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Article ; Online: Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses.

Napoli, Marco / Deshpande, Avani A / Chakravarti, Deepavali / Rajapakshe, Kimal / Gunaratne, Preethi H / Coarfa, Cristian / Flores, Elsa R

Cancer research communications

2024 Volume 4, Issue 2, Page(s) 264–278

Abstract: The p53 family member TP63 encodes two sets of N-terminal isoforms, TAp63 and ΔNp63 isoforms. They each regulate diverse biological functions in epidermal morphogenesis and in cancer. In the skin, where their activities have been extensively ... ...

Abstract	The p53 family member TP63 encodes two sets of N-terminal isoforms, TAp63 and ΔNp63 isoforms. They each regulate diverse biological functions in epidermal morphogenesis and in cancer. In the skin, where their activities have been extensively characterized, TAp63 prevents premature aging by regulating the quiescence and genomic stability of stem cells required for wound healing and hair regeneration, while ΔNp63 controls maintenance and terminal differentiation of epidermal basal cells. This functional diversity is surprising given that these isoforms share a high degree of similarity, including an identical sequence for a DNA-binding domain. To understand the mechanisms of the transcriptional programs regulated by each p63 isoform and leading to diverse biological functions, we performed genome-wide analyses using p63 isoform-specific chromatin immunoprecipitation, RNA sequencing, and metabolomics of TAp63-/- and ΔNp63-/- mouse epidermal cells. Our data indicate that TAp63 and ΔNp63 physically and functionally interact with distinct transcription factors for the downstream regulation of their target genes, thus ultimately leading to the regulation of unique transcriptional programs and biological processes. Our findings unveil novel transcriptomes regulated by the p63 isoforms to control diverse biological functions, including the cooperation between TAp63 and NRF2 in the modulation of metabolic pathways and response to oxidative stress providing a mechanistic explanation for the TAp63 knock out phenotypes. Significance: The p63 isoforms, TAp63 and ΔNp63, control epithelial morphogenesis and tumorigenesis through the interaction with distinct transcription factors and the subsequent regulation of unique transcriptional programs.
MeSH term(s)	Mice ; Animals ; NF-E2-Related Factor 2/genetics ; Genome-Wide Association Study ; Neoplasms/genetics ; Protein Isoforms/genetics ; Epidermis/metabolism
Chemical Substances	NF-E2-Related Factor 2 ; Protein Isoforms
Language	English
Publishing date	2024-01-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2767-9764
ISSN (online)	2767-9764
DOI	10.1158/2767-9764.CRC-23-0358
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Article ; Online: Laminin Alpha 2 Enhances the Protective Effect of Exosomes on Human iPSC-Derived Cardiomyocytes in an In Vitro Ischemia-Reoxygenation Model.

Mesquita, Fernanda C P / King, Madelyn / da Costa Lopez, Patricia Luciana / Thevasagayampillai, Shiyanth / Gunaratne, Preethi H / Hochman-Mendez, Camila

International journal of molecular sciences

2024 Volume 25, Issue 7

Abstract: Ischemic heart disease, a leading cause of death worldwide, manifests clinically as myocardial infarction. Contemporary therapies using mesenchymal stromal cells (MSCs) and their derivative (exosomes, EXOs) were developed to decrease the progression of ... ...

Abstract	Ischemic heart disease, a leading cause of death worldwide, manifests clinically as myocardial infarction. Contemporary therapies using mesenchymal stromal cells (MSCs) and their derivative (exosomes, EXOs) were developed to decrease the progression of cell damage during ischemic injury. Laminin alpha 2 (LAMA2) is an important extracellular matrix protein of the heart. Here, we generated MSC-derived exosomes cultivated under LAMA2 coating to enhance human-induced pluripotent stem cell (hiPSC)-cardiomyocyte recognition of LAMA2-EXOs, thus, increasing cell protection during ischemia reoxygenation. We mapped the mRNA content of LAMA2 and gelatin-EXOs and identified 798 genes that were differentially expressed, including genes associated with cardiac muscle development and extracellular matrix organization. Cells were treated with LAMA2-EXOs 2 h before a 4 h ischemia period (1% O
MeSH term(s)	Humans ; Myocytes, Cardiac ; Exosomes ; Induced Pluripotent Stem Cells ; Carbon Dioxide ; Endothelial Cells ; Ischemia ; Laminin
Chemical Substances	laminin alpha 2 ; Carbon Dioxide (142M471B3J) ; Laminin
Language	English
Publishing date	2024-03-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25073773
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Article ; Online: Transfection of Unmodified MicroRNA Using Monolayer-Coated Au Nanoparticles as Gene-Delivery Vehicles.

Hoang, Johnson / Patil, Sagar L / Srinoi, Pannaree / Liu, Tingting / Marquez, Maria D / Khantamat, Orawan / Tuntiwechapikul, Wirote / Gunaratne, Preethi H / Lee, T Randall

ACS applied bio materials

2023 Volume 7, Issue 1, Page(s) 230–237

Abstract: This article describes a monolayer-coated gold nanoparticle-based transfection system for the delivery of microRNA (miRNA) into human osteosarcoma (HOS) cells. Two distinct ammonium-terminated adsorbates were used in this study, which provided a platform ...

Abstract	This article describes a monolayer-coated gold nanoparticle-based transfection system for the delivery of microRNA (miRNA) into human osteosarcoma (HOS) cells. Two distinct ammonium-terminated adsorbates were used in this study, which provided a platform for ionic bonding of the miRNA onto gold nanoparticles (AuNPs). The custom-designed monolayer-coated gold nanoparticles were characterized by dynamic light scattering, gel mobility shift assay, transmission electron microscopy, ultraviolet-visible spectrometry, zeta potential, and X-ray photoelectron spectroscopy. The miRNA-loaded gold nanoparticles were transfected, and the level of intracellular miRNA delivered and taken up by cells was measured by Taqman qPCR. The overall analysis indicated a successful delivery of miRNA into the HOS cells at an ∼11,000-fold increase compared to nontreated cells.
MeSH term(s)	Humans ; Gold/chemistry ; MicroRNAs/genetics ; Metal Nanoparticles/chemistry ; Transfection ; Gene Transfer Techniques
Chemical Substances	Gold (7440-57-5) ; MicroRNAs
Language	English
Publishing date	2023-12-22
Publishing country	United States
Document type	Journal Article
ISSN	2576-6422
ISSN (online)	2576-6422
DOI	10.1021/acsabm.3c00837
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Article ; Online: Fn14 promotes myoblast fusion during regenerative myogenesis.

Tomaz da Silva, Meiricris / Joshi, Aniket S / Castillo, Micah B / Koike, Tatiana E / Roy, Anirban / Gunaratne, Preethi H / Kumar, Ashok

Life science alliance

2023 Volume 6, Issue 12

Abstract: Skeletal muscle regeneration involves coordinated activation of an array of signaling pathways. Fibroblast growth factor-inducible 14 (Fn14) is a bona fide receptor for the TWEAK cytokine. Levels of Fn14 are increased in the skeletal muscle of mice after ...

Abstract	Skeletal muscle regeneration involves coordinated activation of an array of signaling pathways. Fibroblast growth factor-inducible 14 (Fn14) is a bona fide receptor for the TWEAK cytokine. Levels of Fn14 are increased in the skeletal muscle of mice after injury. However, the cell-autonomous role of Fn14 in muscle regeneration remains unknown. Here, we demonstrate that global deletion of the Fn14 receptor in mice attenuates muscle regeneration. Conditional ablation of Fn14 in myoblasts but not in differentiated myofibers of mice inhibits skeletal muscle regeneration. Fn14 promotes myoblast fusion without affecting the levels of myogenic regulatory factors in the regenerating muscle. Fn14 deletion in myoblasts hastens initial differentiation but impairs their fusion. The overexpression of Fn14 in myoblasts results in the formation of myotubes having an increased diameter after induction of differentiation. Ablation of Fn14 also reduces the levels of various components of canonical Wnt and calcium signaling both in vitro and in vivo. Forced activation of Wnt signaling rescues fusion defects in Fn14-deficient myoblast cultures. Collectively, our results demonstrate that Fn14-mediated signaling positively regulates myoblast fusion and skeletal muscle regeneration.
MeSH term(s)	Animals ; Mice ; Cell Communication ; Cell Differentiation ; Muscle Development ; Myoblasts/metabolism ; Wnt Signaling Pathway ; TWEAK Receptor/metabolism
Chemical Substances	Tnfrsf12a protein, mouse ; TWEAK Receptor
Language	English
Publishing date	2023-10-09
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202302312
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Article ; Online: Co-delivery of novel bispecific and trispecific engagers by an amplicon vector augments the therapeutic effect of an HSV-based oncolytic virotherapy.

Ravirala, Divya / Mistretta, Brandon / Gunaratne, Preethi H / Pei, Guangsheng / Zhao, Zhongming / Zhang, Xiaoliu

Journal for immunotherapy of cancer

2021 Volume 9, Issue 7

Abstract: Background: Although oncolytic virotherapy has shown substantial promises as a new treatment modality for many malignancies, further improvement on its therapeutic efficacy will likely bring more clinical benefits. One plausible way of enhancing the ... ...

Abstract	Background: Although oncolytic virotherapy has shown substantial promises as a new treatment modality for many malignancies, further improvement on its therapeutic efficacy will likely bring more clinical benefits. One plausible way of enhancing the therapeutic effect of virotherapy is to enable it with the ability to concurrently engage the infiltrating immune cells to provide additional antitumor mechanisms. Here, we report the construction and evaluation of two novel chimeric molecules (bispecific chimeric engager proteins, BiCEP and trispecific chimeric engager protein, TriCEP) that can engage both natural killer (NK) and T cells with tumor cells for enhanced antitumor activities. Methods: BiCEP was constructed by linking orthopoxvirus major histocompatibility complex class I-like protein, which can selectively bind to NKG2D with a high affinity to a mutant form of epidermal growth factor (EGF) that can strongly bind to EGF receptor. TriCEP is similarly constructed except that it also contains a modified form of interleukin-2 that can only function as a tethered form. As NKG2D is expressed on both NK and CD8 Results: Both BiCEP and TriCEP showed the ability to engage NK and T cells to kill tumor cells in vitro. Coadministration of BiCEP and TriCEP with an oncolytic herpes simplex virus enhanced the overall antitumor effect. Furthermore, single-cell RNA sequencing analysis revealed that TriCEP not only engaged NK and T cells to kill tumor cells, it also promotes the infiltration and activation of these important immune cells. Conclusions: These novel chimeric molecules exploit the ability of the oncolytic virotherapy in altering the tumor microenvironment with increased infiltration of important immune cells such as NK and T cells for cancer immunotherapy. The ability of BiCEP and TriCEP to engage both NK and T cells makes them an ideal choice for arming an oncolytic virotherapy.
MeSH term(s)	Antibodies, Bispecific/metabolism ; Humans ; Oncolytic Virotherapy/methods ; Oncolytic Viruses/genetics ; Simplexvirus/drug effects ; Simplexvirus/genetics
Chemical Substances	Antibodies, Bispecific
Language	English
Publishing date	2021-07-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2719863-7
ISSN	2051-1426 ; 2051-1426
ISSN (online)	2051-1426
ISSN	2051-1426
DOI	10.1136/jitc-2021-002454
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Article ; Online: Embryonic stem cell microRNAs: defining factors in induced pluripotent (iPS) and cancer (CSC) stem cells?

Gunaratne, Preethi H

Current stem cell research & therapy

2009 Volume 4, Issue 3, Page(s) 168–177

Abstract: The discovery of microRNAs (miRNAs - small non-coding RNAs of approximately 22 nt) heralded a new and exciting era in biology. During this period miRNAs have gone from ignominy due to their origin mainly in 'junk DNA' to notoriety where they can be at ... ...

Abstract	The discovery of microRNAs (miRNAs - small non-coding RNAs of approximately 22 nt) heralded a new and exciting era in biology. During this period miRNAs have gone from ignominy due to their origin mainly in 'junk DNA' to notoriety where they can be at once characterized as being all powerful (a single miRNA can target and potentially silence several hundred genes) and yet marginal (a given gene can be targeted by several miRNAs such that a given miRNA typically exerts a modest repression) [1-4]. The emerging paradox is exemplified by miRNAs that are prominently expressed in embryonic stem (ES) cells. The collective importance of miRNAs is firmly established by the fact that Dicer-/- mouse embryos die on day 7.5 due to defects in differentiation [5]. However, oppositely correlated expression that is expected of conventional repressors is increasingly being defied in multiple systems in relation to miRNA-mRNA target pairs. This is most evident in ES cells where miR-290-295 and 302 clusters the most abundant ES cell miRNAs are found to be driven by pluripotency genes Oct4, Nanog and Sox2 and also target these genes in 'incoherent feed-forward loops' [7]. Here the miRNAs are co-expressed and positively correlated with these targets that they repress suggesting that one of their primary roles is to fine tune gene expression rather than act as ON/OFF switches. On the other hand, let-7 family members that are notably low in ES cells and rapidly induced upon differentiation exhibit more conventional anti-correlated expression patterns with their targets [7-8]. In an intricately designed auto-regulatory loop, LIN28, a key 'keeper' of the pluripotent state binds and represses the processing of let-7 (a key 'keeper' of the differentiated state) [9-11]. One of the let-7 family members, let-7g targets and represses LIN28 through four 3'-UTR binding sites [12]. We propose that LIN28/let-7 pair has the potential to act as a 'toggle switch' that balances the decision to maintain pluripotency vs. differentiation. We also propose that the c-Myc/E2F driven miR17-92 cluster that together controls the G1 to S transition is fundamental for ES self-renewal and cell proliferation [13-18]. In that context it is no surprise that LIN28 and c-Myc (and therefore let-7 and miR-17-92 by association) and more recently Oct4/Sox2 regulated miR-302 has been shown to be among a handful of factors shown to be necessary and sufficient to convert differentiated cells to induced pluripotent stem (iPS) cells [19-29]. It is also no surprise that activation of miR-17-92 (OncomiRs) and down-regulation of let-7 (tumor suppressors) is a recurring theme in relation to cancers from multiple systems [30-48]. We speculate that the LIN28/let-7; c-MYC-E2F/miR-17-92 and Oct4/Sox2/miR-302-cyclin D1 networks are fundamental to properties of pluripotency and self-renewal associated with embryonic stem cells. We also speculate that ES cell miRNA-mRNA associations may also regulate tissue homeostasis and regeneration in the fully developed adult. Consequently, the appropriate regulation of LIN28/let-7; c-MYC-E2F/miR-17-92 and Oct4/Sox2/miR-302-cyclin D1 gene networks will be critical for the success of regenerative strategies that involve iPS cells. Any perturbation in key ES cell miRNA-mRNA networks during any of the above processes maybe a hallmark of (CSCs).
MeSH term(s)	Animals ; Cell Differentiation/genetics ; Embryonic Stem Cells/physiology ; Gene Expression Regulation ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Multigene Family ; Neoplasms/genetics ; Neoplasms/pathology ; Neoplastic Stem Cells/physiology ; Pluripotent Stem Cells/physiology ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
Chemical Substances	MicroRNAs ; RNA, Messenger
Language	English
Publishing date	2009-04-03
Publishing country	United Arab Emirates
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2251937-3
ISSN	2212-3946 ; 1574-888X
ISSN (online)	2212-3946
ISSN	1574-888X
DOI	10.2174/157488809789057400
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Article: Curcumin Reduces Adipose Tissue Inflammation and Alters Gut Microbiota in Diet‐Induced Obese Male Mice

Islam, Tariful / Koboziev, Iurii / Albracht‐Schulte, Kembra / Mistretta, Brandon / Scoggin, Shane / Yosofvand, Mohammad / Moussa, Hanna / Zabet‐Moghaddam, Masoud / Ramalingam, Latha / Gunaratne, Preethi H. / Moustaid‐Moussa, Naima

Molecular nutrition & food research. 2021 Nov., v. 65, no. 22

2021

Abstract: SCOPE: Obesity prevalence continues to increase and contribute to metabolic diseases, potentially by driving systemic inflammation. Curcumin is an anti‐inflammatory spice with claimed health benefits. However, mechanisms by which curcumin may reduce ... ...

Abstract	SCOPE: Obesity prevalence continues to increase and contribute to metabolic diseases, potentially by driving systemic inflammation. Curcumin is an anti‐inflammatory spice with claimed health benefits. However, mechanisms by which curcumin may reduce obesity‐associated inflammation are poorly understood; thus, it is hypothesized that benefits of curcumin consumption may occur through reduced white adipose tissue (WAT) inflammation and/or beneficial changes in gut bacteria. METHODS AND RESULTS: Male B6 mice are fed high‐fat diets (HFD, 45% kcal fat) or HFD supplemented with 0.4% (w/w) curcumin (HFC) for 14 weeks. Curcumin supplementation significantly reduces adiposity and total macrophage infiltration in WAT, compared to HFD group, consistent with reduced mRNA levels of M1 (Cd80, Cd38, Cd11c) and M2 (Arginase‐1) macrophage markers. Moreover, curcumin supplementation reduces expression of other key pro‐inflammatory genes, such as NF‐κB p65 subunit (p65), Stat1, Tlr4, and Il6, in WAT (p < 0.05). Using microbial 16S RNA sequencing, it is demonstrated that the relative abundance of the Lactococcus, Parasutterella, and Turicibacter genera are increased in the HFC group versus HFD. CONCLUSIONS: Curcumin exerts protective metabolic effects in dietary obesity, in part through downregulation of adipose tissue inflammation, which may be mediated by alterations in composition of gut microbiota, and metabolism of curcumin into curcumin‐O‐glucuronide.
Keywords	Lactococcus ; adiposity ; curcumin ; digestive system ; food research ; inflammation ; interleukin-6 ; intestinal microorganisms ; macrophages ; males ; metabolism ; obesity ; spices ; white adipose tissue
Language	English
Dates of publication	2021-11
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2160372-8
ISSN	1613-4133 ; 1613-4125
ISSN (online)	1613-4133
ISSN	1613-4125
DOI	10.1002/mnfr.202100274
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Article ; Online: Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer.

Mistretta, Brandon / Rankothgedera, Sakuni / Castillo, Micah / Rao, Mitchell / Holloway, Kimberly / Bhardwaj, Anjana / El Noafal, Maha / Albarracin, Constance / El-Zein, Randa / Rezaei, Hengameh / Su, Xiaoping / Akbani, Rehan / Shao, Xiaoshan M / Czerniecki, Brian J / Karchin, Rachel / Bedrosian, Isabelle / Gunaratne, Preethi H

Frontiers in immunology

2023 Volume 14, Page(s) 1188831

Abstract: Introduction: We present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer. ...

Abstract	Introduction: We present here a strategy to identify immunogenic neoantigen candidates from unique amino acid sequences at the junctions of fusion proteins which can serve as targets in the development of tumor vaccines for the treatment of breastcancer. Method: We mined the sequence reads of breast tumor tissue that are usually discarded as discordant paired-end reads and discovered cancer specific fusion transcripts using tissue from cancer free controls as reference. Binding affinity predictions of novel peptide sequences crossing the fusion junction were analyzed by the MHC Class I binding predictor, MHCnuggets. CD8+ T cell responses against the 15 peptides were assessed through in vitro Enzyme Linked Immunospot (ELISpot). Results: We uncovered 20 novel fusion transcripts from 75 breast tumors of 3 subtypes: TNBC, HER2+, and HR+. Of these, the NSFP1-LRRC37A2 fusion transcript was selected for further study. The 3833 bp chimeric RNA predicted by the consensus fusion junction sequence is consistent with a read-through transcription of the 5'-gene NSFP1-Pseudo gene NSFP1 (NSFtruncation at exon 12/13) followed by trans-splicing to connect withLRRC37A2 located immediately 3' through exon 1/2. A total of 15 different 8-mer neoantigen peptides discovered from the NSFP1 and LRRC37A2 truncations were predicted to bind to a total of 35 unique MHC class I alleles with a binding affinity of IC50<500nM.); 1 of which elicited a robust immune response. Conclusion: Our data provides a framework to identify immunogenic neoantigen candidates from fusion transcripts and suggests a potential vaccine strategy to target the immunogenic neopeptides in patients with tumors carrying the NSFP1-LRRC37A2 fusion.
MeSH term(s)	Humans ; Animals ; Female ; Breast Neoplasms/genetics ; Cancer Vaccines ; Genes, MHC Class I ; Mammary Neoplasms, Animal ; Breast
Chemical Substances	Cancer Vaccines
Language	English
Publishing date	2023-09-06
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1188831
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Article ; Online: Direct reprogramming of cardiomyocytes into cardiac Purkinje-like cells.

Prodan, Nicole / Ershad, Faheem / Reyes-Alcaraz, Arfaxad / Li, Luge / Mistretta, Brandon / Gonzalez, Lei / Rao, Zhoulyu / Yu, Cunjiang / Gunaratne, Preethi H / Li, Na / Schwartz, Robert J / McConnell, Bradley K

iScience

2022 Volume 25, Issue 11, Page(s) 105402

Abstract: Currently, there are no treatments that ameliorate cardiac cell death, the underlying basis of cardiovascular disease. An unexplored cell type in cardiac regeneration is cardiac Purkinje cells; specialized cells from the cardiac conduction system (CCS) ... ...

Abstract	Currently, there are no treatments that ameliorate cardiac cell death, the underlying basis of cardiovascular disease. An unexplored cell type in cardiac regeneration is cardiac Purkinje cells; specialized cells from the cardiac conduction system (CCS) responsible for propagating electrical signals. Purkinje cells have tremendous potential as a regenerative treatment because they may intrinsically integrate with the CCS of a recipient myocardium, resulting in more efficient electrical conduction in diseased hearts. This study is the first to demonstrate an effective protocol for the direct reprogramming of human cardiomyocytes into cardiac Purkinje-like cells using small molecules. The cells generated were genetically and functionally similar to native cardiac Purkinje cells, where expression of key cardiac Purkinje genes such as
Language	English
Publishing date	2022-10-20
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.105402
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Article ; Conference proceedings: Advances in genome biology and technology.

Gunaratne, Preethi H

Expert review of molecular diagnostics

2004 Volume 4, Issue 6, Page(s) 757–760

MeSH term(s)	Animals ; Biotechnology ; Expressed Sequence Tags ; Gene Expression Profiling/methods ; Genome ; Genomic Library ; Genomics/methods ; Humans ; Stem Cells/metabolism
Language	English
Publishing date	2004-11
Publishing country	England
Document type	Congresses
ZDB-ID	2112530-2
ISSN	1744-8352 ; 1473-7159
ISSN (online)	1744-8352
ISSN	1473-7159
DOI	10.1586/14737159.4.6.757
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