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Darsi SP, Baishya S, Nagati V, Bharani KK, Cheekatla SS, Darsi SK, Kamireddy AR, Barra RR, Devarasetti AK, Surampudi S, Singireddy JR, Kandula SK, Pasupulati AK. Safety assessment of rat embryonic fraction for in vivo regenerative therapy. Biol Open 2024; 13:bio060266. [PMID: 38984587 PMCID: PMC11360137 DOI: 10.1242/bio.060266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 07/03/2024] [Indexed: 07/11/2024] Open
Abstract
Regenerative therapy is considered a novel option for treating various diseases, whereas a developing embryo is a prime source of molecules that help repair diseased tissue and organs. Organoid culture studies also confirmed the inherent biological functions of several embryonic factors. However, the in vivo safety and efficacy of embryonic protein fraction (EPF) were not validated. In this study, we investigated the effectiveness of EPF on healthy adult rats. We obtained embryos from Sprague-Dawley (SD) female rats of E14, E16, and E19 embryonic days and collected protein lysate. This lysate was administered intravenously into adult SD rats on sequential days. We collected blood and performed hematological and biochemical parameters of rats that received EPF. C-reactive protein levels, interleukin-6, blood glucose levels, serum creatinine, blood urea, total leucocyte counts, and % of neutrophils and lymphocytes were comparable between rats receiving EPF and saline. Histological examination of rats' tissues administered with EPF is devoid of abnormalities. Our study revealed that intravenous administration of EPF to healthy adult rats showed that EPF is non-immunogenic, non-inflammatory, non-tumorigenic, and safe for in vivo applications. Our analysis suggests that EPF or its components could be recommended for validating its therapeutic abilities in organ regenerative therapy.
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Affiliation(s)
- Sivarama Prasad Darsi
- Department of Biotechnology, School of Life Sciences, Gitam University, Visakhapatnam, AP, India530045
| | - Somorita Baishya
- Department of Biochemistry, University of Hyderabad, Hyderabad, TG, India500046
| | - Veerababu Nagati
- Department of Biochemistry, University of Hyderabad, Hyderabad, TG, India500046
| | - Kala Kumar Bharani
- Department of Veterinary Pharmacology and Toxicology, P.V. Narasimha Rao University of Veterinary Sciences, Rajendra Nagar, TG, India500030
| | | | - Sujesh Kumar Darsi
- Department of General Medicine, ESI Corporation, Gunadala, Vijayawada, AP, India520004
| | - Adi Reddy Kamireddy
- Department of Internal Medicine, Banner Health Center, Maricopa, AZ, USA85138
| | - Ram Reddy Barra
- Department of Physiology, Apollo Institute of Medical Sciences and Research, Hyderabad, TG 500090, India
| | - Ashok Kumar Devarasetti
- Department of Veterinary Biochemistry, P.V. Narasimha Rao University of Veterinary Sciences, Mamnoor, Warangal, TG, India506166
| | - Sreedhar Surampudi
- Department of Biochemistry, Aware College of Medical Lab Technology, Bairamalguda, Hyderabad 500035, India
| | - Jayaram Reddy Singireddy
- Department of Urology, Hyderabad Kidney & Laparoscopic Centre, Malakpet, Hyderabad, TG 500036, India
| | - Siva Kumar Kandula
- Department of Biotechnology, School of Life Sciences, Gitam University, Visakhapatnam, AP, India530045
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2
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Indu S, Devi AN, Sahadevan M, Sengottaiyan J, Basu A, K SR, Kumar PG. Expression profiling of stemness markers in testicular germline stem cells from neonatal and adult Swiss albino mice during their transdifferentiation in vitro. Stem Cell Res Ther 2024; 15:93. [PMID: 38561834 PMCID: PMC10985951 DOI: 10.1186/s13287-024-03701-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Spermatogonial stem cells (SSCs) were considered to be stem cells with limited potencies due to their existence in adult organisms. However, the production of spermatogonial stem cell colonies with broader differentiation capabilities in primary germ cell cultures from mice of select genetic backgrounds (C57BL6/Tg14, ddY, FVB and 129/Ola) indicated that SSCs from these strains were pluripotent. METHODS We established primary cultures of SSCs from neonatal and adult Swiss 3T3 Albino mice. Stemness of SSC colonies were evaluated by performing real-time PCR and immunofluorescence analysis for a panel of chosen stemness markers. Differentiation potentials of SSCs were examined by attempting the generation of embryoid bodies and evaluating the expression of ectodermal, mesodermal and endodermal markers using immunofluorescence and real-time PCR analysis. RESULTS Spermatogonial stem cells from neonatal and mature mice testes colonised in vitro and formed compact spermatogonial stem cell colonies in culture. The presence of stem cell markers ALPL, ITGA6 and CD9 indicated stemness in these colonies. The differentiation potential of these SSC colonies was demonstrated by their transformation into embryoid bodies upon withdrawal of growth factors from the culture medium. SSC colonies and embryoid bodies formed were evaluated using immunofluorescence and real-time PCR analysis. Embryoid body like structures derived from both neonatal and adult mouse testis were quite similar in terms of the expression of germ layer markers. CONCLUSION These results strongly suggest that SSC-derived EB-like structures could be used for further differentiation into cells of interest in cell-based therapeutics.
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Affiliation(s)
- Sivankutty Indu
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, 695 014, Kerala, India
| | - Anandavally N Devi
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, 695 014, Kerala, India
| | - Mahitha Sahadevan
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, 695 014, Kerala, India
| | - Jeeva Sengottaiyan
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, 695 014, Kerala, India
- Department of Biotechnology, University of Kerala, Karyavattom Campus, Thiruvananthapuram, 695581, Kerala, India
| | - Asmita Basu
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, 695 014, Kerala, India
- Department of Biotechnology, University of Kerala, Karyavattom Campus, Thiruvananthapuram, 695581, Kerala, India
| | - Shabith Raj K
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, 695 014, Kerala, India
- Department of Biotechnology, University of Kerala, Karyavattom Campus, Thiruvananthapuram, 695581, Kerala, India
| | - Pradeep G Kumar
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, 695 014, Kerala, India.
- Department of Biotechnology, University of Kerala, Karyavattom Campus, Thiruvananthapuram, 695581, Kerala, India.
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3
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Yücel AD, Gladyshev VN. The long and winding road of reprogramming-induced rejuvenation. Nat Commun 2024; 15:1941. [PMID: 38431638 PMCID: PMC10908844 DOI: 10.1038/s41467-024-46020-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Organismal aging is inherently connected to the aging of its constituent cells and systems. Reducing the biological age of the organism may be assisted by reducing the age of its cells - an approach exemplified by partial cell reprogramming through the expression of Yamanaka factors or exposure to chemical cocktails. It is crucial to protect cell type identity during partial reprogramming, as cells need to retain or rapidly regain their functions following the treatment. Another critical issue is the ability to quantify biological age as reprogrammed older cells acquire younger states. We discuss recent advances in reprogramming-induced rejuvenation and offer a critical review of this procedure and its relationship to the fundamental nature of aging. We further comparatively analyze partial reprogramming, full reprogramming and transdifferentiation approaches, assess safety concerns and emphasize the importance of distinguishing rejuvenation from dedifferentiation. Finally, we highlight translational opportunities that the reprogramming-induced rejuvenation approach offers.
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Affiliation(s)
- Ali Doğa Yücel
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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4
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Burke M, Wong K, Talyansky Y, Mhatre SD, Mitchell C, Juran CM, Olson M, Iyer J, Puukila S, Tahimic CGT, Christenson LK, Lowe M, Rubinstein L, Shirazi-Fard Y, Sowa MB, Alwood JS, Ronca AE, Paul AM. Sexual dimorphism during integrative endocrine and immune responses to ionizing radiation in mice. Sci Rep 2024; 14:7334. [PMID: 38409284 PMCID: PMC10897391 DOI: 10.1038/s41598-023-33629-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/16/2023] [Indexed: 02/28/2024] Open
Abstract
Exposure to cosmic ionizing radiation is an innate risk of the spaceflight environment that can cause DNA damage and altered cellular function. In astronauts, longitudinal monitoring of physiological systems and interactions between these systems are important to consider for mitigation strategies. In addition, assessments of sex-specific biological responses in the unique environment of spaceflight are vital to support future exploration missions that include both females and males. Here we assessed sex-specific, multi-system immune and endocrine responses to simulated cosmic radiation. For this, 24-week-old, male and female C57Bl/6J mice were exposed to simplified five-ion, space-relevant galactic cosmic ray (GCRsim) radiation at 15 and 50 cGy, to simulate predicted radiation exposures that would be experienced during lunar and Martian missions, respectively. Blood and adrenal tissues were collected at 3- and 14-days post-irradiation for analysis of immune and endocrine biosignatures and pathways. Sexually dimorphic adrenal gland weights and morphology, differential total RNA expression with corresponding gene ontology, and unique immune phenotypes were altered by GCRsim. In brief, this study offers new insights into sexually dimorphic immune and endocrine kinetics following simulated cosmic radiation exposure and highlights the necessity for personalized translational approaches for astronauts during exploration missions.
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Affiliation(s)
- Marissa Burke
- Department of Human Factors and Behavioral Neurobiology, Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kelly Wong
- University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yuli Talyansky
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Siddhita D Mhatre
- KBR, Houston, TX, 77002, USA
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Carol Mitchell
- Department of Human Factors and Behavioral Neurobiology, Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA
| | - Cassandra M Juran
- Department of Human Factors and Behavioral Neurobiology, Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
| | - Makaila Olson
- Department of Human Factors and Behavioral Neurobiology, Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA
| | - Janani Iyer
- KBR, Houston, TX, 77002, USA
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Universities Space Research Association, Mountain View, CA, 94043, USA
| | - Stephanie Puukila
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Oak Ridge Associated Universities, Oak Ridge, TN, 37830, USA
| | - Candice G T Tahimic
- Department of Biology, University of North Florida, Jacksonville, FL, 32224, USA
| | - Lane K Christenson
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Moniece Lowe
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
- Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Linda Rubinstein
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Universities Space Research Association, Mountain View, CA, 94043, USA
- The Joseph Sagol Neuroscience Center, Sheba Research Hospital, Ramat Gan 52621, Israel
| | - Yasaman Shirazi-Fard
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Marianne B Sowa
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Joshua S Alwood
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - April E Ronca
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
- Departments of Obstetrics & Gynecology, Wake Forest Medical School, Winston-Salem, NC, USA.
| | - Amber M Paul
- Department of Human Factors and Behavioral Neurobiology, Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA.
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA.
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Nogueira IPM, Costa GMJ, Lacerda SMDSN. Avian iPSC Derivation to Recover Threatened Wild Species: A Comprehensive Review in Light of Well-Established Protocols. Animals (Basel) 2024; 14:220. [PMID: 38254390 PMCID: PMC10812705 DOI: 10.3390/ani14020220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) were first generated by Yamanaka in 2006, revolutionizing research by overcoming limitations imposed by the use of embryonic stem cells. In terms of the conservation of endangered species, iPSC technology presents itself as a viable alternative for the manipulation of target genetics without compromising specimens. Although iPSCs have been successfully generated for various species, their application in nonmammalian species, particularly avian species, requires further in-depth investigation to cover the diversity of wild species at risk and their different protocol requirements. This study aims to provide an overview of the workflow for iPSC induction, comparing well-established protocols in humans and mice with the limited information available for avian species. Here, we discuss the somatic cell sources to be reprogrammed, genetic factors, delivery methods, enhancers, a brief history of achievements in avian iPSC derivation, the main approaches for iPSC characterization, and the future perspectives and challenges for the field. By examining the current protocols and state-of-the-art techniques employed in iPSC generation, we seek to contribute to the development of efficient and species-specific iPSC methodologies for at-risk avian species. The advancement of iPSC technology holds great promise for achieving in vitro germline competency and, consequently, addressing reproductive challenges in endangered species, providing valuable tools for basic research, bird genetic preservation and rescue, and the establishment of cryobanks for future conservation efforts.
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Affiliation(s)
| | | | - Samyra Maria dos Santos Nassif Lacerda
- Laboratory of Cellular Biology, Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (I.P.M.N.); (G.M.J.C.)
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6
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Kim H, Choi H, Lee D, Kim J. A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing. Genes Genomics 2024; 46:1-11. [PMID: 38032470 DOI: 10.1007/s13258-023-01473-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Understanding gene regulatory networks (GRNs) is essential for unraveling the molecular mechanisms governing cellular behavior. With the advent of high-throughput transcriptome measurement technology, researchers have aimed to reverse engineer the biological systems, extracting gene regulatory rules from their outputs, which represented by gene expression data. Bulk RNA sequencing, a widely used method for measuring gene expression, has been employed for GRN reconstruction. However, it falls short in capturing dynamic changes in gene expression at the level of individual cells since it averages gene expression across mixed cell populations. OBJECTIVE In this review, we provide an overview of 15 GRN reconstruction tools and discuss their respective strengths and limitations, particularly in the context of single cell RNA sequencing (scRNA-seq). METHODS Recent advancements in scRNA-seq break new ground of GRN reconstruction. They offer snapshots of the individual cell transcriptomes and capturing dynamic changes. We emphasize how these technological breakthroughs have enhanced GRN reconstruction. CONCLUSION GRN reconstructors can be classified based on their requirement for cellular trajectory, which represents a dynamical cellular process including differentiation, aging, or disease progression. Benchmarking studies support the superiority of GRN reconstructors that do not require trajectory analysis in identifying regulator-target relationships. However, methods equipped with trajectory analysis demonstrate better performance in identifying key regulatory factors. In conclusion, researchers should select a suitable GRN reconstructor based on their specific research objectives.
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Affiliation(s)
- Hyeonkyu Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea
| | - Hwisoo Choi
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea
| | - Daewon Lee
- School of Art and Technology, Chung-Ang University, 4726 Seodong-Daero, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea.
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul, 06978, Republic of Korea.
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7
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Wang J, Ford JC, Mitra AK. Defining the Role of Metastasis-Initiating Cells in Promoting Carcinogenesis in Ovarian Cancer. BIOLOGY 2023; 12:1492. [PMID: 38132318 PMCID: PMC10740540 DOI: 10.3390/biology12121492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Ovarian cancer is the deadliest gynecological malignancy with a high prevalence of transcoelomic metastasis. Metastasis is a multi-step process and only a small percentage of cancer cells, metastasis-initiating cells (MICs), have the capacity to finally establish metastatic lesions. These MICs maintain a certain level of stemness that allows them to differentiate into other cell types with distinct transcriptomic profiles and swiftly adapt to external stresses. Furthermore, they can coordinate with the microenvironment, through reciprocal interactions, to invade and establish metastases. Therefore, identifying, characterizing, and targeting MICs is a promising strategy to counter the spread of ovarian cancer. In this review, we provided an overview of OC MICs in the context of characterization, identification through cell surface markers, and their interactions with the metastatic niche to promote metastatic colonization.
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Affiliation(s)
- Ji Wang
- Indiana University School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA; (J.W.); (J.C.F.)
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202, USA
| | - James C. Ford
- Indiana University School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA; (J.W.); (J.C.F.)
| | - Anirban K. Mitra
- Indiana University School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA; (J.W.); (J.C.F.)
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202, USA
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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8
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Aich M, Ansari AH, Ding L, Iesmantavicius V, Paul D, Choudhary C, Maiti S, Buchholz F, Chakraborty D. TOBF1 modulates mouse embryonic stem cell fate through regulating alternative splicing of pluripotency genes. Cell Rep 2023; 42:113177. [PMID: 37751355 DOI: 10.1016/j.celrep.2023.113177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/28/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Embryonic stem cells (ESCs) can undergo lineage-specific differentiation, giving rise to different cell types that constitute an organism. Although roles of transcription factors and chromatin modifiers in these cells have been described, how the alternative splicing (AS) machinery regulates their expression has not been sufficiently explored. Here, we show that the long non-coding RNA (lncRNA)-associated protein TOBF1 modulates the AS of transcripts necessary for maintaining stem cell identity in mouse ESCs. Among the genes affected is serine/arginine splicing factor 1 (SRSF1), whose AS leads to global changes in splicing and expression of a large number of downstream genes involved in the maintenance of ESC pluripotency. By overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and AS upon its knockout, we describe local nuclear territories where these distinct events converge. Collectively, these contribute to the maintenance of mouse ESC identity.
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Affiliation(s)
- Meghali Aich
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Asgar Hussain Ansari
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Vytautas Iesmantavicius
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Deepanjan Paul
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Souvik Maiti
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Debojyoti Chakraborty
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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9
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Tajer B, Savage AM, Whited JL. The salamander blastema within the broader context of metazoan regeneration. Front Cell Dev Biol 2023; 11:1206157. [PMID: 37635872 PMCID: PMC10450636 DOI: 10.3389/fcell.2023.1206157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Throughout the animal kingdom regenerative ability varies greatly from species to species, and even tissue to tissue within the same organism. The sheer diversity of structures and mechanisms renders a thorough comparison of molecular processes truly daunting. Are "blastemas" found in organisms as distantly related as planarians and axolotls derived from the same ancestral process, or did they arise convergently and independently? Is a mouse digit tip blastema orthologous to a salamander limb blastema? In other fields, the thorough characterization of a reference model has greatly facilitated these comparisons. For example, the amphibian Spemann-Mangold organizer has served as an amazingly useful comparative template within the field of developmental biology, allowing researchers to draw analogies between distantly related species, and developmental processes which are superficially quite different. The salamander limb blastema may serve as the best starting point for a comparative analysis of regeneration, as it has been characterized by over 200 years of research and is supported by a growing arsenal of molecular tools. The anatomical and evolutionary closeness of the salamander and human limb also add value from a translational and therapeutic standpoint. Tracing the evolutionary origins of the salamander blastema, and its relatedness to other regenerative processes throughout the animal kingdom, will both enhance our basic biological understanding of regeneration and inform our selection of regenerative model systems.
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Affiliation(s)
| | | | - Jessica L. Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
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10
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Wood S, Ishida K, Hagerty JR, Karahodza A, Dennis JN, Jolly ER. Characterization of Schistosome Sox Genes and Identification of a Flatworm Class of Sox Regulators. Pathogens 2023; 12:690. [PMID: 37242360 PMCID: PMC10222431 DOI: 10.3390/pathogens12050690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Schistosome helminths infect over 200 million people across 78 countries and are responsible for nearly 300,000 deaths annually. However, our understanding of basic genetic pathways crucial for schistosome development is limited. The sex determining region Y-box 2 (Sox2) protein is a Sox B type transcriptional activator that is expressed prior to blastulation in mammals and is necessary for embryogenesis. Sox expression is associated with pluripotency and stem cells, neuronal differentiation, gut development, and cancer. Schistosomes express a Sox-like gene expressed in the schistosomula after infecting a mammalian host when schistosomes have about 900 cells. Here, we characterized and named this Sox-like gene SmSOXS1. SmSoxS1 protein is a developmentally regulated activator that localizes to the anterior and posterior ends of the schistosomula and binds to Sox-specific DNA elements. In addition to SmSoxS1, we have also identified an additional six Sox genes in schistosomes, two Sox B, one SoxC, and three Sox genes that may establish a flatworm-specific class of Sox genes with planarians. These data identify novel Sox genes in schistosomes to expand the potential functional roles for Sox2 and may provide interesting insights into early multicellular development of flatworms.
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Affiliation(s)
- Stephanie Wood
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Kenji Ishida
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - James R. Hagerty
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Anida Karahodza
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Janay N. Dennis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Emmitt R. Jolly
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
- Center for Global Health and Disease, Case Western Reserve University, Cleveland, OH 44106, USA
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11
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Lee E, Cheung J, Bialkowska AB. Krüppel-like Factors 4 and 5 in Colorectal Tumorigenesis. Cancers (Basel) 2023; 15:cancers15092430. [PMID: 37173904 PMCID: PMC10177156 DOI: 10.3390/cancers15092430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
Krüppel-like factors (KLFs) are transcription factors regulating various biological processes such as proliferation, differentiation, migration, invasion, and homeostasis. Importantly, they participate in disease development and progression. KLFs are expressed in multiple tissues, and their role is tissue- and context-dependent. KLF4 and KLF5 are two fascinating members of this family that regulate crucial stages of cellular identity from embryogenesis through differentiation and, finally, during tumorigenesis. They maintain homeostasis of various tissues and regulate inflammation, response to injury, regeneration, and development and progression of multiple cancers such as colorectal, breast, ovarian, pancreatic, lung, and prostate, to name a few. Recent studies broaden our understanding of their function and demonstrate their opposing roles in regulating gene expression, cellular function, and tumorigenesis. This review will focus on the roles KLF4 and KLF5 play in colorectal cancer. Understanding the context-dependent functions of KLF4 and KLF5 and the mechanisms through which they exert their effects will be extremely helpful in developing targeted cancer therapy.
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Affiliation(s)
- Esther Lee
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jacky Cheung
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Agnieszka B Bialkowska
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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12
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Mishra-Gorur K, Barak T, Kaulen LD, Henegariu O, Jin SC, Aguilera SM, Yalbir E, Goles G, Nishimura S, Miyagishima D, Djenoune L, Altinok S, Rai DK, Viviano S, Prendergast A, Zerillo C, Ozcan K, Baran B, Sencar L, Goc N, Yarman Y, Ercan-Sencicek AG, Bilguvar K, Lifton RP, Moliterno J, Louvi A, Yuan S, Deniz E, Brueckner M, Gunel M. Pleiotropic role of TRAF7 in skull-base meningiomas and congenital heart disease. Proc Natl Acad Sci U S A 2023; 120:e2214997120. [PMID: 37043537 PMCID: PMC10120005 DOI: 10.1073/pnas.2214997120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/27/2023] [Indexed: 04/13/2023] Open
Abstract
While somatic variants of TRAF7 (Tumor necrosis factor receptor-associated factor 7) underlie anterior skull-base meningiomas, here we report the inherited mutations of TRAF7 that cause congenital heart defects. We show that TRAF7 mutants operate in a dominant manner, inhibiting protein function via heterodimerization with wild-type protein. Further, the shared genetics of the two disparate pathologies can be traced to the common origin of forebrain meninges and cardiac outflow tract from the TRAF7-expressing neural crest. Somatic and inherited mutations disrupt TRAF7-IFT57 interactions leading to cilia degradation. TRAF7-mutant meningioma primary cultures lack cilia, and TRAF7 knockdown causes cardiac, craniofacial, and ciliary defects in Xenopus and zebrafish, suggesting a mechanistic convergence for TRAF7-driven meningiomas and developmental heart defects.
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Affiliation(s)
- Ketu Mishra-Gorur
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Tanyeri Barak
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Leon D. Kaulen
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | | | - Sheng Chih Jin
- Department of Genetics, Yale School of Medicine, New Haven, CT06510
| | | | - Ezgi Yalbir
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Gizem Goles
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Sayoko Nishimura
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | | | - Lydia Djenoune
- Cardiology Division, Department of Medicine, Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA02129
| | - Selin Altinok
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Devendra K. Rai
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Stephen Viviano
- Department of Pediatrics, Yale School of Medicine, New Haven, CT06510
| | - Andrew Prendergast
- Department of Internal Medicine, Section of Cardiology, Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT06510
| | - Cynthia Zerillo
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Kent Ozcan
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Burcin Baran
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Leman Sencar
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Nukte Goc
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | - Yanki Yarman
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
| | | | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, CT06510
| | - Richard P. Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT06510
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY10065
| | - Jennifer Moliterno
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT06510
| | - Angeliki Louvi
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
- Department of Neuroscience, Yale School of Medicine, New Haven, CT06510
| | - Shiaulou Yuan
- Cardiology Division, Department of Medicine, Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA02129
| | - Engin Deniz
- Department of Pediatrics, Yale School of Medicine, New Haven, CT06510
| | - Martina Brueckner
- Department of Pediatrics, Yale School of Medicine, New Haven, CT06510
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT06510
- Department of Genetics, Yale School of Medicine, New Haven, CT06510
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT06510
- Department of Neuroscience, Yale School of Medicine, New Haven, CT06510
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13
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Sattarov R, Toresson H, Orbjörn C, Mattsson-Carlgren N. Direct Conversion of Fibroblast into Neurons for Alzheimer's Disease Research: A Systematic Review. J Alzheimers Dis 2023; 95:805-828. [PMID: 37661882 PMCID: PMC10578293 DOI: 10.3233/jad-230119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is a prevalent neurodegenerative disorder without a cure. Innovative disease models, such as induced neurons (iNs), could enhance our understanding of AD mechanisms and accelerate treatment development. However, a review of AD human iN studies is necessary to consolidate knowledge. OBJECTIVE The objective of this review is to examine the current body of literature on AD human iN cells and provide an overview of the findings to date. METHODS We searched two databases for relevant studies published between 2010 and 2023, identifying nine studies meeting our criteria. RESULTS Reviewed studies indicate the feasibility of generating iNs directly from AD patients' fibroblasts using chemical induction or viral vectors. These cells express mature neuronal markers, including MAP-2, NeuN, synapsin, and tau. However, most studies were limited in sample size and primarily focused on autosomal dominant familial AD (FAD) rather than the more common sporadic forms of AD. Several studies indicated that iNs derived from FAD fibroblasts exhibited abnormal amyloid-β metabolism, a characteristic feature of AD in humans. Additionally, elevated levels of hyperphosphorylated tau, another hallmark of AD, were reported in some studies. CONCLUSION Although only a limited number of small-scale studies are currently available, AD patient-derived iNs hold promise as a valuable model for investigating AD pathogenesis. Future research should aim to conduct larger studies, particularly focusing on sporadic AD cases, to enhance the clinical relevance of the findings for the broader AD patient population. Moreover, these cells can be utilized in screening potential novel treatments for AD.
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Affiliation(s)
- Roman Sattarov
- Department of Clinical Sciences Malmö, Clinical Memory Research Unit, Lund University, Lund, Sweden
| | - Håkan Toresson
- Department of Clinical Sciences Malmö, Clinical Memory Research Unit, Lund University, Lund, Sweden
| | - Camilla Orbjörn
- Department of Clinical Sciences Malmö, Clinical Memory Research Unit, Lund University, Lund, Sweden
| | - Niklas Mattsson-Carlgren
- Department of Clinical Sciences Malmö, Clinical Memory Research Unit, Lund University, Lund, Sweden
- Department of Neurology, Skåne University Hospital, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
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14
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Effect of Long-Term Cryopreservation on the Stemness of Stem Cells of Apical Papilla. Int J Dent 2022; 2022:6004350. [PMID: 36606134 PMCID: PMC9810390 DOI: 10.1155/2022/6004350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/29/2022] Open
Abstract
Stem cells of apical papilla (SCAPs) are considered a subpopulation of dental stem cells with unique properties. They originate from a developing tissue, the apical papilla of developing teeth, a characteristic that enhances their stemness. Banking of these stem cells can offer a source of dental stem cells for future regenerative therapies. Until now, only the effect of six months' cryopreservation on SCAPs has been studied. In this study, the long-term (19 months) effect of cryopreservation on SCAPs was examined by means of estimation of their differentiation's capacity, flow cytometry immunophenotypical characterization, and molecular characterization of the main transcriptional factors that coincide with pluripotency. As was indicated from our results, 19-month cryopreservation of SCAPs did not affect negatively their stemness; since no significant difference was observed on their typical fibroblast-like morphology, they retained their differentiation capacity, and no discrepancies were found either on immunophenotypical level or molecular level.
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15
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Chousal JN, Sohni A, Vitting-Seerup K, Cho K, Kim M, Tan K, Porse B, Wilkinson MF, Cook-Andersen H. Progression of the pluripotent epiblast depends upon the NMD factor UPF2. Development 2022; 149:dev200764. [PMID: 36255229 PMCID: PMC9687065 DOI: 10.1242/dev.200764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that degrades RNAs harboring in-frame stop codons in specific contexts. Loss of NMD factors leads to embryonic lethality in organisms spanning the phylogenetic scale, but the mechanism remains unknown. Here, we report that the core NMD factor, UPF2, is required for expansion of epiblast cells within the inner cell mass of mice in vivo. We identify NMD target mRNAs in mouse blastocysts - both canonical and alternatively processed mRNAs - including those encoding cell cycle arrest and apoptosis factors, raising the possibility that NMD is essential for embryonic cell proliferation and survival. In support, the inner cell mass of Upf2-null blastocysts rapidly regresses with outgrowth and is incompetent for embryonic stem cell derivation in vitro. In addition, we uncovered concordant temporal- and lineage-specific regulation of NMD factors and mRNA targets, indicative of a shift in NMD magnitude during peri-implantation development. Together, our results reveal developmental and molecular functions of the NMD pathway in the early embryo.
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Affiliation(s)
- Jennifer N. Chousal
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Abhishek Sohni
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
- Section for Bioinformatics, Health Technology, Technical University of Denmark (DTU), 2800 Kongens Lyngby, Denmark
| | - Kyucheol Cho
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew Kim
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kun Tan
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
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16
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Lo JHH, Edwards M, Langerman J, Sridharan R, Plath K, Smale ST. Oct4:Sox2 binding is essential for establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cells. Genes Dev 2022; 36:1079-1095. [PMID: 36418052 PMCID: PMC9744233 DOI: 10.1101/gad.350113.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022]
Abstract
Much has been learned about the mechanisms of action of pluripotency factors Oct4 and Sox2. However, as with other regulators of cell identity, little is known about the impact of disrupting their binding motifs in a native environment or the characteristics of genes they regulate. By quantitatively examining dynamic ranges of gene expression instead of focusing on conventional measures of differential expression, we found that Oct4 and Sox2 enhancer binding is strongly enriched near genes subject to large dynamic ranges of expression among cell types, with binding sites near these genes usually within superenhancers. Mutagenesis of representative Oct4:Sox2 motifs near such active, dynamically regulated genes revealed critical roles in transcriptional activation during reprogramming, with more limited roles in transcriptional maintenance in the pluripotent state. Furthermore, representative motifs near silent genes were critical for establishing but not maintaining the fully silent state, while genes whose transcript levels varied by smaller magnitudes among cell types were unaffected by nearby Oct4:Sox2 motifs. These results suggest that Oct4 and Sox2 directly establish both active and silent transcriptional states in pluripotent cells at a large number of genes subject to dynamic regulation during mammalian development, but are less important than expected for maintaining transcriptional states.
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Affiliation(s)
- Jerry Hung-Hao Lo
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Miguel Edwards
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Justin Langerman
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Kathrin Plath
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Stephen T Smale
- Molecular Biology Institute, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Broad Stem Cell Research Center, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
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17
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Johnson AL, Laterra J, Lopez-Bertoni H. Exploring glioblastoma stem cell heterogeneity: Immune microenvironment modulation and therapeutic opportunities. Front Oncol 2022; 12:995498. [PMID: 36212415 PMCID: PMC9532940 DOI: 10.3389/fonc.2022.995498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Despite its growing use in cancer treatment, immunotherapy has been virtually ineffective in clinical trials for gliomas. The inherently cold tumor immune microenvironment (TIME) in gliomas, characterized by a high ratio of pro-tumor to anti-tumor immune cell infiltrates, acts as a seemingly insurmountable barrier to immunotherapy. Glioma stem cells (GSCs) within these tumors are key contributors to this cold TIME, often functioning indirectly through activation and recruitment of pro-tumor immune cell types. Furthermore, drivers of GSC plasticity and heterogeneity (e.g., reprogramming transcription factors, epigenetic modifications) are associated with induction of immunosuppressive cell states. Recent studies have identified GSC-intrinsic mechanisms, including functional mimicry of immune suppressive cell types, as key determinants of anti-tumor immune escape. In this review, we cover recent advancements in our understanding of GSC-intrinsic mechanisms that modulate GSC-TIME interactions and discuss cutting-edge techniques and bioinformatics platforms available to study immune modulation at high cellular resolution with exploration of both malignant (i.e., GSC) and non-malignant (i.e., immune) cell fractions. Finally, we provide insight into the therapeutic opportunities for targeting immunomodulatory GSC-intrinsic mechanisms to potentiate immunotherapy response in gliomas.
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Affiliation(s)
- Amanda L. Johnson
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: John Laterra, ; Hernando Lopez-Bertoni,
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: John Laterra, ; Hernando Lopez-Bertoni,
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18
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Majood M, Garg P, Chaurasia R, Agarwal A, Mohanty S, Mukherjee M. Carbon Quantum Dots for Stem Cell Imaging and Deciding the Fate of Stem Cell Differentiation. ACS OMEGA 2022; 7:28685-28693. [PMID: 36033677 PMCID: PMC9404166 DOI: 10.1021/acsomega.2c03285] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/01/2022] [Indexed: 05/12/2023]
Abstract
Nanotechnology advancements and applications have paved the way for new possibilities in regenerative medicine and tissue engineering. It is a relatively new field that has the potential to improve stem cell differentiation and therapy greatly. Numerous studies have demonstrated that nanomaterials can function as a physiological niche for the formation and differentiation of stem cells. However, quantum dots (QDs), such as carbon quantum dots (CQDs) and graphene quantum dots (GQDs), have shown considerable promise in the field of regenerative medicine. To date, most research has focused on stem cell tracking and imaging using CQDs. However, their interaction with stem cells and the associated possibility for differentiation by selectively focusing chemical signals to a particular lineage has received scant attention. In this mini-review, we attempt to categorize a few pathways linked with the role of CQDs in stem cell differentiation.
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Affiliation(s)
- Misba Majood
- Amity
Institute of Click Chemistry Research and Studies, Amity University Uttar Pradeshs, Noida 201313, India
| | - Piyush Garg
- Amity
Institute of Click Chemistry Research and Studies, Amity University Uttar Pradeshs, Noida 201313, India
| | - Radhika Chaurasia
- Amity
Institute of Click Chemistry Research and Studies, Amity University Uttar Pradeshs, Noida 201313, India
| | - Aakanksha Agarwal
- Amity
Institute of Click Chemistry Research and Studies, Amity University Uttar Pradeshs, Noida 201313, India
| | - Sujata Mohanty
- Stem
Cells Facility, DBT-Centre of Excellence, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Monalisa Mukherjee
- Amity
Institute of Click Chemistry Research and Studies, Amity University Uttar Pradeshs, Noida 201313, India
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19
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Karakota M, Gounari E, Koliakou I, Papaioannou M, Papanikolaou NA, Koliakos G. Induced differentiation and molecular characterization of monocytes-derived multipotential cells generated from commonly discarded leukapheresis filters. Tissue Cell 2022; 77:101825. [DOI: 10.1016/j.tice.2022.101825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
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20
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Borziak K, Finkelstein J. Gene Expression Markers of Prognostic Importance for Prostate Cancer Risk in Patients with Benign Prostate Hyperplasia. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:73-76. [PMID: 36086411 DOI: 10.1109/embc48229.2022.9871422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Comparative analyses utilizing publicly available big data have the potential to generate novel hypotheses and knowledge. However, this approach is underutilized in the realm of cancer research, particularly for prostate cancer. While the general progression of prostate cancer is now well understood, how individual cell types transition from healthy, to pre-cancerous, to cancerous cell types, remains to be further elucidated. To address this, we re-analyzed two publicly available single-cell RNA-seq datasets of prostate cancer and benign prostate hyperplasia cell types. The differential expression analysis of 15,505 epithelial cell profiles across 18,638 genes revealed 791 genes that were up regulated in prostate cancer epithelial cells. Here we report six markers that show significant upregulation in prostate cancer cells relative to BPH epithelial cells: HPN (5.62X), RAC3 (3.51X), CD24 (2.18X), HOXC6 (1.77X), AGR2 (1.71X), and IGFBP2 (1.28X). In particular, the significant differential expression of AGR2 further supports its clinical relevance in supplementing prostate-specific antigen screening for detecting prostate cancer. These findings have the potential to further advance our knowledge of genes governing the development of cancer in prostate epithelial cells. Clinical Relevance- Our results establish the importance of 6 prostate cancer markers (HPN, RAC3, CD24, HOXC6, AGR2, and IGFBP3) in distinguishing between prostate cancer epithelial cells and benign prostate hyperplasia epithelial cells.
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21
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Dos Santos T, Galipeau M, Schukarucha Gomes A, Greenberg M, Larsen M, Lee D, Maghera J, Mulchandani CM, Patton M, Perera I, Polishevska K, Ramdass S, Shayeganpour K, Vafaeian K, Van Allen K, Wang Y, Weisz T, Estall JL, Mulvihill EE, Screaton RA. Islet Biology During COVID-19: Progress and Perspectives. Can J Diabetes 2022; 46:419-427. [PMID: 35589534 PMCID: PMC8608413 DOI: 10.1016/j.jcjd.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/28/2021] [Accepted: 11/01/2021] [Indexed: 01/08/2023]
Abstract
The coronavirus-2019 (COVID-19) pandemic has had significant impact on research directions and productivity in the past 2 years. Despite these challenges, since 2020, more than 2,500 peer-reviewed articles have been published on pancreatic islet biology. These include updates on the roles of isocitrate dehydrogenase, pyruvate kinase and incretin hormones in insulin secretion, as well as the discovery of inceptor and signalling by circulating RNAs. The year 2020 also brought advancements in in vivo and in vitro models, including a new transgenic mouse for assessing beta-cell proliferation, a "pancreas-on-a-chip" to study glucose-stimulated insulin secretion and successful genetic editing of primary human islet cells. Islet biologists evaluated the functionality of stem-cell-derived islet-like cells coated with semipermeable biomaterials to prevent autoimmune attack, revealing the importance of cell maturation after transplantation. Prompted by observations that COVID-19 symptoms can worsen for people with obesity or diabetes, researchers examined how islets are directly affected by severe acute respiratory syndrome coronavirus 2. Herein, we highlight novel functional insights, technologies and therapeutic approaches that emerged between March 2020 and July 2021, written for both scientific and lay audiences. We also include a response to these advancements from patient stakeholders, to help lend a broader perspective to developments and challenges in islet research.
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Affiliation(s)
- Theodore Dos Santos
- Alberta Diabetes Institute & Department of Pharmacology, Li Ka Shing Centre for Health Research Innovation, University of Alberta, Edmonton, Alberta, Canada
| | - Maria Galipeau
- Department of Molecular Biology, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada; Institut de recherches cliniques de Montréal, Cardiometabolic Disease Centre, Montréal, Québec, Canada
| | - Amanda Schukarucha Gomes
- Alberta Diabetes Institute & Department of Pharmacology, Li Ka Shing Centre for Health Research Innovation, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Daniel Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Jasmine Maghera
- Alberta Diabetes Institute & Department of Pharmacology, Li Ka Shing Centre for Health Research Innovation, University of Alberta, Edmonton, Alberta, Canada
| | | | - Megan Patton
- Toronto General Hospital, Toronto, Ontario, Canada
| | - Ineli Perera
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Kateryna Polishevska
- Alberta Diabetes Institute and Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | | | - Kasra Shayeganpour
- Alberta Diabetes Institute and Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | | | - Kyle Van Allen
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Yufeng Wang
- University Health Network, Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Tom Weisz
- Toronto General Hospital, Toronto, Ontario, Canada
| | - Jennifer L Estall
- Department of Molecular Biology, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada; Institut de recherches cliniques de Montréal, Cardiometabolic Disease Centre, Montréal, Québec, Canada
| | - Erin E Mulvihill
- Energy Substrate Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada; Department of Biochemistry, Immunology and Microbiology, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert A Screaton
- Sunnybrook Research Institute, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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22
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Schock EN, York JR, LaBonne C. The developmental and evolutionary origins of cellular pluripotency in the vertebrate neural crest. Semin Cell Dev Biol 2022; 138:36-44. [PMID: 35534333 DOI: 10.1016/j.semcdb.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 11/30/2022]
Abstract
Neural crest cells are central to vertebrate development and evolution, endowing vertebrates with a "new head" that resulted in morphological, physiological, and behavioral features that allowed vertebrates to become active predators. One remarkable feature of neural crest cells is their multi-germ layer potential that allows for the formation of both ectodermal (pigmentation, peripheral glia, sensory neurons) and mesenchymal (connective tissue, cartilage/bone, dermis) cell types. Understanding the cellular and evolutionary origins of this broad cellular potential in the neural crest has been a long-standing focus for developmental biologists. Here, we review recent work that has demonstrated that neural crest cells share key features with pluripotent blastula stem cells, including expression of the Yamanaka stem cell factors (Oct3/4, Klf4, Sox2, c-Myc). These shared features suggest that pluripotency is either retained in the neural crest from blastula stages or subsequently reactivated as the neural crest forms. We highlight the cellular and molecular parallels between blastula stem cells and neural crest cells and discuss the work that has led to current models for the cellular origins of broad potential in the crest. Finally, we explore how these themes can provide new insights into how and when neural crest cells and pluripotency evolved in vertebrates and the evolutionary relationship between these populations.
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Affiliation(s)
| | | | - Carole LaBonne
- Dept. of Molecular Biosciences; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, United States.
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23
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Zibetti C. Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. Cells 2022; 11:cells11050806. [PMID: 35269428 PMCID: PMC8908986 DOI: 10.3390/cells11050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.
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Affiliation(s)
- Cristina Zibetti
- Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway
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24
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Deshpande RP, Sharma S, Liu Y, Pandey PR, Pei X, Wu K, Wu SY, Tyagi A, Zhao D, Mo YY, Watabe K. LncRNA IPW inhibits growth of ductal carcinoma in situ by downregulating ID2 through miR-29c. Breast Cancer Res 2022; 24:6. [PMID: 35078502 PMCID: PMC8787949 DOI: 10.1186/s13058-022-01504-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/11/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Ductal carcinoma in situ (DCIS) of breast is the noninvasive lesion that has propensity to progress to the malignant form. At present, it is still unknown which lesions can potentially progress to invasive forms. In this study, we aimed to identify key lncRNAs involved in DCIS growth. METHODS We employ disease-related lncProfiler array to identify IPW in specimens of DCIS and matching control samples and validate the observations in three DCIS-non-tumorigenic cell lines. Further, we examine the mechanism of IPW action and the downstream signaling in in vitro and in vivo assays. Importantly, we screened a library containing 390 natural compounds to identify candidate compound selectively inhibiting IPW low DCIS cells. RESULTS We identified lncRNA IPW as a novel tumor suppressor critical for inhibiting DCIS growth. Ectopic expression of IPW in DCIS cells strongly inhibited cell proliferation, colony formation and cell cycle progression while silencing IPW in primary breast cells promoted their growth. Additionally, orthotropic implantation of cells with ectopic expression of IPW exhibited decreased tumor growth in vivo. Mechanistically, IPW epigenetically enhanced miR-29c expression by promoting H3K4me3 enrichment in its promoter region. Furthermore, we identified that miR-29c negatively regulated a stemness promoting gene, ID2, and diminished self-renewal ability of DCIS cells. Importantly, we screened a library containing 390 natural compounds and identified toyocamycin as a compound that selectively inhibited the growth of DCIS with low expression of IPW, while it did not affect DCIS with high IPW expression. Toyocamycin also suppressed genes associated with self-renewal ability and inhibited DCIS growth in vivo. CONCLUSION Our findings revealed a critical role of the IPW-miR-29c-ID2 axis in DCIS formation and suggested potential clinical use of toyocamycin for the treatment of DCIS.
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MESH Headings
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Carcinoma, Intraductal, Noninfiltrating/drug therapy
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/metabolism
- Cell Line, Tumor
- Female
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- Humans
- Inhibitor of Differentiation Protein 2/metabolism
- MicroRNAs/genetics
- MicroRNAs/metabolism
- RNA, Long Noncoding/genetics
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Affiliation(s)
| | | | - Yin Liu
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC, 27157, USA
| | - Puspa Raj Pandey
- Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Xinhong Pei
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC, 27157, USA
| | - Kerui Wu
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC, 27157, USA
| | - Shih-Ying Wu
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC, 27157, USA
| | - Abhishek Tyagi
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC, 27157, USA
| | - Dan Zhao
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC, 27157, USA
| | - Yin-Yuan Mo
- Department of Pharmacology and Toxicology, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Kounosuke Watabe
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC, 27157, USA.
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25
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Yousefi S, Akbarzadeh M, Soleimanirad J, Hamdi K, Farzadi L, Ghasemzadeh A, Mahdipour M, Rahbarghazi R, Nouri M. Combination of Estradiol with Leukemia Inhibitory Factor Stimulates Granulosa Cells Differentiation into Oocyte-Like Cells. Adv Pharm Bull 2021; 11:712-718. [PMID: 34888218 PMCID: PMC8642804 DOI: 10.34172/apb.2021.080] [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: 02/11/2020] [Revised: 04/29/2020] [Accepted: 07/26/2020] [Indexed: 11/16/2022] Open
Abstract
Purpose: Previous studies have documented that cumulus granulosa cells (GCs) can trans-differentiation into different non-ovarian cells, showing their multipotentiality to repopulate the injured cells in ovarian tissue. The current experiment is aimed to assess the differentiation capacity of human cumulus GCs toward the oocyte-like phenotype in vitro. Methods: GCs were isolated from healthy female volunteers subjected to in vitro fertilization or intra-cytoplasmic sperm injection (IVF-ICSI). The effect of different media supplemented with leukemia inhibitory factors (LIFs), 5 ng/mL estradiol, and 0.005 IU/mL follicle-stimulating hormone (FSH) were investigated to the differentiation of GCs toward oocyte-like phenotype via monitoring the expression of Oct3/4 and GATA-4 using flow cytometry analysis. The expression of genes such as FIGLA, NOBOX, and SYCP3 was measured by real-time polymerase chain reaction (PCR) assay. We also assess morphological adaptation by using bright-field microscopic imaging. Results: Exposure of GCs to LIFs increased the number of cells expressing stemness factor Oct3/4 coincided with the suppression of GATA-4 after 7 days (P < 0.05). We found that the transcript level of all genes FIGLA, Nobox, and SYCP-3 decreased in cells after treatment with a FSH (P < 0.05). According to our data, the incubation of GCs with estradiol increased the expression of genes related to the oocyte-like phenotype. Conclusion: Our finding revealed that the combination of LIFs and estradiol could induce the GCs’ oogenesis capacity and thereby is possibly suggested as a therapeutic strategy during the occurrence of gynecological disorders.
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Affiliation(s)
- Soudabe Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Akbarzadeh
- Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Soleimanirad
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kobra Hamdi
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Laya Farzadi
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Aalie Ghasemzadeh
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Mahdipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Nouri
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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26
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Piret SE, Attallah AA, Gu X, Guo Y, Gujarati NA, Henein J, Zollman A, Hato T, Ma'ayan A, Revelo MP, Dickman KG, Chen CH, Shun CT, Rosenquist TA, He JC, Mallipattu SK. Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation. Kidney Int 2021; 100:1250-1267. [PMID: 34634362 PMCID: PMC8608748 DOI: 10.1016/j.kint.2021.08.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/06/2021] [Accepted: 08/20/2021] [Indexed: 11/24/2022]
Abstract
Loss of fatty acid β-oxidation (FAO) in the proximal tubule is a critical mediator of acute kidney injury and eventual fibrosis. However, transcriptional mediators of FAO in proximal tubule injury remain understudied. Krüppel-like factor 15 (KLF15), a highly enriched zinc-finger transcription factor in the proximal tubule, was significantly reduced in proximal tubule cells after aristolochic acid I (AAI) treatment, a proximal tubule-specific injury model. Proximal tubule specific knockout of Klf15 exacerbated proximal tubule injury and kidney function decline compared to control mice during the active phase of AAI treatment, and after ischemia-reperfusion injury. Furthermore, along with worsening proximal tubule injury and kidney function decline, knockout mice exhibited increased kidney fibrosis as compared to control mice during the remodeling phase after AAI treatment. RNA-sequencing of kidney cortex demonstrated increased transcripts involved in immune system and integrin signaling pathways and decreased transcripts encompassing metabolic pathways, specifically FAO, and PPARα signaling, in knockout versus control mice after AAI treatment. In silico and experimental chromatin immunoprecipitation studies collectively demonstrated that KLF15 occupied the promoter region of key FAO genes, CPT1A and ACAA2, in close proximity to transcription factor PPARα binding sites. While the loss of Klf15 reduced the expression of Cpt1a and Acaa2 and led to compromised FAO, induction of KLF15 partially rescued loss of FAO in AAI-treated cells. Klf15, Ppara, Cpt1a, and Acaa2 expression was also decreased in other mouse kidney injury models. Tubulointerstitial KLF15 independently correlated with eGFR, PPARA and CPT1A appearance in expression arrays from human kidney biopsies. Thus, proximal tubule-specific loss of Klf15 exacerbates acute kidney injury and fibrosis, likely due to loss of interaction with PPARα leading to loss of FAO gene transcription.
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Affiliation(s)
- Sian E Piret
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Ahmed A Attallah
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Xiangchen Gu
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA; Department of Nephrology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China
| | - Yiqing Guo
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Nehaben A Gujarati
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Justina Henein
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Amy Zollman
- Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Takashi Hato
- Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Monica P Revelo
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Kathleen G Dickman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Chung-Hsin Chen
- Department of Urology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Tung Shun
- Department of Forensic Medicine and Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Thomas A Rosenquist
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - John C He
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sandeep K Mallipattu
- Division of Nephrology, Department of Medicine, Stony Brook University, Stony Brook, New York, USA; Renal Division, Northport VA Medical Center, Northport, New York, USA.
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27
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Hsu LJ, Liu CL, Kuo ML, Shen CN, Shen CR. An Alternative Cell Therapy for Cancers: Induced Pluripotent Stem Cell (iPSC)-Derived Natural Killer Cells. Biomedicines 2021; 9:1323. [PMID: 34680440 PMCID: PMC8533510 DOI: 10.3390/biomedicines9101323] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/18/2022] Open
Abstract
Cell therapy is usually defined as the treatment or prevention of human disease by supplementation with cells that have been selected, manipulated, and pharmacologically treated or altered outside the body (ex vivo). Induced pluripotent stem cells (iPSCs), with their unique characteristics of indefinite expansion in cultures and genetic modifications, represent an ideal cell source for differentiation into specialized cell types. Cell therapy has recently become one of the most promising therapeutic approaches for cancers, and different immune cell types are selected as therapeutic platforms. Natural killer (NK) cells are shown to be effective tumor cell killers and do not cause graft-vs-host disease (GVHD), making them excellent candidates for, and facilitating the development of, "off-the-shelf" cell therapies. In this review, we summarize the progress in the past decade in the advent of iPSC technology and review recent developments in gene-modified iPSC-NK cells as readily available "off-the-shelf" cellular therapies.
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Affiliation(s)
- Li-Jie Hsu
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- PhD Program in Biotechnology Industry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Chao-Lin Liu
- Department of Chemical Engineering, Ming Chi University of Technology, New Taipei 243, Taiwan;
- Biochemical Technology R&D Center, Ming Chi University of Technology, New Taipei 243, Taiwan
| | - Ming-Ling Kuo
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Center of Molecular and Clinical Immunology, Chang Gung University, Taoyuan 333, Taiwan
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Lin-Kou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Department of Pediatrics, New Taipei Municipal TuCheng Hospital, New Taipei 236, Taiwan
| | - Chia-Ning Shen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan;
| | - Chia-Rui Shen
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- PhD Program in Biotechnology Industry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Center of Molecular and Clinical Immunology, Chang Gung University, Taoyuan 333, Taiwan
- Department of Ophthalmology, Lin-Kou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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28
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Cakmak C, Zempel H. A perspective on human cell models for POLG-spectrum disorders: advantages and disadvantages of CRISPR-Cas-based vs. patient-derived iPSC models. MED GENET-BERLIN 2021; 33:245-249. [PMID: 38835703 PMCID: PMC11006303 DOI: 10.1515/medgen-2021-2090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/21/2021] [Indexed: 06/06/2024]
Abstract
Neurogenetic diseases represent a broad group of diseases with variable genetic causes and clinical manifestations. Among these, polymerase-gamma (POLG)-spectrum disorders are relatively frequent with an estimated disease frequency of ∼1:10.000. Also, mutations in the POLG gene are by far the most important cause for mitochondriopathy. POLG-spectrum disorders usually result in progressive loss of brain function and may involve severe and deadly encephalopathy, seizures, and neuromuscular disease, as well as cardiac and hepatic failure in some cases. Onset of disease may range from birth to late adulthood, and disease duration ranges from weeks in severe cases to decades. There is no curative treatment; current animal models do not faithfully recapitulate human disease, complicating preclinical therapeutic studies. Human-based preclinical model systems must be developed to understand the human disease mechanisms and develop therapeutic approaches. In this review, we provide an overview of the current approaches to model neurogenetic disorders in a human cellular and neuronal environment with a focus on POLG-spectrum disorders. We discuss the necessity of using neuronal cells and the advantages and pitfalls of currently available cell model approaches, namely (i) CRISPR-based (i. e., genetically engineered) and induced pluripotent stem cell (iPSC) (i. e., stem cell like)-derived neuronal models and (ii) the reprogramming of patient-derived cells into iPSCs and derived neurons. Despite the fact that cell models are by definition in vitro systems incapable of recapitulating all aspects of human disease, they are still the reasonable point of start to discover disease mechanisms and develop therapeutic approaches to treat neurogenetic diseases.
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Affiliation(s)
- Cagla Cakmak
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Hans Zempel
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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29
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Palla G, Pollner P, Börcsök J, Major A, Molnár B, Csabai I. Hierarchy and control of ageing-related methylation networks. PLoS Comput Biol 2021; 17:e1009327. [PMID: 34534207 PMCID: PMC8480875 DOI: 10.1371/journal.pcbi.1009327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/29/2021] [Accepted: 08/05/2021] [Indexed: 11/28/2022] Open
Abstract
DNA methylation provides one of the most widely studied biomarkers of ageing. Since the methylation of CpG dinucleotides function as switches in cellular mechanisms, it is plausible to assume that by proper adjustment of these switches age may be tuned. Though, adjusting hundreds of CpG methylation levels coherently may never be feasible and changing just a few positions may lead to biologically unstable state. A prominent example of methylation-based age estimators is provided by Horvath's clock, based on 353 CpG dinucleotides, showing a high correlation (not necessarily causation) with chronological age across multiple tissue types. On this small subset of CpG dinucleotides we demonstrate how the adjustment of one methylation level leads to a cascade of changes at other sites. Among the studied subset, we locate the most important CpGs (and related genes) that may have a large influence on the rest of the sub-system. According to our analysis, the structure of this network is way more hierarchical compared to what one would expect based on ensembles of uncorrelated connections. Therefore, only a handful of CpGs is enough to modify the system towards a desired state. When propagation of the change over the network is taken into account, the resulting modification in the predicted age can be significantly larger compared to the effect of isolated CpG perturbations. By adjusting the most influential single CpG site and following the propagation of methylation level changes we can reach up to 5.74 years in virtual age reduction, significantly larger than without taking into account of the network control. Extending our approach to the whole methylation network may identify key nodes that have controller role in the ageing process.
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Affiliation(s)
- Gergely Palla
- Health Services Management Training Centre, Semmelweis University, Budapest, Hungary
- MTA-ELTE Statistical and Biological Physics Research Group, Dept. of Biological Physics, Eötvös University, Budapest, Hungary
| | - Péter Pollner
- Health Services Management Training Centre, Semmelweis University, Budapest, Hungary
- MTA-ELTE Statistical and Biological Physics Research Group, Dept. of Biological Physics, Eötvös University, Budapest, Hungary
| | - Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - András Major
- Dept. of Physics of Complex Systems, ELTE Eötvös University, Budapest, Hungary
| | - Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - István Csabai
- Dept. of Physics of Complex Systems, ELTE Eötvös University, Budapest, Hungary
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30
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Ealy AD, Speckhart SL, Wooldridge LK. Cytokines That Serve as Embryokines in Cattle. Animals (Basel) 2021; 11:ani11082313. [PMID: 34438770 PMCID: PMC8388520 DOI: 10.3390/ani11082313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary This review will explore how some cytokines also influence early embryonic development. We term these types of molecules as embryokines. Understanding how cytokines serve as embryokines could offer new opportunities to improve embryo development and the overall health of the embryo so that pregnancies will be retained after embryo transfer and so that viable offspring are produced. At least two cytokines may offer these benefits to bovine embryos produced in vitro. Additional cytokines also are identified in this review that may contain beneficial activities on bovine embryos. Abstract The term “embryokine” has been used to denote molecules produced by the endometrium, oviduct, or by embryo itself that will influence embryo development. Several cytokines have been identified as embryokines in cattle and other mammals. This review will describe how these cytokines function as embryokines, with special emphasis being placed on their actions on in vitro produced (IVP) bovine embryos. Embryokines are being explored for their ability to overcome the poor development rates of IVP embryos and to limit post-transfer pregnancy retention efficiencies that exist in IVP embryos. This review will focus on describing two of the best-characterized cytokines, colony-stimulating factor 2 and interleukin 6, for their ability to modify bovine embryo quality and confirmation, promote normal fetal development, and generate healthy calves. Additional cytokines will also be discussed for their potential to serve as embryokines.
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Affiliation(s)
- Alan D. Ealy
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, USA;
- Correspondence:
| | - Savannah L. Speckhart
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, USA;
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31
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Srivastava M. Beyond Casual Resemblances: Rigorous Frameworks for Comparing Regeneration Across Species. Annu Rev Cell Dev Biol 2021; 37:415-440. [PMID: 34288710 DOI: 10.1146/annurev-cellbio-120319-114716] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The majority of animal phyla have species that can regenerate. Comparing regeneration across animals can reconstruct the molecular and cellular evolutionary history of this process. Recent studies have revealed some similarity in regeneration mechanisms, but rigorous comparative methods are needed to assess whether these resemblances are ancestral pathways (homology) or are the result of convergent evolution (homoplasy). This review aims to provide a framework for comparing regeneration across animals, focusing on gene regulatory networks (GRNs), which are substrates for assessing process homology. The homology of the wound-induced activation of Wnt signaling and of adult stem cells are discussed as examples of ongoing studies of regeneration that enable comparisons in a GRN framework. Expanding the study of regeneration GRNs in currently studied species and broadening taxonomic sampling for these approaches will identify processes that are unifying principles of regeneration biology across animals. These insights are important both for evolutionary studies of regeneration and for human regenerative medicine. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mansi Srivastava
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;
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32
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Borziak K, Finkelstein J. Identification of Liver Cancer Stem Cell Stemness Markers Using a Comparative Analysis of Public Data Sets. STEM CELLS AND CLONING-ADVANCES AND APPLICATIONS 2021; 14:9-17. [PMID: 34168465 PMCID: PMC8216768 DOI: 10.2147/sccaa.s307043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022]
Abstract
Purpose Comparative reanalysis of single-cell transcriptomics data to gain useful novel insights into cancer stem cells (CSCs), which are a rare subset of cells within tumors, characterized by their capability to self-renew and differentiate, and their role in tumorigenicity. Patients and Methods This project utilized publically available liver single-cell RNA-seq datasets of liver cancer and liver progenitor cell types to demonstrate how shared large amounts of data can generate new and valuable information. The data were analyzed using EdgeR differential expression analysis, with focus on a set of 34 known stemness markers. Results We showed that the expression of stemness markers SOX9, KRT19, KRT7, and CD24, and Yamanaka factors Oct4 and SOX2 in CSCs was significantly elevated relative to progenitor cell types, potentially explaining their increased differentiation and replication potential. Conclusion These results help to further document the complementary expression changes that give CSCs their distinct phenotypic profile. Our findings have potential significance to advance our knowledge of the important genes relevant to CSCs.
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Affiliation(s)
- Kirill Borziak
- Center for Biomedical and Population Health Informatics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joseph Finkelstein
- Center for Biomedical and Population Health Informatics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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Yaglova NV, Obernikhin SS, Tsomartova DA, Nazimova SV, Yaglov VV, Tsomartova ES, Chereshneva EV, Ivanova MY, Lomanovskaya TA. Impaired Morphogenesis and Function of Rat Adrenal Zona Glomerulosa by Developmental Low-Dose Exposure to DDT Is Associated with Altered Oct4 Expression. Int J Mol Sci 2021; 22:6324. [PMID: 34204839 PMCID: PMC8231536 DOI: 10.3390/ijms22126324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
Dichlorodiphenyltrichloroethane (DDT) is a persistent organic pollutant and one of the most widespread endocrine disrupting chemicals. The impact of low-dose exposure to DDT on the morphogenesis of the adrenal gland is still poorly understood. The development and function of zona glomerulosa in rats has been found to be associated with changes in the expression of the transcription factor Oct4 (Octamer 4), which is the most important player in cell pluripotency. The aim of the study was to investigate the morphogenesis and function of rat adrenal zona glomerulosa in rats exposed to low doses of DDT during prenatal and postnatal development and to determine the possible role of Oct4 in DDT-mediated structural and functional changes. The DDT-exposed rats demonstrated slower development and lower functional activity of the zona glomerulosa during the pubertal period associated with higher expression of Oct4. Further, accelerated growth and restoration of hormone production was associated with, firstly, a decrease in Oct4 expressing cells and secondly, the loss of the inverse relationship between basal aldosterone levels and the number of Oct4 expressing cells. Thus, the transcriptional factor Oct4 exhibited an altered pattern of expression in the DDT-exposed rats during postnatal development. The results of the study uncover a novel putative mechanism by which low doses of DDT disrupt the development of adrenal zona glomerulosa.
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Affiliation(s)
- Nataliya V. Yaglova
- Laboratory of Endocrine System Development, Federal State Budgetary Scientific Institution “Research Institute of Human Morphology”, 117418 Moscow, Russia; (S.S.O.); (D.A.T.); (S.V.N.); (V.V.Y.); (E.S.T.)
| | - Sergey S. Obernikhin
- Laboratory of Endocrine System Development, Federal State Budgetary Scientific Institution “Research Institute of Human Morphology”, 117418 Moscow, Russia; (S.S.O.); (D.A.T.); (S.V.N.); (V.V.Y.); (E.S.T.)
| | - Dibakhan A. Tsomartova
- Laboratory of Endocrine System Development, Federal State Budgetary Scientific Institution “Research Institute of Human Morphology”, 117418 Moscow, Russia; (S.S.O.); (D.A.T.); (S.V.N.); (V.V.Y.); (E.S.T.)
- Department of Histology, Cytology, and Embryology, Federal State Funded Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (E.V.C.); (M.Y.I.); (T.A.L.)
| | - Svetlana V. Nazimova
- Laboratory of Endocrine System Development, Federal State Budgetary Scientific Institution “Research Institute of Human Morphology”, 117418 Moscow, Russia; (S.S.O.); (D.A.T.); (S.V.N.); (V.V.Y.); (E.S.T.)
| | - Valentin V. Yaglov
- Laboratory of Endocrine System Development, Federal State Budgetary Scientific Institution “Research Institute of Human Morphology”, 117418 Moscow, Russia; (S.S.O.); (D.A.T.); (S.V.N.); (V.V.Y.); (E.S.T.)
| | - Elina S. Tsomartova
- Laboratory of Endocrine System Development, Federal State Budgetary Scientific Institution “Research Institute of Human Morphology”, 117418 Moscow, Russia; (S.S.O.); (D.A.T.); (S.V.N.); (V.V.Y.); (E.S.T.)
- Department of Histology, Cytology, and Embryology, Federal State Funded Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (E.V.C.); (M.Y.I.); (T.A.L.)
| | - Elizaveta V. Chereshneva
- Department of Histology, Cytology, and Embryology, Federal State Funded Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (E.V.C.); (M.Y.I.); (T.A.L.)
| | - Marina Y. Ivanova
- Department of Histology, Cytology, and Embryology, Federal State Funded Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (E.V.C.); (M.Y.I.); (T.A.L.)
| | - Tatiana A. Lomanovskaya
- Department of Histology, Cytology, and Embryology, Federal State Funded Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (E.V.C.); (M.Y.I.); (T.A.L.)
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Mahjoor M, Afkhami H, Mollaei M, Nasr A, Shahriary S, Khorrami S. MicroRNA-30c delivered by bone marrow-mesenchymal stem cells induced apoptosis and diminished cell invasion in U-251 glioblastoma cell line. Life Sci 2021; 279:119643. [PMID: 34048811 DOI: 10.1016/j.lfs.2021.119643] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Glioblastoma multiform (GBM) is the most belligerent and prevalent brain malignancy among adults. Due to the blood-brain barrier (BBB), drug administration is confronted by massive challenges, making resectional surgery the only treatment pipeline. MicroRNAs have recently absorbed the attention of studies for correlating with the progression of various malignancies. miR-30c has been reported to play a role in cell proliferation, metabolism, and apoptosis process. For instance, miR-30c has been reported to regulate apoptosis through the TNF-related apoptosis-inducing ligand (TRAIL). miR-30c also targets IL-6, which further induces apoptosis. Besides, miR-30c inhibits glioma proliferation and its migratory ability. Besides, the overexpression of miR-30c arrested cells at G0 as well as dampening their migration and invasion. However, it has been shown that the expression level of miR-30c was low in glioma. MSCs can migrate toward tumor cells which is called tumor-tropism, in which they are capable of delivering engineered miR-30c based on gap junction and non-intimacy mechanisms. MATERIAL AND METHODS MiR-30c was cloned into pCDH-CMV-MCS-EF1-copGFP vector utilizing XbaI and EcoRI in order to construct pCDH-miR-30c. Then psPAX2, pMD2.G, and pCDH-miR-30c were co-transfected into Hek-293T to yield lenti-miR-30c virus particles. Next, bone marrow-mesenchymal stem cells (BM-MSCs) were Transduced with lenti-miR-30c. Thereafter, we co-cultured U-251 cell line with BM-MCSs-miR-30c and evaluated the apoptosis rate and the relative expression level of IL-6, Klf4, Sox2, c-Myc, and Oct4 using Real-Time PCR and flow cytometry. RESULTS Wound healing assays represented low migratory ability in U-251 cells treated with BM-MSCs-miR-30c. Plus, apoptosis assay using Annexin V/7AAD showed an increased number of apoptotic U-251 cells following the treatment. miR-30 targeted IL-6 and induced apoptosis. It also impacted on the self-renewal and the anti-apoptotic cluster of genes, namely Klf4, Sox2, c-Myc, and Oct4, to induce apoptosis and dwindle the migration and invasion.
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Affiliation(s)
- Mohamad Mahjoor
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Afkhami
- Department of Medical Microbiology, Faculty of Medicine, Shahed University of Medical Sciences, Tehran, Iran
| | - Mojtaba Mollaei
- Department of Immunology, School of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Atieh Nasr
- Bachelor Student of Biochemistry, Department of Biochemistry, Islamic Azad University of Najafabad, Esfahan, Iran
| | - Shamin Shahriary
- Bachelor Student of Microbiology, Department of Microbiology, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Samaneh Khorrami
- Department of Immunology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Sheng Y, Ma R, Yu C, Wu Q, Zhang S, Paulsen K, Zhang J, Ni H, Huang Y, Zheng Y, Qian Z. Role of c-Myc haploinsufficiency in the maintenance of HSCs in mice. Blood 2021; 137:610-623. [PMID: 33538795 PMCID: PMC8215193 DOI: 10.1182/blood.2019004688] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
This study was conducted to determine the dosage effect of c-Myc on hematopoiesis and its distinct role in mediating the Wnt/β-catenin pathway in hematopoietic stem cell (HSC) and bone marrow niche cells. c-Myc haploinsufficiency led to ineffective hematopoiesis by inhibiting HSC self-renewal and quiescence and by promoting apoptosis. We have identified Nr4a1, Nr4a2, and Jmjd3, which are critical for the maintenance of HSC functions, as previously unrecognized downstream targets of c-Myc in HSCs. c-Myc directly binds to the promoter regions of Nr4a1, Nr4a2, and Jmjd3 and regulates their expression. Our results revealed that Nr4a1 and Nr4a2 mediates the function of c-Myc in regulating HSC quiescence, whereas all 3 genes contribute to the function of c-Myc in the maintenance of HSC survival. Adenomatous polyposis coli (Apc) is a negative regulator of the Wnt/β-catenin pathway. We have provided the first evidence that Apc haploinsufficiency induces a blockage of erythroid lineage differentiation through promoting secretion of IL6 in bone marrow endothelial cells. We found that c-Myc haploinsufficiency failed to rescue defective function of Apc-deficient HSCs in vivo but it was sufficient to prevent the development of severe anemia in Apc-heterozygous mice and to significantly prolong the survival of those mice. Furthermore, we showed that c-Myc-mediated Apc loss induced IL6 secretion in endothelial cells, and c-Myc haploinsufficiency reversed the negative effect of Apc-deficient endothelial cells on erythroid cell differentiation. Our studies indicate that c-Myc has a context-dependent role in mediating the function of Apc in hematopoiesis.
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Affiliation(s)
- Yue Sheng
- Department of Medicine and
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, University of Florida, Gainesville, FL
- Department of Medicine and
| | - Rui Ma
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL
| | - Chunjie Yu
- Department of Medicine and
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, University of Florida, Gainesville, FL
- Department of Medicine and
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL
| | - Qiong Wu
- Department of Medicine and
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, University of Florida, Gainesville, FL
- Department of Medicine and
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL
| | - Steven Zhang
- Department of Radiation Oncology, UF Health Cancer Center, University of Florida, Gainesville, FL
| | - Kimberly Paulsen
- Department of Medicine and
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, University of Florida, Gainesville, FL
| | - Jiwang Zhang
- Oncology Institute, Cardinal Bernardin Cancer Center, Department of Cancer Biology, Loyola University Medical Center, Maywood, IL
| | - Hongyu Ni
- Department of Pathology, University of Illinois at Chicago, Chicago, IL
| | - Yong Huang
- Department of Medicine, University of Virginia, Charlottesville, VA; and
| | - Yi Zheng
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH
| | - Zhijian Qian
- Department of Medicine and
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, University of Florida, Gainesville, FL
- Department of Medicine and
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Mehravar M, Ghaemimanesh F, Poursani EM. An Overview on the Complexity of OCT4: at the Level of DNA, RNA and Protein. Stem Cell Rev Rep 2021; 17:1121-1136. [PMID: 33389631 DOI: 10.1007/s12015-020-10098-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 10/22/2022]
Abstract
OCT4 plays critical roles in self-renewal and pluripotency maintenance of embryonic stem cells, and is considered as one of the main stemness markers. It also has pivotal roles in early stages of embryonic development. Most studies on OCT4 have focused on the expression and function of OCT4A, which is the biggest isoform of OCT4 known so far. Recently, many studies have shown that OCT4 has various transcript variants, protein isoforms, as well as pseudogenes. Distinguishing the expression and function of these variants and isoforms is a big challenge in expression profiling studies of OCT4. Understanding how OCT4 is functioning in different contexts, depends on knowing of where and when each of OCT4 transcripts, isoforms and pseudogenes are expressed. Here, we review OCT4 known transcripts, isoforms and pseudogenes, as well as its interactions with other proteins, and emphasize the importance of discriminating each of them in order to understand the exact function of OCT4 in stem cells, normal development and development of diseases.
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Affiliation(s)
- Majid Mehravar
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Fatemeh Ghaemimanesh
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ensieh M Poursani
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Lee SA, Li KN, Tumbar T. Stem cell-intrinsic mechanisms regulating adult hair follicle homeostasis. Exp Dermatol 2020; 30:430-447. [PMID: 33278851 DOI: 10.1111/exd.14251] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
Adult hair follicle stem cells (HFSCs) undergo dynamic and periodic molecular changes in their cellular states throughout the hair homeostatic cycle. These states are tightly regulated by cell-intrinsic mechanisms and by extrinsic signals from the microenvironment. HFSCs are essential not only for fuelling hair growth, but also for skin wound healing. Increasing evidence suggests an important role of HFSCs in organizing multiple skin components around the hair follicle, thus functioning as an organizing centre during adult skin homeostasis. Here, we focus on recent findings on cell-intrinsic mechanisms of HFSC homeostasis, which include transcription factors, histone modifications, DNA regulatory elements, non-coding RNAs, cell metabolism, cell polarity and post-transcriptional mRNA processing. Several transcription factors are now known to participate in well-known signalling pathways that control hair follicle homeostasis, as well as in super-enhancer activities to modulate HFSC and progenitor lineage progression. Interestingly, HFSCs have been shown to secrete molecules that are important in guiding the organization of several skin components around the hair follicle, including nerves, arrector pili muscle and vasculature. Finally, we discuss recent technological advances in the field such as single-cell RNA sequencing and live imaging, which revealed HFSC and progenitor heterogeneity and brought new light to understanding crosstalking between HFSCs and the microenvironment. The field is well on its way to generate a comprehensive map of molecular interactions that should serve as a solid theoretical platform for application in hair and skin disease and ageing.
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Affiliation(s)
- Seon A Lee
- Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Kefei Nina Li
- Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Tudorita Tumbar
- Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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Embryonic stem cell-like subpopulations are present within Schwannoma. J Clin Neurosci 2020; 81:201-209. [PMID: 33222917 DOI: 10.1016/j.jocn.2020.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/10/2020] [Accepted: 09/13/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND There is accumulating evidence of the presence of embryonic stem cell (ESC)-like cells in benign tumors. AIM This study aimed to identify ESC-like cells in Schwannoma using the induced-pluripotent stem cell (iPSC) markers OCT4, SOX2, NANOG, KLF4 and c-MYC. METHODS Immunohistochemical (IHC) staining (n = 20) and RT-qPCR (n = 6) were performed on Schwannoma tissue samples (STS) to investigate protein and mRNA expression of these iPSC markers, respectively. Immunofluorescence (IF) staining was performed to investigate co-localization of the iPSC markers with CD34, α-SMA and CD133. RESULTS IHC staining and RT-qPCR demonstrated protein and mRNA expression of all five iPSC markers, respectively. IF staining showed expression of SOX2, KLF4 and c-MYC on the tumor cells and the endothelium of the tumor microvessels which also expressed OCT4, while NANOG was exclusively expressed on the endothelium of the tumor microvessels. The OCT4+/CD34+ endothelium expressed CD133. CONCLUSION We have identified a putative OCT4+/SOX2+/NANOG+/KLF4+/c-MYC+/CD133+ ESC-like subpopulation on the endothelium of tumor microvessels and an OCT4-/SOX2+/NANOG-/KLF4+/c-MYC+/CD133+ ESC-like subpopulation, within Schwannoma.
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Wang Y, Yi N, Hu Y, Zhou X, Jiang H, Lin Q, Chen R, Liu H, Gu Y, Tong C, Lu M, Zhang J, Zhang B, Peng L, Li L. Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:696-711. [PMID: 32769060 PMCID: PMC7412763 DOI: 10.1016/j.omtn.2020.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/05/2020] [Accepted: 07/06/2020] [Indexed: 12/23/2022]
Abstract
Cardiomyocyte differentiation derived from embryonic stem cells (ESCs) is a complex process involving molecular regulation of multiple levels. In this study, we first identify and compare differentially expressed gene (DEG) signatures of ESC-derived cardiomyocyte differentiation (ESCDCD) in humans and mice. Then, the multiscale embedded gene co-expression network analysis (MEGENA) of the human ESCDCD dataset is performed to identify 212 significantly co-expressed gene modules, which capture well the regulatory information of cardiomyocyte differentiation. Three modules respectively involved in the regulation of stem cell pluripotency, Wnt, and calcium pathways are enriched in the DEG signatures of the differentiation phase transition in the two species. Three human-specific cardiomyocyte differentiation phase transition modules are identified. Moreover, the potential regulation mechanisms of transcription factors during cardiomyocyte differentiation are also illustrated. Finally, several novel key drivers of ESCDCD are identified with the evidence of their expression during mouse embryonic cardiomyocyte differentiation. Using an integrative network analysis, the core molecular signatures and gene subnetworks (modules) underlying cardiomyocyte lineage commitment are identified in both humans and mice. Our findings provide a global picture of gene-gene co-regulation and identify key regulators during ESCDCD.
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Affiliation(s)
- Yumei Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Na Yi
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Yi Hu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Hanyu Jiang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Qin Lin
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Rou Chen
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Huan Liu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Yanqiong Gu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Chang Tong
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Min Lu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Junfang Zhang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Luying Peng
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China.
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Institute of Medical Genetics, Tongji University, Shanghai 200092, China; Department of Medical Genetics, Tongji University School of Medicine, Shanghai 200092, China; Heart Health Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China.
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Lee H, Nowosiad P, Dutan Polit LM, Price J, Srivastava DP, Thuret S. Apolipoprotein E expression pattern in human induced pluripotent stem cells during in vitro neural induction. F1000Res 2020; 9:353. [PMID: 32685135 PMCID: PMC7355222 DOI: 10.12688/f1000research.23580.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 11/20/2022] Open
Abstract
Apolipoprotein E (APOE) is a multifunctional protein that plays significant roles in important cellular mechanisms in peripheral tissues and is as well expressed in the central nervous system, notably by adult neural stem cells (NSCs) in the hippocampus. Evidence from animal studies suggest that APOE is critical for adult NSC maintenance. However, whether APOE has the potential to play a similar role in human NSCs has not been directly investigated. To address this question, we conducted a focused study characterising APOE gene and protein expression in an in vitro model of neural differentiation utilising human induced pluripotent stem cells. We found that APOE gene expression was dramatically decreased as the cells became more differentiated, indicating that APOE expression levels reflect the degree of cellular differentiation during neural induction. Furthermore, qualitative analysis results of immunocytochemistry showed that intracellular localisation of APOE protein becomes more pronounced as neural differentiation progresses. Taken together, our findings suggest a potential role for APOE in human NSC maintenance and justify further investigations being carried out to understand whether changes in APOE levels can directly impact the neurogenic capacity of human stem cells.
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Affiliation(s)
- Hyunah Lee
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Paulina Nowosiad
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Lucia M Dutan Polit
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Sandrine Thuret
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
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Moudgil A, Wilkinson MN, Chen X, He J, Cammack AJ, Vasek MJ, Lagunas T, Qi Z, Lalli MA, Guo C, Morris SA, Dougherty JD, Mitra RD. Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells. Cell 2020; 182:992-1008.e21. [PMID: 32710817 PMCID: PMC7510185 DOI: 10.1016/j.cell.2020.06.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/14/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022]
Abstract
Cellular heterogeneity confounds in situ assays of transcription factor (TF) binding. Single-cell RNA sequencing (scRNA-seq) deconvolves cell types from gene expression, but no technology links cell identity to TF binding sites (TFBS) in those cell types. We present self-reporting transposons (SRTs) and use them in single-cell calling cards (scCC), a novel assay for simultaneously measuring gene expression and mapping TFBS in single cells. The genomic locations of SRTs are recovered from mRNA, and SRTs deposited by exogenous, TF-transposase fusions can be used to map TFBS. We then present scCC, which map SRTs from scRNA-seq libraries, simultaneously identifying cell types and TFBS in those same cells. We benchmark multiple TFs with this technique. Next, we use scCC to discover BRD4-mediated cell-state transitions in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single-cell resolution, establishing a new method for studying TF biology in situ.
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Affiliation(s)
- Arnav Moudgil
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Michael N Wilkinson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Xuhua Chen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - June He
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Alexander J Cammack
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Michael J Vasek
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Tomás Lagunas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Zongtai Qi
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Matthew A Lalli
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Chuner Guo
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
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Roberts MS, Anstine LJ, Finke VS, Bryson BL, Webb BM, Weber-Bonk KL, Seachrist DD, Majmudar PR, Keri RA. KLF4 defines the efficacy of the epidermal growth factor receptor inhibitor, erlotinib, in triple-negative breast cancer cells by repressing the EGFR gene. Breast Cancer Res 2020; 22:66. [PMID: 32552913 PMCID: PMC7301986 DOI: 10.1186/s13058-020-01305-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is characterized by high rates of recurrence and poor overall survival. This is due, in part, to a deficiency of targeted therapies, making it essential to identify therapeutically targetable driver pathways of this disease. While epidermal growth factor receptor (EGFR) is expressed in 60% of TNBCs and drives disease progression, attempts to inhibit EGFR in unselected TNBC patients have had a marginal impact on outcomes. Hence, we sought to identify the mechanisms that dictate EGFR expression and inhibitor response to provide a path for improving the utility of these drugs. In this regard, the majority of TNBCs express low levels of the transcription factor, Krüppel-like factor 4 (KLF4), while a small subset is associated with high expression. KLF4 and EGFR have also been reported to have opposing actions in TNBC. Thus, we tested whether KLF4 controls the expression of EGFR and cellular response to its pharmacological inhibition. Methods KLF4 was transiently overexpressed in MDA-MB-231 and MDA-MB-468 cells or silenced in MCF10A cells. Migration and invasion were assessed using modified Boyden chamber assays, and proliferation was measured by EdU incorporation. Candidate downstream targets of KLF4, including EGFR, were identified using reverse phase protein arrays of MDA-MB-231 cells following enforced KLF4 expression. The ability of KLF4 to suppress EGFR gene and protein expression and downstream signaling was assessed by RT-PCR and western blot, respectively. ChIP-PCR confirmed KLF4 binding to the EGFR promoter. Response to erlotinib in the context of KLF4 overexpression or silencing was assessed using cell number and dose-response curves. Results We report that KLF4 is a major determinant of EGFR expression and activity in TNBC cells. KLF4 represses transcription of the EGFR gene, leading to reduced levels of total EGFR, its activated/phosphorylated form (pEGFR), and its downstream signaling intermediates. Moreover, KLF4 suppression of EGFR is a necessary intermediary step for KLF4 to inhibit aggressive TNBC phenotypes. Most importantly, KLF4 dictates the sensitivity of TNBC cells to erlotinib, an FDA-approved inhibitor of EGFR. Conclusions KLF4 is a major regulator of the efficacy of EGFR inhibitors in TNBC cells that may underlie the variable effectiveness of such drugs in patients.
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Affiliation(s)
- Melyssa S Roberts
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Lindsey J Anstine
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Viviane S Finke
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Benjamin L Bryson
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Bryan M Webb
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kristen L Weber-Bonk
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Darcie D Seachrist
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Parth R Majmudar
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Ruth A Keri
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA. .,Department of Genetics and Genome Sciences and Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, OH, 44106, USA.
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Brighi C, Cordella F, Chiriatti L, Soloperto A, Di Angelantonio S. Retinal and Brain Organoids: Bridging the Gap Between in vivo Physiology and in vitro Micro-Physiology for the Study of Alzheimer's Diseases. Front Neurosci 2020; 14:655. [PMID: 32625060 PMCID: PMC7311765 DOI: 10.3389/fnins.2020.00655] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Recent progress in tissue engineering has led to increasingly complex approaches to investigate human neurodegenerative diseases in vitro, such as Alzheimer's disease, aiming to provide more functional and physiological models for the study of their pathogenesis, and possibly the identification of novel diagnostic biomarkers and therapeutic targets. Induced pluripotent stem cell-derived cortical and retinal organoids represent a novel class of in vitro three-dimensional models capable to recapitulate with a high similarity the structure and the complexity of the native brain and retinal tissues, thus providing a framework for better mimicking in a dish the patient's disease features. This review aims to discuss progress made over the years in the field of in vitro three-dimensional cell culture systems, and the benefits and disadvantages related to a possible application of organoids for the study of neurodegeneration associated with Alzheimer's disease, providing a promising breakthrough toward a personalized medicine approach and the reduction in the use of humanized animal models.
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Affiliation(s)
- Carlo Brighi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Federica Cordella
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Luigi Chiriatti
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | | | - Silvia Di Angelantonio
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
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44
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Vykuntham NG, Suran S, Siripini S, John S, Kumar P, Paithankar K, Amere Subbarao S. Altered molecular pathways decides the treatment outcome of Hsp90 inhibitors against breast cancer cells. Toxicol In Vitro 2020; 65:104828. [DOI: 10.1016/j.tiv.2020.104828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 02/06/2023]
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45
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Lee H, Nowosiad P, Dutan Polit LM, Price J, Srivastava DP, Thuret S. Apolipoprotein E expression pattern in human induced pluripotent stem cells during in vitro neural induction. F1000Res 2020; 9:353. [PMID: 32685135 PMCID: PMC7355222 DOI: 10.12688/f1000research.23580.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 09/23/2023] Open
Abstract
Apolipoprotein E (APOE) is a multifunctional protein that plays significant roles in important cellular mechanisms in peripheral tissues and is as well expressed in the central nervous system, notably by adult neural stem cells (NSCs) in the hippocampus. Evidence from animal studies suggest that APOE is critical for adult NSC maintenance. However, whether APOE has the potential to play a similar role in human NSCs has not been directly investigated. To address this question, we conducted a focused study characterising APOE gene and protein expression in an in vitro model of neural differentiation utilising human induced pluripotent stem cells. We found that APOE gene expression was dramatically decreased as the cells became more differentiated, indicating that APOE expression levels reflect the degree of cellular differentiation during neural induction. Furthermore, qualitative analysis results of immunocytochemistry showed that intracellular localisation of APOE protein becomes more pronounced as neural differentiation progresses. Taken together, our findings suggest a potential role for APOE in human NSC maintenance and justify further investigations being carried out to understand whether changes in APOE levels can directly impact the neurogenic capacity of human stem cells.
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Affiliation(s)
- Hyunah Lee
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Paulina Nowosiad
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Lucia M. Dutan Polit
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Deepak P. Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Sandrine Thuret
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
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46
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Lo JHT, U KP, Yiu T, Ong MTY, Lee WYW. Sarcopenia: Current treatments and new regenerative therapeutic approaches. J Orthop Translat 2020; 23:38-52. [PMID: 32489859 PMCID: PMC7256062 DOI: 10.1016/j.jot.2020.04.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022] Open
Abstract
Sarcopenia is characterized by loss of muscle and reduction in muscle strength that contributes to higher mortality rate and increased incidence of fall and hospitalization in the elderly. Mitochondria dysfunction and age-associated inflammation in muscle are two of the main attributors to sarcopenia progression. Recent clinical trials on sarcopenia therapies such as physical exercise, nutraceutical, and pharmaceutical interventions have revealed that exercise is the only effective strategy shown to alleviate sarcopenia. Unlike nutraceutical and pharmaceutical interventions that showed controversial results in sarcopenia alleviation, exercise was found to restore mitochondria homeostasis and dampen inflammatory responses via a complex exchange of myokines and osteokines signalling between muscle and bone. However, as exercise have limited benefit to immobile patients, the use of stem cells and their secretome are being suggested to be novel therapeutics that can be catered to a larger patient population owing to their mitochondria restoration effects and immune modulatory abilities. As such, we reviewed the potential pros and cons associated with various stem cell types/secretome in sarcopenia treatment and the regulatory and production barriers that need to be overcome to translate such novel therapeutic agents into bedside application. Translational potential: This review summarizes the causes underlying sarcopenia from the perspective of mitochondria dysfunction and age-associated inflammation, and the progress of clinical trials for the treatment of sarcopenia. We also propose therapeutic potential of stem cell therapy and bioactive secretome for sarcopenia.
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Affiliation(s)
- Jessica Hiu-Tung Lo
- Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China.,Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China
| | - Kin Pong U
- Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China.,Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China
| | - Tszlam Yiu
- Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China.,Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China
| | - Michael Tim-Yun Ong
- Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China
| | - Wayne Yuk-Wai Lee
- Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China.,Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, PR China
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Lanigan TM, Kopera HC, Saunders TL. Principles of Genetic Engineering. Genes (Basel) 2020; 11:E291. [PMID: 32164255 PMCID: PMC7140808 DOI: 10.3390/genes11030291] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/28/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic engineering is the use of molecular biology technology to modify DNA sequence(s) in genomes, using a variety of approaches. For example, homologous recombination can be used to target specific sequences in mouse embryonic stem (ES) cell genomes or other cultured cells, but it is cumbersome, poorly efficient, and relies on drug positive/negative selection in cell culture for success. Other routinely applied methods include random integration of DNA after direct transfection (microinjection), transposon-mediated DNA insertion, or DNA insertion mediated by viral vectors for the production of transgenic mice and rats. Random integration of DNA occurs more frequently than homologous recombination, but has numerous drawbacks, despite its efficiency. The most elegant and effective method is technology based on guided endonucleases, because these can target specific DNA sequences. Since the advent of clustered regularly interspaced short palindromic repeats or CRISPR/Cas9 technology, endonuclease-mediated gene targeting has become the most widely applied method to engineer genomes, supplanting the use of zinc finger nucleases, transcription activator-like effector nucleases, and meganucleases. Future improvements in CRISPR/Cas9 gene editing may be achieved by increasing the efficiency of homology-directed repair. Here, we describe principles of genetic engineering and detail: (1) how common elements of current technologies include the need for a chromosome break to occur, (2) the use of specific and sensitive genotyping assays to detect altered genomes, and (3) delivery modalities that impact characterization of gene modifications. In summary, while some principles of genetic engineering remain steadfast, others change as technologies are ever-evolving and continue to revolutionize research in many fields.
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Affiliation(s)
- Thomas M. Lanigan
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huira C. Kopera
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas L. Saunders
- Biomedical Research Core Facilities, Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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48
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Ashokachakkaravarthy K, Pottakkat B. Mitotic quiescence in hepatic cancer stem cells: An incognito mode. Oncol Rev 2020; 14:452. [PMID: 32153726 PMCID: PMC7036709 DOI: 10.4081/oncol.2020.452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/02/2020] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma represents one of the most aggressive cancers with high recurrence rates. The high recurrence is a major problem in the management of this disease. Cancer stem cells (CSCs) are often regarded as the basis of cancer recurrence. The anti-proliferative therapy kills the proliferating cells but induces mitotic quiescence in CSCs which remain as residual dormant CSCs. Later on, withdrawal of treatment reactivates the residual CSCs from dormancy to produce new cancer cells. The proliferation of these newly formed cancer cells initiates new tumor formation in the liver leading to tumor recurrence. HCC cells evade the immune surveillance via modulating the key immune cells by alpha feto-protein (AFP) secreted from CSCs or hepatic progenitor cells. This AFP mediated immune evasion assists in establishing new tumors by cancer cells in the liver. In this review, we will summarise the CSC mechanisms of recurrence, mitotic quiescence, dormancy and reactivation of CSCs, metastasis and immune evasion of hepatocellular carcinoma.
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Affiliation(s)
- Kandasamy Ashokachakkaravarthy
- Department of Surgical Gastroenterology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India
| | - Biju Pottakkat
- Department of Surgical Gastroenterology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India
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49
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Anuja K, Kar M, Chowdhury AR, Shankar G, Padhi S, Roy S, Akhter Y, Rath AK, Banerjee B. Role of telomeric RAP1 in radiation sensitivity modulation and its interaction with CSC marker KLF4 in colorectal cancer. Int J Radiat Biol 2020; 96:790-802. [PMID: 31985344 DOI: 10.1080/09553002.2020.1721609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Aims: Radiotherapy is predominantly used as one of the treatment modalities to treat local tumor in colorectal cancer (CRC). Hindrance in disease treatment can be attributed to radio-tolerance of cancer stem cells (CSCs) subsistence in the tumor. Understanding the radio-resistant property of CSCs might help in the accomplishment of targeted radiotherapy treatment and increased disease-free survival. Telomeric RAP1 contributes in modulation of various transcription factors leading to aberrant cell proliferation and tumor cell migration. Therefore, we investigated the role of RAP1 in maintaining resistance phenotype and acquired stemness in radio-resistant cells.Main methods: Characterization of HCT116 derived radio-resistant cell (HCT116RR) was performed by cell survival and DNA damage profiling. RAP1 silenced cells were investigated for DNA damage and expression of CSC markers through western blotting and Real-time PCR post-irradiation. Molecular docking and co-immunoprecipitation study were performed to investigate RAP1 and KLF4 interaction followed by RAP1 protein status profiling in CRC patient.Key findings: We established radio-resistant cells, which showed tolerance to radiotherapy and elevated expression of CSC markers along with RAP1. RAP1 silencing showed enhanced DNA damage and reduced expression of CSC markers post-irradiation. We observed strong physical interaction between RAP1 and KLF4 protein. Furthermore, higher RAP1 expression was observed in the tumor of CRC patients. Dataset analysis also revealed that high expression of RAP1 expression is associated with poor prognosis.Significance: We conclude that higher expression of RAP1 implicates its possible role in promoting radio-resistance in CRC cells by modulating DNA damage and CSC phenotype.
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Affiliation(s)
- Kumari Anuja
- Molecular Stress and Stem Cell Biology Group, School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Madhabananda Kar
- Department of Surgical Oncology, All India Institute of Medical Sciences (AIIMS), Bhubaneswar, India
| | - Amit Roy Chowdhury
- Molecular Stress and Stem Cell Biology Group, School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Gauri Shankar
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Swatishree Padhi
- Molecular Stress and Stem Cell Biology Group, School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Souvick Roy
- Molecular Stress and Stem Cell Biology Group, School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | | | - Birendranath Banerjee
- Molecular Stress and Stem Cell Biology Group, School of Biotechnology, KIIT University, Bhubaneswar, India
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50
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King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen BA. Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells. eLife 2020; 9:41279. [PMID: 32043966 PMCID: PMC7077988 DOI: 10.7554/elife.41279] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
In embryonic stem cells (ESCs), a core transcription factor (TF) network establishes the gene expression program necessary for pluripotency. To address how interactions between four key TFs contribute to cis-regulation in mouse ESCs, we assayed two massively parallel reporter assay (MPRA) libraries composed of binding sites for SOX2, POU5F1 (OCT4), KLF4, and ESRRB. Comparisons between synthetic cis-regulatory elements and genomic sequences with comparable binding site configurations revealed some aspects of a regulatory grammar. The expression of synthetic elements is influenced by both the number and arrangement of binding sites. This grammar plays only a small role for genomic sequences, as the relative activities of genomic sequences are best explained by the predicted occupancy of binding sites, regardless of binding site identity and positioning. Our results suggest that the effects of transcription factor binding sites (TFBS) are influenced by the order and orientation of sites, but that in the genome the overall occupancy of TFs is the primary determinant of activity. Transcription factors are proteins that flip genetic switches; their role is to control when and where genes are active. They do this by binding to short stretches of DNA called cis-regulatory sequences. Each sequence can have several binding sites for different transcription factors, but it is largely unclear whether the transcription factors binding to the same regulatory sequence actually work together. It is possible that each transcription factor may work independently and there only needs to be critical mass of transcription factors bound to throw the genetic switch. If this is the case, the most important features of a cis-regulatory sequence should be the number of binding sites it contains, and how tightly the transcription factors bind to those sites. The more transcription factors and the more strongly they bind, the more active the gene should be. An alternative option is that certain transcription factors may work better together, enhancing each other's effects such that the total effect is more than the sum of its parts. If this is true, the order, orientation and spacing of the binding sites within a sequence should matter more than the number. One way to investigate to distinguish between these possibilities is to study mouse embryonic stem cells, which have a core set of four transcription factors. Looking directly at a real genome, however, can be confusing and it is difficult to measure the effects of different cis-regulatory sequences because genes differ in so many other ways. To tackle this problem, King et al. created a synthetic set of cis-regulatory sequences based on the four core transcription factors found in mouse stem cells. The synthetic set had every combination of two, three or four of the binding sites, with each site either facing forwards or backwards along the DNA strand. King et al. attached each of the synthetic cis-regulatory sequences to a reporter gene to find out how well each sequence performed. This revealed that the cis-regulatory sequences with the most binding sites and the tightest binding affinities work best, suggesting that transcription factors mainly work independently. There was evidence of some interaction between some transcription factors, because, of the synthetic sequences with four binding sites, some worked better than others, and there were patterns in the most effective binding site combinations. However, these effects were small and when King et al. went on to test sequences from the real mouse genome, the most important factor by far was the number of binding sites. Synthetic libraries of DNA sequences allow researchers to examine gene regulation more clearly than is possible in real genomes. Yet this approach does have its limitations and it is impossible to capture every type of cis-regulatory sequence in one library. The next step to extend this work is to combine the two approaches, taking sequences from the real genome and manipulating them one by one. This could help to unravel the rules that govern how cis-regulatory sequences work in real cells.
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Affiliation(s)
- Dana M King
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - Clarice Kit Yee Hong
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - James L Shepherdson
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - David M Granas
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - Brett B Maricque
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - Barak A Cohen
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.,Department of Genetics, Washington University in St. Louis, St. Louis, United States
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