161] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/29/2016] [Indexed: 11/25/2022] Open
Abstract
Fanconi anemia (FA) is a rare genetic disorder associated with bone-marrow failure, genome instability and cancer predisposition. Recently, we and others have demonstrated dysfunctional mitochondria with morphological alterations in FA cells accompanied by high reactive oxygen species (ROS) levels. Mitochondrial morphology is regulated by continuous fusion and fission events and the misbalance between these two is often accompanied by autophagy. Here, we provide evidence of impaired autophagy in FA. We demonstrate that FA cells have increased number of autophagic (presumably mitophagic) events and accumulate dysfunctional mitochondria due to an impaired ability to degrade them. Moreover, mitochondrial fission accompanied by oxidative stress (OS) is a prerequisite condition for mitophagy in FA and blocking this pathway may release autophagic machinery to clear dysfunctional mitochondria.
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Affiliation(s)
- Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Stem Cell and Molecular Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Milan Esner
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Maunish Barvalia
- Indian Institute of Technology Madras, Chennai, India.,Current Address: Department of Microbiology and Immunology, University of British Columbia, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Yu Jun Wu
- Yong Loo Lin School of Medicine, Department of Anatomy, National University of Singapore, Singapore
| | - Tomáš Loja
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Huat Bay Boon
- Yong Loo Lin School of Medicine, Department of Anatomy, National University of Singapore, Singapore
| | - Matilde E Lleonart
- Translational Research in Cancer Stem Cells, Vall d´Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Rama S Verma
- Stem Cell and Molecular Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Lumir Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,ICRC- FNUSA, International Clinical Research Center and St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Alex Lyakhovich
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,ICRC- FNUSA, International Clinical Research Center and St. Anne's University Hospital Brno, Brno, Czech Republic
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A simplified protocol for the isolation and culture of cardiomyocytes and progenitor cells from neonatal mouse ventricles. Eur J Cell Biol 2015; 94:444-52. [PMID: 26153430 DOI: 10.1016/j.ejcb.2015.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 01/04/2023] Open
Abstract
The neonatal heart is a very useful tool for the study of biochemical pathways and properties of cardiomyocytes and as it has the potential to regenerate for a brief period of time from birth; it is also useful to study cardiac regeneration. However, as the heart matures, this proficiency for regeneration is reduced. This regenerative potential may be influenced by the microenvironment of the heart in the early stages of postnatal development and therefore, cell cultures derived at this stage may contain functional cardiomyocytes and progenitor cells. The aim of this study was to identify key steps in the isolation and culture of such early stage-neonatal mouse hearts to allow maximum migration of cardiomyocytes from the explant and their maintenance as functional, long term cultures. Explant cultures of mouse ventricles preserved 3-dimensional structure and generated migrating layers of cardiomyocytes that expressed alpha sarcomeric actin which could be further sub-cultured by enzymatic dissociation. Western blotting demonstrated expression of c-KIT, GATA4, alpha sarcomeric actin and connexin43 proteins after 20 days of explant culture. ACTA1, GATA4, and CX43 continued to express in five weeks old explant cultures while the c-KIT protein was expressed up to two passages during sub-culture. Real time PCR and SQRT PCR also demonstrated gene expression of cardiomyocyte markers in long term cultures. Migrating cells from the explants assembled into contracting spheroids after subculture and expressed the c-KIT protein. Progenitor markers CD44, CD90, and extracellular proteins, periostin and vimentin demonstrated the preservation of cellular heterogeneity in such cultures. Supplementation with Hydrocortisone maintained a cardioprotective environment and reduced the non-myocyte population. This is an optimized and efficient method for the generation of neonatal heart cultures that is not labor intensive and does not require supplementation with cytokines.
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Santhakumar R, Vidyasekar P, Verma RS. Cardiogel: a nano-matrix scaffold with potential application in cardiac regeneration using mesenchymal stem cells. PLoS One 2014; 9:e114697. [PMID: 25521816 PMCID: PMC4270637 DOI: 10.1371/journal.pone.0114697] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/13/2014] [Indexed: 01/05/2023] Open
Abstract
3-Dimensional conditions for the culture of Bone Marrow-derived Stromal/Stem Cells (BMSCs) can be generated with scaffolds of biological origin. Cardiogel, a cardiac fibroblast-derived Extracellular Matrix (ECM) has been previously shown to promote cardiomyogenic differentiation of BMSCs and provide protection against oxidative stress. To determine the matrix composition and identify significant proteins in cardiogel, we investigated the differences in the composition of this nanomatrix and a BMSC-derived ECM scaffold, termed as ‘mesogel’. An optimized protocol was developed that resulted in efficient decellularization while providing the maximum yield of ECM. The proteins were sequentially solubilized using acetic acid, Sodium Dodecyl Sulfate (SDS) and Dithiothreitol (DTT). These proteins were then analyzed using surfactant-assisted in-solution digestion followed by nano-liquid chromatography and tandem mass spectrometry (nLC-MS/MS). The results of these analyses revealed significant differences in their respective compositions and 17 significant ECM/matricellular proteins were differentially identified between cardiogel and mesogel. We observed that cardiogel also promoted cell proliferation, adhesion and migration while enhancing cardiomyogenic differentiation and angiogenesis. In conclusion, we developed a reproducible method for efficient extraction and solubilization of in vitro cultured cell-derived extracellular matrix. We report several important proteins differentially identified between cardiogel and mesogel, which can explain the biological properties of cardiogel. We also demonstrated the cardiomyogenic differentiation and angiogenic potential of cardiogel even in the absence of any external growth factors. The transplantation of Bone Marrow derived Stromal/Stem Cells (BMSCs) cultured on such a nanomatrix has potential applications in regenerative therapy for Myocardial Infarction (MI).
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Affiliation(s)
- Rajalakshmi Santhakumar
- Stem cell and Molecular Biology Lab, Department of Biotechnology, Indian Institute of Technology Madras (IITM), Chennai, Tamil Nadu, India
| | - Prasanna Vidyasekar
- Stem cell and Molecular Biology Lab, Department of Biotechnology, Indian Institute of Technology Madras (IITM), Chennai, Tamil Nadu, India
| | - Rama Shanker Verma
- Stem cell and Molecular Biology Lab, Department of Biotechnology, Indian Institute of Technology Madras (IITM), Chennai, Tamil Nadu, India
- * E-mail:
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Epanchintsev A, Shyamsunder P, Verma RS, Lyakhovich A. IL-6, IL-8, MMP-2, MMP-9 are overexpressed in Fanconi anemia cells through a NF-κB/TNF-α dependent mechanism. Mol Carcinog 2014; 54:1686-99. [PMID: 25358651 DOI: 10.1002/mc.22240] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/14/2014] [Accepted: 09/15/2014] [Indexed: 11/05/2022]
Abstract
Fanconi anemia (FA) is a rare autosomal recessive genetic disorder associated with a bone-marrow failure, genome instability, hypersensitivity to DNA crosslinking agents and a predisposition to cancer. Mutations have been documented in 16 FA genes that participate in the FA-BRCA DNA repair pathway, a fundamental pathway in the development of the disease and the presentation of its symptoms. FA cells have been characterized by an overproduction of cytokines, MAPKs, and Interleukins. Through this study we have identified the overexpression of additional secretory factors such as IL-6, IL-8, MMP-2, and MMP-9 in FA cells and in cells depleted of FANCA or FANCC and proved that their expression is under the control of NF-κB/TNF-α signaling pathways. We also demonstrated that these overexpressed secretory factors were effective in promoting the proliferation, migration, and invasion of surrounding tumor cells a fundamental event in the process of epithelial mesenchymal transition (EMT) and that they also modulated the expression of EMT markers such as E-cadherin and SNAIL. Overall our data suggest that the upregulation of EMT promoting factors in FA may contribute to predisposing FA patients to cancer, thereby providing new insights into possible therapeutic interventions.
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Affiliation(s)
- Alexey Epanchintsev
- Institute of Genetics and Molecular and Cellular Biology, Department of Functional Genomics and Cancer Biology, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale Illkirch Cedex, France
| | - Pavithra Shyamsunder
- Department of Biotechnology, Stem Cell and Molecular Biology Laboratory, Indian Institute of Technology Madras, Chennai, India
| | - Rama S Verma
- Department of Biotechnology, Stem Cell and Molecular Biology Laboratory, Indian Institute of Technology Madras, Chennai, India
| | - Alex Lyakhovich
- Novosibirsk Institute of Molecular Biology and Biophysics, Novosibirsk, Russia.,Cancer & Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore.,Queen's University Belfast, Belfast, UK
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