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Ijee S, Chambayil K, Chaudhury AD, Bagchi A, Modak K, Das S, Benjamin ESB, Rani S, Paul DZ, Nath A, Roy D, Palani D, Priyanka S, Ravichandran R, Kumary BK, Sivamani Y, S. V, Babu D, Nakamura Y, Thamodaran V, Balasubramanian P, Velayudhan SR. Efficient deletion of microRNAs using CRISPR/Cas9 with dual guide RNAs. Front Mol Biosci 2024; 10:1295507. [PMID: 38628442 PMCID: PMC11020096 DOI: 10.3389/fmolb.2023.1295507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/27/2023] [Indexed: 04/19/2024] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that play crucial roles in gene regulation, exerting post-transcriptional silencing, thereby influencing cellular function, development, and disease. Traditional loss-of-function methods for studying miRNA functions, such as miRNA inhibitors and sponges, present limitations in terms of specificity, transient effects, and off-target effects. Similarly, CRISPR/Cas9-based editing of miRNAs using single guide RNAs (sgRNAs) also has limitations in terms of design space for generating effective gRNAs. In this study, we introduce a novel approach that utilizes CRISPR/Cas9 with dual guide RNAs (dgRNAs) for the rapid and efficient generation of short deletions within miRNA genomic regions. Through the expression of dgRNAs through single-copy lentiviral integration, this approach achieves over a 90% downregulation of targeted miRNAs within a week. We conducted a comprehensive analysis of various parameters influencing efficient deletion formation. In addition, we employed doxycycline (Dox)-inducible expression of Cas9 from the AAVS1 locus, enabling homogeneous, temporal, and stage-specific editing during cellular differentiation. Compared to miRNA inhibitory methods, the dgRNA-based approach offers higher specificity, allowing for the deletion of individual miRNAs with similar seed sequences, without affecting other miRNAs. Due to the increased design space, the dgRNA-based approach provides greater flexibility in gRNA design compared to the sgRNA-based approach. We successfully applied this approach in two human cell lines, demonstrating its applicability for studying the mechanisms of human erythropoiesis and pluripotent stem cell (iPSC) biology and differentiation. Efficient deletion of miR-451 and miR-144 resulted in blockage of erythroid differentiation, and the deletion of miR-23a and miR-27a significantly affected iPSC survival. We have validated the highly efficient deletion of genomic regions by editing protein-coding genes, resulting in a significant impact on protein expression. This protocol has the potential to be extended to delete multiple miRNAs within miRNA clusters, allowing for future investigations into the cooperative effects of the cluster members on cellular functions. The protocol utilizing dgRNAs for miRNA deletion can be employed to generate efficient pooled libraries for high-throughput comprehensive analysis of miRNAs involved in different biological processes.
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Affiliation(s)
- Smitha Ijee
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Karthik Chambayil
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Sree Chitra Tirunal Institute of Science and Medical Technology, Thiruvananthapuram, India
| | - Anurag Dutta Chaudhury
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Regional Centre for Biotechnology, New Delhi, India
| | - Abhirup Bagchi
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Kirti Modak
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Regional Centre for Biotechnology, New Delhi, India
| | - Saswati Das
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Esther Sathya Bama Benjamin
- Sree Chitra Tirunal Institute of Science and Medical Technology, Thiruvananthapuram, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Sonam Rani
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Daniel Zechariah Paul
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Aneesha Nath
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Debanjan Roy
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Dhavapriya Palani
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Sweety Priyanka
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | | | - Betty K. Kumary
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Yazhini Sivamani
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Vijayanand S.
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Dinesh Babu
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Vasanth Thamodaran
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Tata Institute of Genetics and Society, Bengaluru, India
| | | | - Shaji R. Velayudhan
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
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Benjamin ESB, Vinod E, Illangeswaran RSS, Rajamani BM, Vidhyadharan RT, Bagchi A, Maity A, Mohan A, Parasuraman G, Amirtham SM, Abraham A, Velayudhan SR, Balasubramanian P. Immortalised chronic myeloid leukemia (CML) derived mesenchymal stromal cells (MSCs) line retains the immunomodulatory and chemoprotective properties of CML patient-derived MSCs. Cell Signal 2024; 116:111067. [PMID: 38281615 DOI: 10.1016/j.cellsig.2024.111067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 01/30/2024]
Abstract
Despite the success of Tyrosine kinase inhibitors (TKIs) in treating chronic myeloid leukemia (CML), leukemic stem cells (LSCs) persist, contributing to relapse and resistance. CML Mesenchymal Stromal Cells (MSCs) help in LSC maintenance and protection from TKIs. However, the limited passage and self-differentiation abilities of primary CML MSCs hinder extensive research. To overcome this, we generated and characterized an immortalised CML patient-derived MSC (iCML MSC) line and assessed its role in LSC maintenance. We also compared the immunophenotype and differentiation potential between primary CML MSCs at diagnosis, post-treatment, and with normal bone marrow MSCs. Notably, CML MSCs exhibited enhanced chondrogenic differentiation potential compared to normal MSCs. The iCML MSC line retained the trilineage differentiation potential and was genetically stable, enabling long-term investigations. Functional studies demonstrated that iCML MSCs protected CML CD34+ cells from imatinib-induced apoptosis, recapitulating the bone marrow microenvironment-mediated resistance observed in patients. iCML MSC-conditioned media enabled CML CD34+ and AML blast cells to proliferate rapidly, with no impact on healthy donor CD34+ cells. Gene expression profiling revealed dysregulated genes associated with calcium metabolism in CML CD34+ cells cocultured with iCML MSCs, providing insights into potential therapeutic targets. Further, cytokine profiling revealed that the primary CML MSC lines abundantly secreted 25 cytokines involved in immune regulation, supporting the hypothesis that CML MSCs create an immune modulatory microenvironment that promotes growth and protects against TKIs. Our study establishes the utility of iCML MSCs as a valuable model to investigate leukemic-stromal interactions and study candidate genes involved in mediating TKI resistance in CML LSCs.
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Affiliation(s)
- Esther Sathya Bama Benjamin
- Department of Haematology, Christian Medical College, Ranipet campus, India; Sree Chitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram, India
| | - Elizabeth Vinod
- Department of Physiology, Christain Medical College, Vellore, India; Centre for Stem Cell Research (A Unit of inStem, Bengaluru), CMC Campus, Vellore, India
| | | | | | | | - Abhirup Bagchi
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), CMC Campus, Vellore, India
| | - Arnab Maity
- Department of Haematology, Christian Medical College, Ranipet campus, India
| | - Ajith Mohan
- Department of Haematology, Christian Medical College, Ranipet campus, India
| | | | | | - Aby Abraham
- Department of Haematology, Christian Medical College, Ranipet campus, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College, Ranipet campus, India; Centre for Stem Cell Research (A Unit of inStem, Bengaluru), CMC Campus, Vellore, India
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Rajendiran V, Devaraju N, Haddad M, Ravi NS, Panigrahi L, Paul J, Gopalakrishnan C, Wyman S, Ariudainambi K, Mahalingam G, Periyasami Y, Prasad K, George A, Sukumaran D, Gopinathan S, Pai AA, Nakamura Y, Balasubramanian P, Ramalingam R, Thangavel S, Velayudhan SR, Corn JE, Mackay JP, Marepally S, Srivastava A, Crossley M, Mohankumar KM. Base editing of key residues in the BCL11A-XL-specific zinc finger domains derepresses fetal globin expression. Mol Ther 2024; 32:663-677. [PMID: 38273654 PMCID: PMC10928131 DOI: 10.1016/j.ymthe.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
BCL11A-XL directly binds and represses the fetal globin (HBG1/2) gene promoters, using 3 zinc-finger domains (ZnF4, ZnF5, and ZnF6), and is a potential target for β-hemoglobinopathy treatments. Disrupting BCL11A-XL results in derepression of fetal globin and high HbF, but also affects hematopoietic stem and progenitor cell (HSPC) engraftment and erythroid maturation. Intriguingly, neurodevelopmental patients with ZnF domain mutations have elevated HbF with normal hematological parameters. Inspired by this natural phenomenon, we used both CRISPR-Cas9 and base editing at specific ZnF domains and assessed the impacts on HbF production and hematopoietic differentiation. Generating indels in the various ZnF domains by CRISPR-Cas9 prevented the binding of BCL11A-XL to its site in the HBG1/2 promoters and elevated the HbF levels but affected normal hematopoiesis. Far fewer side effects were observed with base editing- for instance, erythroid maturation in vitro was near normal. However, we observed a modest reduction in HSPC engraftment and a complete loss of B cell development in vivo, presumably because current base editing is not capable of precisely recapitulating the mutations found in patients with BCL11A-XL-associated neurodevelopment disorders. Overall, our results reveal that disrupting different ZnF domains has different effects. Disrupting ZnF4 elevated HbF levels significantly while leaving many other erythroid target genes unaffected, and interestingly, disrupting ZnF6 also elevated HbF levels, which was unexpected because this region does not directly interact with the HBG1/2 promoters. This first structure/function analysis of ZnF4-6 provides important insights into the domains of BCL11A-XL that are required to repress fetal globin expression and provide framework for exploring the introduction of natural mutations that may enable the derepression of single gene while leaving other functions unaffected.
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Affiliation(s)
- Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Mahdi Haddad
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Lokesh Panigrahi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Joshua Paul
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Chandrasekar Gopalakrishnan
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Stacia Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA
| | | | - Gokulnath Mahalingam
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Dhiyaneshwaran Sukumaran
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Sandhiya Gopinathan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Rajasekaran Ramalingam
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Shaji R Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Jacon E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA; Institute of Molecular Health Sciences, Department of Biology, Zurich, Switzerland
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India.
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Nandy K, Babu D, Rani S, Joshi G, Ijee S, George A, Palani D, Premkumar C, Rajesh P, Vijayanand S, David E, Murugesan M, Velayudhan SR. Efficient gene editing in induced pluripotent stem cells enabled by an inducible adenine base editor with tunable expression. Sci Rep 2023; 13:21953. [PMID: 38081875 PMCID: PMC10713686 DOI: 10.1038/s41598-023-42174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
The preferred method for disease modeling using induced pluripotent stem cells (iPSCs) is to generate isogenic cell lines by correcting or introducing pathogenic mutations. Base editing enables the precise installation of point mutations at specific genomic locations without the need for deleterious double-strand breaks used in the CRISPR-Cas9 gene editing methods. We created a bulk population of iPSCs that homogeneously express ABE8e adenine base editor enzyme under a doxycycline-inducible expression system at the AAVS1 safe harbor locus. These cells enabled fast, efficient and inducible gene editing at targeted genomic regions, eliminating the need for single-cell cloning and screening to identify those with homozygous mutations. We could achieve multiplex genomic editing by creating homozygous mutations in very high efficiencies at four independent genomic loci simultaneously in AAVS1-iABE8e iPSCs, which is highly challenging with previously described methods. The inducible ABE8e expression system allows editing of the genes of interest within a specific time window, enabling temporal control of gene editing to study the cell or lineage-specific functions of genes and their molecular pathways. In summary, the inducible ABE8e system provides a fast, efficient and versatile gene-editing tool for disease modeling and functional genomic studies.
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Affiliation(s)
- Krittika Nandy
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Dinesh Babu
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Sonam Rani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Gaurav Joshi
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Anila George
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Chitra Premkumar
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Praveena Rajesh
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Mohankumar Murugesan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Shaji R Velayudhan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India.
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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Rani S, Thamodaran V, Nandy K, Fouzia NA, Maddali M, Rajesh P, Vijayanand S, David E, Velayudhan SR. Establishment and characterization of CSCRi006-A: an induced pluripotent stem cell line generated from a patient with Diamond-Blackfan Anemia (DBA) carrying ribosomal protein S19 (RPS19) mutation. Hum Cell 2023; 36:2204-2213. [PMID: 37603219 DOI: 10.1007/s13577-023-00946-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/21/2023] [Indexed: 08/22/2023]
Abstract
Diamond-Blackfan anemia (DBA) is a congenital hypoplastic anemia characterized by ineffective erythropoiesis. DBA is majorly caused by mutations in the ribosomal protein (RP) genes (Gadhiya and Wills in Diamond-Blackfan Anemia, https://www.statpearls.com/ ; 2023). A suitable disease model that yields a continuous supply of erythroid cells is required to study disease pathogenesis and drug discovery. Toward this, we reprogrammed dermal fibroblasts from a DBA patient with a heterozygous mutation c.22-23delAG in the RPS19 gene identified through exome sequencing. To generate induced pluripotent stem cells (iPSCs), we induced episomal expression of the reprogramming factors OTC3/4, L-MYC, LIN28, SOX2, and KLF4, and a p53 shRNA2. The DBA-iPSC line CSCRi006-A generated during this study was extensively characterized for its pluripotency and genome stability. The clone retained normal karyotype and showed high expression levels of pluripotency markers, OCT4, NANOG, SOX2, TRA-I-60, TRA-I-81, and SSEA4. It could differentiate into cells originating from all three germ cell layers, as identified by immunostaining for SOX17 (endoderm), Brachyury (mesoderm), and PAX6 (ectoderm). IPSCs provide a renewable source of cells for in vitro disease modeling. CSCRi006-A, a thoroughly characterized iPSC line carrying heterozygous RPS19 c.22-23delAG mutation, is a valuable cell line for the disease modeling of DBA. This iPSC line can be differentiated into different blood cell types to study the mechanisms of disease development and identify potential treatments.
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Affiliation(s)
- Sonam Rani
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Vasanth Thamodaran
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
- Tata Institute for Genetics and Society, Bangalore, India
| | - Krittika Nandy
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - N A Fouzia
- Department of Hematology, Christian Medical College, Vellore, India
| | - Madhavi Maddali
- Department of Hematology, Christian Medical College, Vellore, India
| | - Praveena Rajesh
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Shaji R Velayudhan
- Centre for Stem Cell Research, Christian Medical College, Vellore, India.
- Department of Hematology, Christian Medical College, Vellore, India.
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Raina K, Joshi G, Modak K, Premkumar C, Priyanka S, Rajesh P, Velayudhan SR, Thummer RP. Generation and characterization of induced pluripotent stem cell line IITGi001-A derived from adult human primary dermal fibroblasts. Stem Cell Res 2023; 71:103159. [PMID: 37392703 DOI: 10.1016/j.scr.2023.103159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/27/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Adult human primary dermal fibroblasts [ATCC (PCS-201-012)] were reprogrammed by transfection of oriP/EBNA-1 based episomal plasmids expressing OCT3/4, SOX2, KLF4, L-MYC, LIN28 and a p53 shRNA (Okita et al., 2011) to give rise to induced pluripotent stem cells (iPSCs). These iPSCs expressed core pluripotency markers, maintained normal karyotype, and showed tri-lineage differentiation potential. Further, the absence of episomal plasmid integration in this iPSC line was confirmed by genomic PCR. In addition, DNA fingerprinting of fibroblast and iPSC DNA by microsatellite analysis confirmed the genetic identity of this cell line. This iPSC line was shown to be free from mycoplasma contamination.
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Affiliation(s)
- Khyati Raina
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Gaurav Joshi
- Department of Hematology, Christian Medical College, Vellore, India
| | - Kirti Modak
- Department of Hematology, Christian Medical College, Vellore, India
| | - Chitra Premkumar
- Center for Stem Cell Research, Christian Medical College, Vellore, India
| | - Sweety Priyanka
- Department of Hematology, Christian Medical College, Vellore, India
| | - Praveena Rajesh
- Center for Stem Cell Research, Christian Medical College, Vellore, India
| | - Shaji R Velayudhan
- Department of Hematology, Christian Medical College, Vellore, India; Center for Stem Cell Research, Christian Medical College, Vellore, India
| | - Rajkumar P Thummer
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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7
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Joshi G, Arthur NBJ, Geetha TS, Datari PVR, Modak K, Roy D, Chaudhury AD, Sundaraganesan P, Priyanka S, Na F, Ramprasad V, Abraham A, Srivastava VM, Srivastava A, Kulkarni UP, George B, Velayudhan SR. Comprehensive laboratory diagnosis of Fanconi anaemia: comparison of cellular and molecular analysis. J Med Genet 2023; 60:801-809. [PMID: 36894310 PMCID: PMC10423531 DOI: 10.1136/jmg-2022-108714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/03/2022] [Indexed: 03/11/2023]
Abstract
BACKGROUND Fanconi anaemia (FA) is a rare inherited bone marrow failure disease caused by germline pathogenic variants in any of the 22 genes involved in the FA-DNA interstrand crosslink (ICL) repair pathway. Accurate laboratory investigations are required for FA diagnosis for the clinical management of the patients. We performed chromosome breakage analysis (CBA), FANCD2 ubiquitination (FANCD2-Ub) analysis and exome sequencing of 142 Indian patients with FA and evaluated the efficiencies of these methods in FA diagnosis. METHODS We performed CBA and FANCD2-Ub analysis in the blood cells and fibroblasts of patients with FA. Exome sequencing with improved bioinformatics to detect the single number variants and CNV was carried out for all the patients. Functional validation of the variants with unknown significance was done by lentiviral complementation assay. RESULTS Our study showed that FANCD2-Ub analysis and CBA on peripheral blood cells could diagnose 97% and 91.5% of FA cases, respectively. Exome sequencing identified the FA genotypes consisting of 45 novel variants in 95.7% of the patients with FA. FANCA (60.2%), FANCL (19.8%) and FANCG (11.7%) were the most frequently mutated genes in the Indian population. A FANCL founder mutation c.1092G>A; p.K364=was identified at a very high frequency (~19%) in our patients. CONCLUSION We performed a comprehensive analysis of the cellular and molecular tests for the accurate diagnosis of FA. A new algorithm for rapid and cost-effective molecular diagnosis for~90% of FA cases has been established.
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Affiliation(s)
- Gaurav Joshi
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | | | | | | | - Kirti Modak
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Debanjan Roy
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anurag Dutta Chaudhury
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | | | - Sweety Priyanka
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Fouzia Na
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | | | - Aby Abraham
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Vivi M Srivastava
- Department of Cytogenetics, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Center for Stem Cell Research, Vellore, Tamil Nadu, India
| | - Uday Prakash Kulkarni
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Biju George
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Center for Stem Cell Research, Vellore, Tamil Nadu, India
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8
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Venkatesan V, Christopher AC, Rhiel M, Azhagiri MKK, Babu P, Walavalkar K, Saravanan B, Andrieux G, Rangaraj S, Srinivasan S, Karuppusamy KV, Jacob A, Bagchi A, Pai AA, Nakamura Y, Kurita R, Balasubramanian P, Pai R, Marepally SK, Mohankumar KM, Velayudhan SR, Boerries M, Notani D, Cathomen T, Srivastava A, Thangavel S. Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies. Mol Ther Nucleic Acids 2023; 32:671-688. [PMID: 37215154 PMCID: PMC10197010 DOI: 10.1016/j.omtn.2023.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Reactivation of fetal hemoglobin (HbF) is a commonly adapted strategy to ameliorate β-hemoglobinopathies. However, the continued production of defective adult hemoglobin (HbA) limits HbF tetramer production affecting the therapeutic benefits. Here, we evaluated deletional hereditary persistence of fetal hemoglobin (HPFH) mutations and identified an 11-kb sequence, encompassing putative repressor region (PRR) to β-globin exon-1 (βE1), as the core deletion that ablates HbA and exhibits superior HbF production compared with HPFH or other well-established targets. PRR-βE1-edited hematopoietic stem and progenitor cells (HSPCs) retained their genome integrity and their engraftment potential to repopulate for long-term hematopoiesis in immunocompromised mice producing HbF positive cells in vivo. Furthermore, PRR-βE1 gene editing is feasible without ex vivo HSPC culture. Importantly, the editing induced therapeutically significant levels of HbF to reverse the phenotypes of both sickle cell disease and β-thalassemia major. These findings imply that PRR-βE1 gene editing of patient HSPCs could lead to improved therapeutic outcomes for β-hemoglobinopathy gene therapy.
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Affiliation(s)
- Vigneshwaran Venkatesan
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Abisha Crystal Christopher
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, 79106 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Faculty, University of Freiburg, 79106 Freiburg, Germany
| | - Manoj Kumar K. Azhagiri
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Prathibha Babu
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Kaivalya Walavalkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Bharath Saravanan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Faculty of Medicine & Medical Center - University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sumathi Rangaraj
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
| | - Saranya Srinivasan
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
| | - Karthik V. Karuppusamy
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Annlin Jacob
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
| | - Abhirup Bagchi
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
| | - Aswin Anand Pai
- Department of Hematology, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 3050074, Japan
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 3050074, Japan
| | | | - Rekha Pai
- Department of Pathology, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Srujan Kumar Marepally
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
| | | | - Shaji R. Velayudhan
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
- Department of Hematology, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Faculty of Medicine & Medical Center - University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Dimple Notani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, 79106 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Faculty, University of Freiburg, 79106 Freiburg, Germany
| | - Alok Srivastava
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
- Department of Hematology, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu 632002, India
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9
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Rajamani BM, Illangeswaran RSS, Benjamin ESB, Balakrishnan B, Jebanesan DZP, Das S, Pai AA, Vidhyadharan RT, Mohan A, Karathedath S, Abraham A, Mathews V, Velayudhan SR, Balasubramanian P. Modulating retinoid-X-receptor alpha (RXRA) expression sensitizes chronic myeloid leukemia cells to imatinib in vitro and reduces disease burden in vivo. Front Pharmacol 2023; 14:1187066. [PMID: 37324449 PMCID: PMC10264673 DOI: 10.3389/fphar.2023.1187066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: The ligand-activated transcription factors, nuclear hormone receptors (NHRs), remain unexplored in hematological malignancies except for retinoic acid receptor alpha (RARA). Methods: Here we profiled the expression of various NHRs and their coregulators in Chronic myeloid leukemia (CML) cell lines and identified a significant differential expression pattern between inherently imatinib mesylate (IM)-sensitive and resistant cell lines. Results: Retinoid-X-receptor alpha (RXRA) was downregulated in CML cell lines inherently resistant to IM and in primary CML CD34+ cells. Pre-treatment with clinically relevant RXRA ligands improved sensitivity to IM in-vitro in both CML cell lines and primary CML cells. This combination effectively reduced the viability and colony-forming capacity of CML CD34+ cells in-vitro. In-vivo, this combination reduced leukemic burden and prolonged survival. Overexpression (OE) of RXRA inhibited proliferation and improved sensitivity to IM in-vitro. In-vivo, RXRA OE cells showed reduced engraftment of cells in the bone marrow, improved sensitivity to IM, and prolonged survival. Both RXRA OE and ligand treatment markedly reduced BCR::ABL1 downstream kinase activation, activating apoptotic cascades and improving sensitivity to IM. Importantly, RXRA OE also led to the disruption of the oxidative capacity of these cells. Conclusion: Combining IM with clinically available RXRA ligands could form an alternative treatment strategy in CML patients with suboptimal response to IM.
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Affiliation(s)
- Bharathi M. Rajamani
- Department of Haematology, Christian Medical College, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | | | - Esther Sathya Bama Benjamin
- Department of Haematology, Christian Medical College, Vellore, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Balaji Balakrishnan
- Department of Haematology, Christian Medical College, Vellore, India
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | | | - Saswati Das
- Department of Haematology, Christian Medical College, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College, Vellore, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | | | - Ajith Mohan
- Department of Haematology, Christian Medical College, Vellore, India
| | | | - Aby Abraham
- Department of Haematology, Christian Medical College, Vellore, India
| | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, India
| | - Shaji R. Velayudhan
- Department of Haematology, Christian Medical College, Vellore, India
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, India
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10
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Dahariya S, Raghuwanshi S, Thamodaran V, Velayudhan SR, Gutti RK. Role of Long Non-Coding RNAs in Human-Induced Pluripotent Stem Cells Derived Megakaryocytes: A p53, HOX Antisense Intergenic RNA Myeloid 1, and miR-125b Interaction Study. J Pharmacol Exp Ther 2023; 384:92-101. [PMID: 36243404 DOI: 10.1124/jpet.121.001095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 12/27/2022] Open
Abstract
Megakaryocytes (MKs) are rare polyploid cells found in the bone marrow and produce platelets. Platelets are small cell fragments that are essential during wound healing and vascular hemostasis. In vitro differentiation of MKs from human-induced pluripotent stem cell-derived CD34+ hematopoietic stem cells (hiPSC-HSCs) could provide an alternative treatment option for thrombocytopenic patients as a platelet source. In this approach, we developed a method to produce functional MKs from hiPSC-HSCs using a xeno-free and feeder-free condition and minimize the variation and risk from animal-derived products in cell culture. We have also investigated the genome-wide expression as well as functional significance of long noncoding RNAs (lncRNAs) in hiPSC-HSC-derived MKs to get insight into MK biology. We have performed lncRNAs expression profiling by using the Human LncProfilers qPCR Array Kit and identified 26 differentially regulated lncRNAs in hiPSC-HSC-derived MKs as compared with those in hiPSC-HSCs. HOX antisense intergenic RNA myeloid 1 (HOTAIRM1) was the most highly upregulated lncRNA in hiPSC-HSC-derived MKs and phorbol 12-myristate 13-acetate (PMA)-induced megakaryocytic-differentiating K562 cells. Furthermore, we have studied the potential mechanism of HOTAIRM1 based on the interactions between HOTAIRM1, p53, and miR-125b in PMA-induced K562 cells. Our results demonstrated that during MK maturation, HOTAIRM1 might be associated with the transcriptional regulation of p53 via acting as a decoy for miR-125b. Thus, the interaction between HOTAIRM1, p53, and miR-125b is likely involved in controlling cell cycling (cyclin D1), reactive oxygen species production, and apoptosis to support terminal maturation of MKs. SIGNIFICANCE STATEMENT: In vitro generation of megakaryocytes (MKs) from human-induced pluripotent stem cell-derived hematopoietic stem cells (hiPSC-HSCs) could provide an alternative source of platelets for treating thrombocytopenic patients. This study has investigated the functional significance of long non-coding RNAs in hiPSC-HSC-derived MKs, which remains unclear. This study's findings suggest that the regulatory role of HOX antisense intergenic RNA myeloid 1 (HOTAIRM1) in p53-mediated regulation of cyclin D1 during megakaryocytopoiesis is to promote MK maturation by decoying miR-125b.
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Affiliation(s)
- Swati Dahariya
- Stem Cell Research Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India (S.D., S.R., R.K.G.) and Centre for Stem Cell Research, Christian Medical College, Vellore, India (V.T., S.R.V.)
| | - Sanjeev Raghuwanshi
- Stem Cell Research Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India (S.D., S.R., R.K.G.) and Centre for Stem Cell Research, Christian Medical College, Vellore, India (V.T., S.R.V.)
| | - Vasanth Thamodaran
- Stem Cell Research Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India (S.D., S.R., R.K.G.) and Centre for Stem Cell Research, Christian Medical College, Vellore, India (V.T., S.R.V.)
| | - Shaji R Velayudhan
- Stem Cell Research Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India (S.D., S.R., R.K.G.) and Centre for Stem Cell Research, Christian Medical College, Vellore, India (V.T., S.R.V.)
| | - Ravi Kumar Gutti
- Stem Cell Research Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India (S.D., S.R., R.K.G.) and Centre for Stem Cell Research, Christian Medical College, Vellore, India (V.T., S.R.V.)
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11
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George A, Ravi NS, Prasad K, Panigrahi L, Koikkara S, Rajendiran V, Devaraju N, Paul J, Pai AA, Nakamura Y, Kurita R, Balasubramanian P, Thangavel S, Marepally S, Velayudhan SR, Srivastava A, Mohankumar KM. Efficient and error-free correction of sickle mutation in human erythroid cells using prime editor-2. Front Genome Ed 2022; 4:1085111. [PMID: 36605051 PMCID: PMC9808041 DOI: 10.3389/fgeed.2022.1085111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Sickle cell anaemia (SCA) is one of the common autosomal recessive monogenic disorders, caused by a transverse point mutation (GAG > GTG) at the sixth codon of the beta-globin gene, which results in haemolytic anaemia due to the fragile RBCs. Recent progress in genome editing has gained attention for the therapeutic cure for SCA. Direct correction of SCA mutation by homology-directed repair relies on a double-strand break (DSB) at the target site and carries the risk of generating beta-thalassaemic mutations if the editing is not error-free. On the other hand, base editors cannot correct the pathogenic SCA mutation resulting from A > T base transversion. Prime editor (PE), the recently described CRISPR/Cas 9 based gene editing tool that enables precise gene manipulations without DSB and unintended nucleotide changes, is a viable approach for the treatment of SCA. However, the major limitation with the use of prime editing is the lower efficiency especially in human erythroid cell lines and primary cells. To overcome these limitations, we developed a modular lenti-viral based prime editor system and demonstrated its use for the precise modelling of SCA mutation and its subsequent correction in human erythroid cell lines. We achieved highly efficient installation of SCA mutation (up to 72%) and its subsequent correction in human erythroid cells. For the first time, we demonstrated the functional restoration of adult haemoglobin without any unintended nucleotide changes or indel formations using the PE2 system. We also validated that the off-target effects mediated by the PE2 system is very minimal even with very efficient on-target conversion, making it a safe therapeutic option. Taken together, the modular lenti-viral prime editor system developed in this study not only expands the range of cell lines targetable by prime editor but also improves the efficiency considerably, enabling the use of prime editor for myriad molecular, genetic, and translational studies.
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Affiliation(s)
- Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lokesh Panigrahi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanya Koikkara
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Joshua Paul
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Aswin Anand Pai
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India,Department of Haematology, Christian Medical College and Hospital, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | | | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Shaji R. Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Department of Haematology, Christian Medical College and Hospital, Vellore, India
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Department of Haematology, Christian Medical College and Hospital, Vellore, India
| | - Kumarasamypet M. Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India,*Correspondence: Kumarasamypet M. Mohankumar,
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12
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Mahalingam G, Rachamalla HK, Arjunan P, Periyasami Y, M S, Thangavel S, Mohankumar KM, Moorthy M, Velayudhan SR, Srivastava A, Marepally S. Optimization of SARS-CoV-2 Pseudovirion Production in Lentivirus Backbone With a Novel Liposomal System. Front Pharmacol 2022; 13:840727. [PMID: 35401169 PMCID: PMC8990231 DOI: 10.3389/fphar.2022.840727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/21/2022] [Indexed: 01/11/2023] Open
Abstract
Due to the fast mutating nature of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the development of novel therapeutics, vaccines, and evaluating the efficacies of existing one’s against the mutated strains is critical for containing the virus. Pseudotyped SARS-CoV-2 viruses are proven to be instrumental in evaluating the efficiencies of therapeutics, owing to their ease in application and safety when compared to handling the live virus. However, a comprehensive protocol that includes selecting transfection reagents, validating different packaging systems for high-throughput screening of neutralizing antibodies, is still a requisite. To this end, we designed and synthesized amide linker-based cationic lipids with varying hydrophilic head groups from dimethyl (Lipo-DME) to methyl, ethylhydroxyl (Lipo-MeOH), and diethylhydroxyl (Lipo-DOH) keeping the hydrophobic tail, stearic acid, as constant. Among the liposomal formulations of these lipids, Lipo-DOH was found to be superior in delivering plasmids and demonstrated comparable transfection efficiencies with commercial standard Lipofectamine 3000. We further used Lipo-DOH for lentivirus and SARS-CoV-2 pseudovirion preparation. For comparing different lentivirus packaging systems, we optimized conditions using Addgene and BEI systems and found that the BEI lenti plasmid system was found to be efficient in making lentiviruses using Lipo-DOH. Using the optimized transfection reagent and the lentivirus system, we developed a robust protocol for the generation of SARS-CoV-2 pseudovirions and characterized their infectivity in human ACE2 expressing HEK-293T cells and neutralizing properties in IgG against spike protein of SARS-CoV-2 positive human sera from individuals recovered from COVID-19.
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Affiliation(s)
- Gokulnath Mahalingam
- Centre for Stem Cell Research (CSCR) (a Unit of InStem, Bengaluru), CMC Campus, Vellore, India
| | | | - Porkizhi Arjunan
- Centre for Stem Cell Research (CSCR) (a Unit of InStem, Bengaluru), CMC Campus, Vellore, India
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (CSCR) (a Unit of InStem, Bengaluru), CMC Campus, Vellore, India
| | - Salma M
- Centre for Stem Cell Research (CSCR) (a Unit of InStem, Bengaluru), CMC Campus, Vellore, India
| | | | | | - Mahesh Moorthy
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - Shaji R. Velayudhan
- Centre for Stem Cell Research (CSCR) (a Unit of InStem, Bengaluru), CMC Campus, Vellore, India
| | - Alok Srivastava
- Centre for Stem Cell Research (CSCR) (a Unit of InStem, Bengaluru), CMC Campus, Vellore, India
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR) (a Unit of InStem, Bengaluru), CMC Campus, Vellore, India
- *Correspondence: Srujan Marepally,
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13
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Ravi NS, Wienert B, Wyman SK, Bell HW, George A, Mahalingam G, Vu JT, Prasad K, Bandlamudi BP, Devaraju N, Rajendiran V, Syedbasha N, Pai AA, Nakamura Y, Kurita R, Narayanasamy M, Balasubramanian P, Thangavel S, Marepally S, Velayudhan SR, Srivastava A, DeWitt MA, Crossley M, Corn JE, Mohankumar KM. Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin. eLife 2022; 11:65421. [PMID: 35147495 PMCID: PMC8865852 DOI: 10.7554/elife.65421] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Naturally occurring point mutations in the HBG promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous HBG proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions and identified novel regulatory regions including a cluster at the –123 region. Base editing at –123 and –124 bp of HBG promoter induced fetal hemoglobin (HbF) to a higher level than disruption of well-known BCL11A binding site in erythroblasts derived from human CD34+ hematopoietic stem and progenitor cells (HSPC). We further demonstrated in vitro that the introduction of –123T > C and –124T > C HPFH-like mutations drives gamma-globin expression by creating a de novo binding site for KLF1. Overall, our findings shed light on so far unknown regulatory elements within the HBG promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin.
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Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Beeke Wienert
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Henry William Bell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anila George
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | - Jonathan T Vu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Kirti Prasad
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | | | - Vignesh Rajendiran
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Nazar Syedbasha
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Japan, Tokyo, Japan
| | | | | | | | - Srujan Marepally
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Mark A DeWitt
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Australia
| | - Jacob E Corn
- Department of Biology, ETH Zurich, Zurich, Switzerland
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14
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Abstract
Induced pluripotent stem cells (iPSCs) generated from patients are a valuable tool for disease modelling, drug screening, and studying the functions of cell/tissue-specific genes. However, for this research, isogenic iPSC lines are important for comparison of phenotypes in the wild type and mutant differentiated cells generated from the iPSCs. The advent of gene editing technologies to correct or generate mutations helps in the generation of isogenic iPSC lines with the same genetic background. Due to the ease of programming, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9-based gene editing tools have gained pace in gene manipulation studies, including investigating complex diseases like cancer. An iPSC line with drug inducible Cas9 expression from the Adeno-Associated Virus Integration Site 1 (AAVS1) safe harbor locus offers a controllable expression of Cas9 with robust gene editing. Here, we describe a stepwise protocol for the generation and characterization of such an iPSC line (AAVS1-PDi-Cas9 iPSC) with a doxycycline (dox)-inducible Cas9 expression cassette from the AAVS1 safe harbor site and efficient editing of target genes with lentiviral vectors expressing gRNAs. This approach with a tunable Cas9 expression that allows investigating gene functions in iPSCs or in the differentiated cells can serve as a versatile tool in disease modelling studies.
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Affiliation(s)
- Vasanth Thamodaran
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College, Vellore, India
| | - Sonam Rani
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College, Vellore, India
| | - Shaji R Velayudhan
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College, Vellore, India.
- Department of Haematology, Christian Medical College, Vellore, India.
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15
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Nath A, Rayabaram J, Ijee S, Bagchi A, Chaudhury AD, Roy D, Chambayil K, Singh J, Nakamura Y, Velayudhan SR. Comprehensive Analysis of microRNAs in Human Adult Erythropoiesis. Cells 2021; 10:3018. [PMID: 34831239 PMCID: PMC8616439 DOI: 10.3390/cells10113018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs, which play an important role in various cellular and developmental processes. The study of miRNAs in erythropoiesis is crucial to uncover the cellular pathways that are modulated during the different stages of erythroid differentiation. Using erythroid cells derived from human CD34+ hematopoietic stem and progenitor cells (HSPCs)and small RNA sequencing, our study unravels the various miRNAs involved in critical cellular pathways in erythroid maturation. We analyzed the occupancy of erythroid transcription factors and chromatin accessibility in the promoter and enhancer regions of the differentially expressed miRNAs to integrate miRNAs in the transcriptional circuitry of erythropoiesis. Analysis of the targets of the differentially expressed miRNAs revealed novel pathways in erythroid differentiation. Finally, we described the application of Clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) based editing of miRNAs to study their function in human erythropoiesis.
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Affiliation(s)
- Aneesha Nath
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
| | - Janakiram Rayabaram
- Department of Haematology, Christian Medical College, Vellore 632004, India; (J.R.); (A.D.C.); (D.R.)
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
| | - Abhirup Bagchi
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
| | - Anurag Dutta Chaudhury
- Department of Haematology, Christian Medical College, Vellore 632004, India; (J.R.); (A.D.C.); (D.R.)
| | - Debanjan Roy
- Department of Haematology, Christian Medical College, Vellore 632004, India; (J.R.); (A.D.C.); (D.R.)
- Manipal Academy of Higher Education, Manipal 576119, India
| | - Karthik Chambayil
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
| | - Jyoti Singh
- National Centre for Cell Science, University of Pune Campus, Pune 411007, India;
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan;
| | - Shaji R. Velayudhan
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, India; (A.N.); (S.I.); (A.B.); (K.C.)
- Department of Haematology, Christian Medical College, Vellore 632004, India; (J.R.); (A.D.C.); (D.R.)
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16
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Christopher AC, Venkatesan V, Karuppusamy KV, Srinivasan S, Babu P, Azhagiri MKK, C K, Bagchi A, Rajendiran V, Ravi NS, Kumar S, Marepally SK, Mohankumar KM, Srivastava A, Velayudhan SR, Thangavel S. Preferential expansion of human CD34+CD133+CD90+ hematopoietic stem cells enhances gene-modified cell frequency for gene therapy. Hum Gene Ther 2021; 33:188-201. [PMID: 34486377 DOI: 10.1089/hum.2021.089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CD34+CD133+CD90+ hematopoietic stem cells (HSCs) are responsible for long-term multi-lineage hematopoiesis and the high frequency of gene-modified HSCs is crucial for the success of hematopoietic stem and progenitor cell (HSPC) gene therapy. However, the ex vivo culture and gene manipulation steps of HSPC graft preparation significantly reduce the frequency of HSCs, thus necessitating large doses of HSPCs and reagents for the manipulation. Here, we identified a combination of small molecules, Resveratrol, UM729, and SR1 that preferentially expands CD34+CD133+CD90+ HSCs over other subpopulations of adult HSPCs in ex vivo culture. The preferential expansion enriches the HSCs in ex vivo culture, enhances the adhesion and results in a 6-fold increase in the long-term engraftment in NSG mice. Further, the culture enriched HSCs are more responsive to gene modification by lentiviral transduction and gene editing, increasing the frequency of gene-modified HSCs up to 10-fold in vivo. The yield of gene-modified HSCs obtained by the culture enrichment is similar to the sort-purification of HSCs and superior to Cyclosporin-H treatment. Our study addresses a critical challenge of low frequency of gene-modified HSCs in HSPC graft by developing and demonstrating a facile HSPC culture condition that increases the frequency of gene-modified cells in vivo. This strategy will improve the outcome of HSPC gene therapy and also simplify the gene manipulation process.
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Affiliation(s)
| | - Vigneshwaran Venkatesan
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India.,Manipal Academy of Higher Education, 76793, Manipal, Karnataka, India;
| | - Karthik V Karuppusamy
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India.,Manipal Academy of Higher Education, 76793, Manipal, Karnataka, India;
| | | | - Prathibha Babu
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India.,Manipal Academy of Higher Education, 76793, Manipal, Karnataka, India;
| | - Manoj Kumar K Azhagiri
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India.,Manipal Academy of Higher Education, 76793, Manipal, Karnataka, India;
| | - Karthik C
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India;
| | - Abhirup Bagchi
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India;
| | | | - Nithin Sam Ravi
- Center for Stem Cell Research, 302927, Vellore, Tamil Nadu, India;
| | - Sanjay Kumar
- Christian Medical College and Hospital Vellore, 30025, Center for Stem Cell Research, Vellore, Tamil Nadu, India;
| | | | | | - Alok Srivastava
- Christian Medical College, Centre for Stem Cell Research, CMC Campus, Bagayam, Vellore, Tamilnadu, India, 632002.,Christian Medical College, Haematology, Ida Scudder Road, Vellore, Tamil Nadu, India, 632004;
| | | | - Saravanabhavan Thangavel
- Center for Stem Cell Research, 302927, Christian Medical College Campus Bagayam,, Vellore, Tamil nadu, India, 632002;
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17
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Bagchi A, Nath A, Thamodaran V, Ijee S, Palani D, Rajendiran V, Venkatesan V, Datari P, Pai AA, Janet NB, Balasubramanian P, Nakamura Y, Srivastava A, Mohankumar KM, Thangavel S, Velayudhan SR. Direct Generation of Immortalized Erythroid Progenitor Cell Lines from Peripheral Blood Mononuclear Cells. Cells 2021; 10:523. [PMID: 33804564 PMCID: PMC7999632 DOI: 10.3390/cells10030523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 02/04/2023] Open
Abstract
Reliable human erythroid progenitor cell (EPC) lines that can differentiate to the later stages of erythropoiesis are important cellular models for studying molecular mechanisms of human erythropoiesis in normal and pathological conditions. Two immortalized erythroid progenitor cells (iEPCs), HUDEP-2 and BEL-A, generated from CD34+ hematopoietic progenitors by the doxycycline (dox) inducible expression of human papillomavirus E6 and E7 (HEE) genes, are currently being used extensively to study transcriptional regulation of human erythropoiesis and identify novel therapeutic targets for red cell diseases. However, the generation of iEPCs from patients with red cell diseases is challenging as obtaining a sufficient number of CD34+ cells require bone marrow aspiration or their mobilization to peripheral blood using drugs. This study established a protocol for culturing early-stage EPCs from peripheral blood (PB) and their immortalization by expressing HEE genes. We generated two iEPCs, PBiEPC-1 and PBiEPC-2, from the peripheral blood mononuclear cells (PBMNCs) of two healthy donors. These cell lines showed stable doubling times with the properties of erythroid progenitors. PBiEPC-1 showed robust terminal differentiation with high enucleation efficiency, and it could be successfully gene manipulated by gene knockdown and knockout strategies with high efficiencies without affecting its differentiation. This protocol is suitable for generating a bank of iEPCs from patients with rare red cell genetic disorders for studying disease mechanisms and drug discovery.
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Affiliation(s)
- Abhirup Bagchi
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Aneesha Nath
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vasanth Thamodaran
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vignesh Rajendiran
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vigneshwaran Venkatesan
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Phaneendra Datari
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Aswin Anand Pai
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Nancy Beryl Janet
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Poonkuzhali Balasubramanian
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 3050074, Japan;
| | - Alok Srivastava
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Kumarasamypet Murugesan Mohankumar
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Saravanabhavan Thangavel
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Shaji R. Velayudhan
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
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18
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Sullivan S, Stacey GN, Akazawa C, Aoyama N, Baptista R, Bedford P, Bennaceur Griscelli A, Chandra A, Elwood N, Girard M, Kawamata S, Hanatani T, Latsis T, Lin S, Ludwig TE, Malygina T, Mack A, Mountford JC, Noggle S, Pereira LV, Price J, Sheldon M, Srivastava A, Stachelscheid H, Velayudhan SR, Ward NJ, Turner ML, Barry J, Song J. Quality control guidelines for clinical-grade human induced pluripotent stem cell lines. Regen Med 2018; 13:859-866. [PMID: 30205750 DOI: 10.2217/rme-2018-0095] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Use of clinical-grade human induced pluripotent stem cell (iPSC) lines as a starting material for the generation of cellular therapeutics requires demonstration of comparability of lines derived from different individuals and in different facilities. This requires agreement on the critical quality attributes of such lines and the assays that should be used. Working from established recommendations and guidance from the International Stem Cell Banking Initiative for human embryonic stem cell banking, and concentrating on those issues more relevant to iPSCs, a series of consensus workshops has made initial recommendations on the minimum dataset required to consider an iPSC line of clinical grade, which are outlined in this report. Continued evolution of this field will likely lead to revision of these guidelines on a regular basis.
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Affiliation(s)
- Stephen Sullivan
- Global Alliance for iPSC Therapies (GAiT), The Jack Copland Centre, Edinburgh, UK
| | - Glyn N Stacey
- International Stem Cell Banking Initiative, 2 High St, Barley, Hertfordshire, UK
| | - Chihiro Akazawa
- Department of Biochemistry and Biophysics, Graduate School of Health Care Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Naoki Aoyama
- Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo, Japan
| | - Ricardo Baptista
- Cell & Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, London, UK
| | - Patrick Bedford
- Centre for Commercialization of Regenerative Medicine (CCRM), Toronto, ON, Canada
| | | | - Amit Chandra
- Centre for Biological Engineering, Loughborough University, Holywell Park, Loughborough, UK
| | - Ngaire Elwood
- Cord Blood Research, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Mathilde Girard
- Yposkesi, 2 Rue Henri Auguste Desbruères, 91100 Corbeil-Essonnes, France
| | - Shin Kawamata
- Foundation Biomedical Research and Innovation (FBRI), Research and Development Center for Cell Therapy, Chuo-ku, Kobe, Japan
| | - Tadaaki Hanatani
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Theodoros Latsis
- APHP-Hopital Paul Brousse Université Paris Sud/ESteam Paris Inserm UMR 935, Villejuif, France
| | - Stephen Lin
- California Institute for Regenerative Medicine (CIRM), Lake Merritt Plaza, 1999 Harrison Street STE 1650, Oakland, CA, USA
| | - Tenneille E Ludwig
- WiCell Research Institute (WiCell Stem Cell Bank), Madison, WI 53719, USA
| | - Tamara Malygina
- Optec LLC, Inzhenernaya Str., 28 Novosibirsk, 630090, Russia
| | - Amanda Mack
- Fujifilm Cellular Dynamics International, 525 Science Dr., Madison, WI 53711, USA
| | - Joanne C Mountford
- Advanced Therapeutics, Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Scott Noggle
- New York Stem Cell Foundation Laboratories, New York, NY 10032, USA
| | - Lygia V Pereira
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Jack Price
- UK Stem Cell Bank, National Institute for Biological Standards and Control, Hertfordshire, UK
| | - Michael Sheldon
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854-8009, USA
| | - Alok Srivastava
- Department of Haematology, Christian Medical College, Vellore- 632004, Tamil Nadu, India.,Centre for Stem Cell Research, Christian Medical College, Vellore- 632004, Tamil Nadu, India
| | - Harald Stachelscheid
- Charité - Universita¨tsmedizin Berlin, Berlin Institute of Health and Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College, Vellore- 632004, Tamil Nadu, India.,Centre for Stem Cell Research, Christian Medical College, Vellore- 632004, Tamil Nadu, India
| | - Natalie J Ward
- Cell & Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, London, UK
| | - Marc L Turner
- Global Alliance for iPSC Therapies (GAiT), The Jack Copland Centre, Edinburgh, UK.,Cell & Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, London, UK.,Advanced Therapeutics, Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Jacqueline Barry
- Global Alliance for iPSC Therapies (GAiT), The Jack Copland Centre, Edinburgh, UK.,Cell & Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, London, UK
| | - Jihwan Song
- Global Alliance for iPSC Therapies (GAiT), The Jack Copland Centre, Edinburgh, UK.,Department of Biomedical Science, CHA Stem Cell Institute, CHA University, Seongnam-si, Gyeonggi-do, Republic of Korea
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19
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Pal R, Mariappan I, Velayudhan SR. Editorial: Induced Pluripotent Stem Cell-Derived Mesenchymal Stem Cells: Ushering of a New Era in Personalized Cell Therapies. Curr Stem Cell Res Ther 2015; 11:97-8. [PMID: 26592539 DOI: 10.2174/1574888x1102160107174225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Manian KV, Aalam SMM, Bharathan SP, Srivastava A, Velayudhan SR. Understanding the Molecular Basis of Heterogeneity in Induced Pluripotent Stem Cells. Cell Reprogram 2015; 17:427-40. [PMID: 26562626 DOI: 10.1089/cell.2015.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reprogramming of somatic cells to generate induced pluripotent stem cells (iPSCs) has considerable latency and generates epigenetically distinct partially and fully reprogrammed clones. To understand the molecular basis of reprogramming and to distinguish the partially reprogrammed iPSC clones (pre-iPSCs), we analyzed several of these clones for their molecular signatures. Using a combination of markers that are expressed at different stages of reprogramming, we found that the partially reprogrammed stable clones have significant morphological and molecular heterogeneity in their response to transition to the fully pluripotent state. The pre-iPSCs had significant levels of OCT4 expression but exhibited variable levels of mesenchymal-to-epithelial transition. These novel molecular signatures that we identified would help in using these cells to understand the molecular mechanisms in the late of stages of reprogramming. Although morphologically similar mouse iPSC clones showed significant heterogeneity, the human iPSC clones isolated initially on the basis of morphology were highly homogeneous with respect to the levels of pluripotency.
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Affiliation(s)
- Kannan V Manian
- 1 Centre for Stem Cell Research, Christian Medical College , Vellore, Tamil Nadu, India .,2 Department of Haematology, Christian Medical College , Vellore, Tamil Nadu, India
| | | | - Sumitha P Bharathan
- 1 Centre for Stem Cell Research, Christian Medical College , Vellore, Tamil Nadu, India .,2 Department of Haematology, Christian Medical College , Vellore, Tamil Nadu, India
| | - Alok Srivastava
- 1 Centre for Stem Cell Research, Christian Medical College , Vellore, Tamil Nadu, India .,2 Department of Haematology, Christian Medical College , Vellore, Tamil Nadu, India
| | - Shaji R Velayudhan
- 1 Centre for Stem Cell Research, Christian Medical College , Vellore, Tamil Nadu, India .,2 Department of Haematology, Christian Medical College , Vellore, Tamil Nadu, India
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Mayuranathan T, Rayabaram J, Das R, Arora N, Edison ES, Chandy M, Srivastava A, Velayudhan SR. Identification of rare and novel deletions that cause (δβ)0-thalassaemia and hereditary persistence of foetal haemoglobin in Indian population. Eur J Haematol 2014; 92:514-20. [DOI: 10.1111/ejh.12276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2014] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Reena Das
- Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Neeraj Arora
- Department of Haematology; Christian Medical College; Vellore India
| | - Eunice S. Edison
- Department of Haematology; Christian Medical College; Vellore India
| | | | - Alok Srivastava
- Department of Haematology; Christian Medical College; Vellore India
- Centre for Stem Cell Research; Christian Medical College; Vellore India
| | - Shaji R. Velayudhan
- Department of Haematology; Christian Medical College; Vellore India
- Centre for Stem Cell Research; Christian Medical College; Vellore India
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Mayuranathan T, Rayabaram J, Edison ES, Srivastava A, Velayudhan SR. A novel deletion of β-globin promoter causing high HbA2 in an Indian population. Haematologica 2012; 97:1445-7. [PMID: 22581004 DOI: 10.3324/haematol.2012.062299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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