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Kumar S, Ahmad A, Kushwaha N, Shokeen N, Negi S, Gautam K, Singh A, Tiwari P, Garg R, Agarwal R, Mohan A, Trikha A, Thakar A, Saini V. Selection of Ideal Reference Genes for Gene Expression Analysis in COVID-19 and Mucormycosis. Microbiol Spectr 2022; 10:e0165622. [PMID: 36377893 PMCID: PMC9769637 DOI: 10.1128/spectrum.01656-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Selection of reference genes during real-time quantitative PCR (qRT-PCR) is critical to determine accurate and reliable mRNA expression. Nonetheless, not a single study has investigated the expression stability of candidate reference genes to determine their suitability as internal controls in SARS-CoV-2 infection or COVID-19-associated mucormycosis (CAM). Using qRT-PCR, we determined expression stability of the nine most commonly used housekeeping genes, namely, TATA-box binding protein (TBP), cyclophilin (CypA), β-2-microglobulin (B2M), 18S rRNA (18S), peroxisome proliferator-activated receptor gamma (PPARG) coactivator 1 alpha (PGC-1α), glucuronidase beta (GUSB), hypoxanthine phosphoribosyltransferase 1 (HPRT-1), β-ACTIN, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in patients with COVID-19 of various severities (asymptomatic, mild, moderate, and severe) and those with CAM. We used statistical algorithms (delta-CT [threshold cycle], NormFinder, BestKeeper, GeNorm, and RefFinder) to select the most appropriate reference gene and observed that clinical severity profoundly influences expression stability of reference genes. CypA demonstrated the most consistent expression irrespective of disease severity and emerged as the most suitable reference gene in COVID-19 and CAM. Incidentally, GAPDH, the most commonly used reference gene, showed the maximum variations in expression and emerged as the least suitable. Next, we determined expression of nuclear factor erythroid 2-related factor 2 (NRF2), interleukin-6 (IL-6), and IL-15 using CypA and GAPDH as internal controls and show that CypA-normalized expression matches well with the RNA sequencing-based expression of these genes. Further, IL-6 expression correlated well with the plasma levels of IL-6 and C-reactive protein, a marker of inflammation. In conclusion, GAPDH emerged as the least suitable and CypA as the most suitable reference gene in COVID-19 and CAM. The results highlight the expression variability of housekeeping genes due to disease severity and provide a strong rationale for identification of appropriate reference genes in other chronic conditions as well. IMPORTANCE Gene expression studies are critical to develop new diagnostics, therapeutics, and prognostic modalities. However, accurate determination of expression requires data normalization with a reference gene, whose expression does not vary across different disease stages. Misidentification of a reference gene can produce inaccurate results. Unfortunately, despite the global impact of COVID-19 and an urgent unmet need for better treatment, not a single study has investigated the expression stability of housekeeping genes across the disease spectrum to determine their suitability as internal controls. Our study identifies CypA and then TBP as the two most suitable reference genes for COVID-19 and CAM. Further, GAPDH, the most commonly used reference gene in COVID-19 studies, turned out to be the least suitable. This work fills an important gap in the field and promises to facilitate determination of an accurate expression of genes to catalyze development of novel molecular diagnostics and therapeutics for improved patient care.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Ayaan Ahmad
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Namrata Kushwaha
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Niti Shokeen
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Sheetal Negi
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Kamini Gautam
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Anup Singh
- Department of Otorhinolaryngology-Head & Neck Surgery, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Pavan Tiwari
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Rakesh Garg
- Department of Onco-Anesthesiology, Intensive Care, Pain and Palliative Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Richa Agarwal
- Department of Onco-Anesthesiology, Intensive Care, Pain and Palliative Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Anant Mohan
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Anjan Trikha
- Department of Onco-Anesthesiology, Intensive Care, Pain and Palliative Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Alok Thakar
- Department of Otorhinolaryngology-Head & Neck Surgery, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vikram Saini
- Laboratory of Infection Biology and Translational Research, Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
- Biosafety Laboratory-3, Centralized Core Research Facility (CCRF), All India Institute of Medical Sciences (AIIMS), New Delhi, India
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Borges AS, Bastos CMS, Dantas DM, Milfont CGB, Brito GMH, Pereira-de-Morais L, Delmondes GA, da Silva RER, Kennedy-Feitosa E, Maia FPA, Lima CMG, Bin Emran T, Coutinho HDM, Menezes IRA, Kerntopf MR, Caruso G, Barbosa R. Effect of Lippia alba (Mill.) N.E. Brown Essential Oil on the Human Umbilical Artery. PLANTS (BASEL, SWITZERLAND) 2022; 11:3002. [PMID: 36365458 PMCID: PMC9659075 DOI: 10.3390/plants11213002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Lippia alba is popularly known as lemon balm, with its essential oil (EO) cited for displaying antimicrobial, sedative, and vasorelaxant effects. Yet, its action on isolated human vessels has not been described in the literature. Thus, we evaluated the vasorelaxant effect of essential oil of L. alba (EOLa) on human umbilical arteries (HUA) isolated in organ baths. HUA rings were isolated, subjected to contractions induced by potassium chloride (KCl), serotonin (5-HT), or histamine (HIST) to record the isometric tension, and then treated with EOLa (30-1000 µg/mL). The EOLa showed a more prominent inhibitory effect on the pharmacomechanical coupling contraction via HIST with an EC50 value of 277.1 ± 8.5 µg/mL and maximum relaxant effect at 600 µg/mL. The addition of tetraethylammonium (TEA) or 4-aminopyridine (4-AP) in HUA preparations did not inhibit EOLa total relaxant effect at 1000 µg/mL. In the presence of gliblenclamide (GLI), the oil relaxed the HUA rings by 90.8% at maximum concentration. The EOLa was also investigated for its effects on voltage-operated calcium channels (VOCCs), where the HUA preincubation with this oil at 1000 μg/mL inhibited BaCl2 (0.1-30 mM)-induced contractions. This study demonstrates for the first time that EOla has a vasorelaxant effect on HUA and its particular blockade of VOCCs.
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Affiliation(s)
- Alex S. Borges
- Biological Chemistry Department, Postgraduate Program in Biological Chemistry, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Carla M. S. Bastos
- Biological Chemistry Department, Postgraduate Program in Biological Chemistry, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Debora M. Dantas
- Biological Chemistry Department, Postgraduate Program in Biological Chemistry, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Cícera G. B. Milfont
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Guilherme M. H. Brito
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Luís Pereira-de-Morais
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Gyllyandeson A. Delmondes
- Nursing Collegiate, Petrolina Campus, Federal University of The San Francisco Vale, Petrolina 56304-205, Pernambuco, Brazil
| | - Renata E. R. da Silva
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Emanuel Kennedy-Feitosa
- Health Science Department, Morphophysiopharmacology Laboratory, Federal Rural University of Semiarid, Mossoró 59625-900, Rio Grande do Norte, Brazil
| | | | - Clara M. G. Lima
- Department of Food Science, Federal University of Lavras, Lavras 37200-900, Minas Gerais, Brazil
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Henrique Douglas M. Coutinho
- Biological Chemistry Department, Postgraduate Program in Biological Chemistry, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Irwin Rose A. Menezes
- Biological Chemistry Department, Postgraduate Program in Biological Chemistry, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Marta R. Kerntopf
- Biological Chemistry Department, Postgraduate Program in Biological Chemistry, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
| | - Gianluca Caruso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Naples, Italy
| | - Roseli Barbosa
- Biological Chemistry Department, Postgraduate Program in Biological Chemistry, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
- Biological Sciences Department, Physiopharmacology of Excitable Cells Laboratory, Pimenta Campus, Regional University of Cariri, Crato 63105-010, Ceará, Brazil
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Physiological Cooperation between Aquaporin 5 and TRPV4. Int J Mol Sci 2022; 23:ijms231911634. [PMID: 36232935 PMCID: PMC9570067 DOI: 10.3390/ijms231911634] [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: 08/03/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Aquaporins—among them, AQP5—are responsible for transporting water across biological membranes, which is an important process in all living organisms. The transient receptor potential channel 4 (TRPV4) is a cation channel that is mostly calcium-permeable and can also be activated by osmotic stimuli. It plays a role in a number of different functions in the body, e.g., the development of bones and cartilage, and it is involved in the body’s osmoregulation, the generation of certain types of sensation (pain), and apoptosis. Our earlier studies on the uterus and the literature data aroused our interest in the physiological role of the cooperation of AQP5 and TRPV4. In this review, we focus on the co-expression and cooperation of AQP5 and TRPV4 in the lung, salivary glands, uterus, adipose tissues, and lens. Understanding the cooperation between AQP5 and TRPV4 may contribute to the development of new drug candidates and the therapy of several disorders (e.g., preterm birth, cataract, ischemia/reperfusion-induced edema, exercise- or cold-induced asthma).
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