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Efremova I, Maslennikov R, Poluektova E, Medvedev O, Kudryavtseva A, Krasnov G, Fedorova M, Romanikhin F, Bakhitov V, Aliev S, Sedova N, Kuropatkina T, Ivanova A, Zharkova M, Pervushova E, Ivashkin V. Gut Microbiota and Biomarkers of Endothelial Dysfunction in Cirrhosis. Int J Mol Sci 2024; 25:1988. [PMID: 38396668 PMCID: PMC10888218 DOI: 10.3390/ijms25041988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Our aim was to study the association of endothelial dysfunction biomarkers with cirrhosis manifestations, bacterial translocation, and gut microbiota taxa. The fecal microbiome was assessed using 16S rRNA gene sequencing. Plasma levels of nitrite, big endothelin-1, asymmetric dimethylarginine (ADMA), presepsin, and claudin were measured as biomarkers of endothelial dysfunction, bacterial translocation, and intestinal barrier dysfunction. An echocardiography with simultaneous determination of blood pressure and heart rate was performed to evaluate hemodynamic parameters. Presepsin, claudin 3, nitrite, and ADMA levels were higher in cirrhosis patients than in controls. Elevated nitrite levels were associated with high levels of presepsin and claudin 3, the development of hemodynamic circulation, hypoalbuminemia, grade 2-3 ascites, overt hepatic encephalopathy, high mean pulmonary artery pressure, increased abundance of Proteobacteria and Erysipelatoclostridium, and decreased abundance of Oscillospiraceae, Subdoligranulum, Rikenellaceae, Acidaminococcaceae, Christensenellaceae, and Anaerovoracaceae. Elevated ADMA levels were associated with higher Child-Pugh scores, lower serum sodium levels, hypoalbuminemia, grade 2-3 ascites, milder esophageal varices, overt hepatic encephalopathy, lower mean pulmonary artery pressure, and low abundance of Erysipelotrichia and Erysipelatoclostridiaceae. High big endothelin-1 levels were associated with high levels of presepsin and sodium, low levels of fibrinogen and cholesterol, hypocoagulation, increased Bilophila and Coprobacillus abundances, and decreased Alloprevotella abundance.
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Affiliation(s)
- Irina Efremova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str. 1-1, 119435 Moscow, Russia; (I.E.); (E.P.)
| | - Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str. 1-1, 119435 Moscow, Russia; (I.E.); (E.P.)
- Scientific Community for the Promotion of the Clinical Study of the Human Microbiome, Pogodinskaya Str. 1-1, 119435 Moscow, Russia
- Consultative and Diagnostic Center 2 of the Moscow Health Department, Millionnaya Str. 6, 107564 Moscow, Russia (N.S.)
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str. 1-1, 119435 Moscow, Russia; (I.E.); (E.P.)
- Scientific Community for the Promotion of the Clinical Study of the Human Microbiome, Pogodinskaya Str. 1-1, 119435 Moscow, Russia
| | - Oleg Medvedev
- Pharmacology Department, Lomonosov Moscow State University, Leninskie Gori 1, 119991 Moscow, Russia; (O.M.)
| | - Anna Kudryavtseva
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, 119991 Moscow, Russia
| | - George Krasnov
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, 119991 Moscow, Russia
| | - Maria Fedorova
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, 119991 Moscow, Russia
| | - Filipp Romanikhin
- Pharmacology Department, Lomonosov Moscow State University, Leninskie Gori 1, 119991 Moscow, Russia; (O.M.)
| | - Vyacheslav Bakhitov
- Consultative and Diagnostic Center 2 of the Moscow Health Department, Millionnaya Str. 6, 107564 Moscow, Russia (N.S.)
| | - Salekh Aliev
- Consultative and Diagnostic Center 2 of the Moscow Health Department, Millionnaya Str. 6, 107564 Moscow, Russia (N.S.)
- First Hospital Surgery Department, Pirogov Russian National Research Medical University, Ostrovityanova Str. 1-7, 117997 Moscow, Russia
| | - Natalia Sedova
- Consultative and Diagnostic Center 2 of the Moscow Health Department, Millionnaya Str. 6, 107564 Moscow, Russia (N.S.)
- Department of Clinical Laboratory Diagnostics, FGBOU DPO “Russian Medical Academy of Continuing Professional Education of the Ministry of Health of the Russian Federation”, Barricadnaya Str. 2/1-2, 125993 Moscow, Russia
| | - Tatiana Kuropatkina
- Pharmacology Department, Lomonosov Moscow State University, Leninskie Gori 1, 119991 Moscow, Russia; (O.M.)
| | - Anastasia Ivanova
- Pharmacology Department, Lomonosov Moscow State University, Leninskie Gori 1, 119991 Moscow, Russia; (O.M.)
| | - Maria Zharkova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str. 1-1, 119435 Moscow, Russia; (I.E.); (E.P.)
| | - Ekaterina Pervushova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str. 1-1, 119435 Moscow, Russia; (I.E.); (E.P.)
| | - Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str. 1-1, 119435 Moscow, Russia; (I.E.); (E.P.)
- Scientific Community for the Promotion of the Clinical Study of the Human Microbiome, Pogodinskaya Str. 1-1, 119435 Moscow, Russia
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Kovaleva A, Poluektova E, Maslennikov R, Karchevskaya A, Shifrin O, Kiryukhin A, Tertychnyy A, Kovalev L, Kovaleva M, Lobanova O, Kudryavtseva A, Krasnov G, Ivashkin V. Intestinal Barrier and Gut Microbiota in Patients with Overlapping Irritable Bowel Syndrome and Functional Dyspepsia. Dig Dis Sci 2023; 68:4166-4174. [PMID: 37752368 DOI: 10.1007/s10620-023-08117-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
BACKGROUND Disturbances in the intestinal barrier and gut dysbiosis have been observed in patients with functional bowel diseases. AIMS To investigate the correlation between biomarkers of intestinal barrier disorders at different layers and the severity of symptoms in patients with overlapping diarrhea-predominant irritable bowel syndrome and functional dyspepsia (IDFO), as well as with gut microbiota taxa. METHODS This study included 45 patients with IDFO and 16 healthy controls. Endoscopy with biopsy of the duodenum and sigmoid colon (SC) was performed to count intraepithelial lymphocytes (IELs) and mucosal eosinophils (subepithelial layer), assess fatty acid binding protein (FABP; epithelial layer) level, and stain for mucin-2 (MUC-2; pre-epithelial layer). Composition of the gut microbiota was evaluated using 16S rRNA gene sequencing. RESULTS Patients with IDFO exhibited an increase in biomarkers of intestinal barrier disorders at all layers studied. IEL count in the duodenum was correlated with the severity of bloating (r = 0.336; p = 0.024) and, in the SC, was correlated with tenesmus severity (r = 0.303; p = 0.042). FABP-1 level in the SC was correlated with the severity of diarrhea (r = 0.577; p = 0.001), and FABP-5 concentration in the SC was correlated with abdominal distension (r = 0.477; p = 0.010). MUC-2 concentration in the duodenum was correlated with the severity of heartburn (r = 0.572; p = 0.025) and burning sensation in the epigastrium (r = 0.518; p = 0.048). All biomarkers of intestinal barrier permeability were correlated with the abundance of some gut microbiota taxa. CONCLUSION Patients with IDFO exhibited disrupted intestinal barrier function in all layers, which was associated with clinical symptom severity and changes in the gut microbiota.
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Affiliation(s)
| | | | | | | | | | | | | | - Leonid Kovalev
- A.N. Bach Institute of Biochemistry, Leninsky Prospekt, 33, Bld. 2, Moscow, Russia, 119071
| | - Marina Kovaleva
- A.N. Bach Institute of Biochemistry, Leninsky Prospekt, 33, Bld. 2, Moscow, Russia, 119071
| | | | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Vavilova St., 32, Bld. 1, Moscow, Russia, 119991
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Vavilova St., 32, Bld. 1, Moscow, Russia, 119991
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Kovaleva A, Poluektova E, Maslennikov R, Karchevskaya A, Shifrin O, Kiryukhin A, Tertychnyy A, Kovalev L, Kovaleva M, Lobanova O, Kudryavtseva A, Krasnov G, Fedorova M, Ivashkin V. Effect of Rebamipide on the Intestinal Barrier, Gut Microbiota Structure and Function, and Symptom Severity Associated with Irritable Bowel Syndrome and Functional Dyspepsia Overlap: A Randomized Controlled Trial. J Clin Med 2023; 12:6064. [PMID: 37763004 PMCID: PMC10531936 DOI: 10.3390/jcm12186064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/30/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Treatment of functional digestive disorders is not always effective. Therefore, a search for new application points for potential drugs is perspective. Our aim is to evaluate the effect of rebamipide on symptom severity, intestinal barrier status, and intestinal microbiota composition and function in patients with diarrheal variant of irritable bowel syndrome overlapping with functional dyspepsia (D-IBSoFD). Sixty patients were randomized to receive trimebutine (TRI group), trimebutine + rebamipide (T + R group), or rebamipide (REB group) for 2 months. At the beginning and end of the study, patients were assessed for general health (SF-36), severity of digestive symptoms (Gastrointestinal Symptom Rating and 7 × 7 scales), state of the intestinal barrier, and composition (16S rRNA gene sequencing) and function (short-chain fatty acid fecal content) of the gut microbiota. The severity of most digestive symptoms was reduced in the REB and T + R groups to levels similar to that observed in the TRI group. The duodenal and sigmoidal lymphocytic and sigmoidal eosinophilic infiltration was decreased only in the REB and T + R groups, not in the TRI group. Serum zonulin levels were significantly decreased only in the REB group. A decrease in intraepithelial lymphocytic infiltration in the duodenum correlated with a decrease in the severity of rumbling and flatulence, while a decrease in infiltration within the sigmoid colon correlated with improved stool consistency and decreased severity of the sensation of incomplete bowel emptying. In conclusion, rebamipide improves the intestinal barrier condition and symptoms in D-IBSoFD. The rebamipide effects are not inferior to those of trimebutine.
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Affiliation(s)
- Aleksandra Kovaleva
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
| | - Elena Poluektova
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
- The Scientific Community for Human Microbiome Research, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia
| | - Roman Maslennikov
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
- The Scientific Community for Human Microbiome Research, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia
| | - Anna Karchevskaya
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
- Laboratory of General and Clinical Neurophysiology, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 5A Butlerova Str., 117485 Moscow, Russia
- N.N. Burdenko National Medical Research Center of Neurosurgery, 16, 4th Tverskaya-Yamskaya St., 125047 Moscow, Russia
| | - Oleg Shifrin
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
| | - Andrey Kiryukhin
- Endoscopy Unit, The Second University Clinic, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia
| | - Aleksandr Tertychnyy
- Institute of Clinical Morphology and Digital Pathology, Sechenov University, Trubetskaya Str., 8, Bld. 2, 119048 Moscow, Russia; (A.T.)
| | - Leonid Kovalev
- Laboratory of Structural Biochemistry of Protein, A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospekt, 33, Bld. 2, 119071 Moscow, Russia
| | - Marina Kovaleva
- Laboratory of Structural Biochemistry of Protein, A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospekt, 33, Bld. 2, 119071 Moscow, Russia
| | - Olga Lobanova
- Institute of Clinical Morphology and Digital Pathology, Sechenov University, Trubetskaya Str., 8, Bld. 2, 119048 Moscow, Russia; (A.T.)
| | - Anna Kudryavtseva
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Bld. 1, 119991 Moscow, Russia
| | - George Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Bld. 1, 119991 Moscow, Russia
| | - Maria Fedorova
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Bld. 1, 119991 Moscow, Russia
| | - Vladimir Ivashkin
- Department of Introduction to Internal Diseases, Gastroenterology and Hepatology, Sechenov University, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia; (A.K.); (E.P.)
- The Scientific Community for Human Microbiome Research, Pogodinskaya Str., 1, Bld. 1, 119435 Moscow, Russia
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Efremova I, Maslennikov R, Poluektova E, Zharkova M, Kudryavtseva A, Krasnov G, Fedorova M, Shirokova E, Kozlov E, Levshina A, Ivashkin V. Gut Dysbiosis and Hemodynamic Changes as Links of the Pathogenesis of Complications of Cirrhosis. Microorganisms 2023; 11:2202. [PMID: 37764046 PMCID: PMC10537778 DOI: 10.3390/microorganisms11092202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
The aim was to evaluate the relationship between gut dysbiosis and hemodynamic changes (hyperdynamic circulation) in cirrhosis, and between hemodynamic changes and complications of this disease. This study included 47 patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. Echocardiography with a simultaneous assessment of blood pressure and heart rate was performed to assess systemic hemodynamics. Patients with hyperdynamic circulation had more severe cirrhosis, lower albumin, sodium and prothrombin levels, higher C-reactive protein, aspartate aminotransferase and total bilirubin levels, and higher incidences of portopulmonary hypertension, ascites, overt hepatic encephalopathy, hypoalbuminemia, hypoprothrombinemia, systemic inflammation, and severe hyperbilirubinemia than patients with normodynamic circulation. Patients with hyperdynamic circulation compared with those with normodynamic circulation had increased abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcaceae, Lactobacillaceae, Fusobacteria, Micrococcaceae, Intestinobacter, Clostridium sensu stricto, Proteus and Rumicoccus, and decreased abundance of Bacteroidetes, Bacteroidaceae, Holdemanella, and Butyrivibrio. The systemic vascular resistance and cardiac output values correlated with the abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcaceae, Lactobacillaceae, Micrococcaceae, and Fusobacteria. Heart rate and cardiac output value were negatively correlated with the abundance of Bacteroidetes. The mean pulmonary artery pressure value was positively correlated with the abundance of Proteobacteria and Micrococcaceae, and negatively with the abundance of Holdemanella.
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Affiliation(s)
- Irina Efremova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
| | - Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
- The Interregional Public Organization “Scientific Community for the Promotion of the Clinical Study of the Human Microbiome”, 119991 Moscow, Russia
- Consultative and Diagnostic Center No. 2, Moscow Health Department, 107564 Moscow, Russia
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
- The Interregional Public Organization “Scientific Community for the Promotion of the Clinical Study of the Human Microbiome”, 119991 Moscow, Russia
| | - Maria Zharkova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
| | - Anna Kudryavtseva
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia (G.K.); (M.F.)
| | - George Krasnov
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia (G.K.); (M.F.)
| | - Maria Fedorova
- Post-Genomic Research Laboratory, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia (G.K.); (M.F.)
| | - Elena Shirokova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
| | - Evgenii Kozlov
- Laboratory of Immunopathology, Department of Clinical Immunology and Allergy, Sechenov University, 119991 Moscow, Russia;
| | - Anna Levshina
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
- Laboratory of Immunopathology, Department of Clinical Immunology and Allergy, Sechenov University, 119991 Moscow, Russia;
| | - Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, 119991 Moscow, Russia (E.P.); (M.Z.); (A.L.); (V.I.)
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Snezhkina A, Pavlov V, Fedorova M, Kalinin D, Pudova E, Kobelyatskaya A, Bakhtogarimov I, Krasnov G, Kudryavtseva A. Comprehensive Genetic Study of Malignant Cervical Paraganglioma. Int J Mol Sci 2023; 24:ijms24098220. [PMID: 37175927 PMCID: PMC10179044 DOI: 10.3390/ijms24098220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Malignant middle ear paraganglioma (MEPGL) is an exceedingly rare tumor of the neuroendocrine system. In general, MEPGLs represent as slow growing and hypervascularized benign neoplasms. The genetic basis of MEPGL tumorigenesis has been poorly investigated. We report a case of malignant MEPGL accompanied by the comprehensive genetic analysis of the primary tumor and metastasis. Based on whole-exome sequencing data, the germline pathogenic mutation p.R230H in the SDHB gene, encoding for subunit B of mitochondrial complex II, was found in a patient. Analysis of somatic mutation spectra revealed five novel variants in different genes, including a potentially deleterious variant in UNC13C that was common for the tumor and metastasis. Identified somatic variants clustered into SBS1 and SBS5 mutational signatures. Of note, the primary tumor was characterized by Ki-67 4% and had an elevated mutational load (1.4/Mb); the metastasis' mutational load was about 4.5 times higher (6.4/Mb). In addition, we revealed somatic loss of the wild-type SDHB allele, as well as loss of heterozygosity (LOH) at the 11p locus. Thus, germline mutation in SDHB combined with somatic LOH seem to be drivers that lead to the tumor's initiation and progression. Other somatic changes identified can be additional disease-causing factors. Obtained results expand our understanding of molecular genetic mechanisms associated with the development of this rare tumor.
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Affiliation(s)
- Anastasiya Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladislav Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitry Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Ildar Bakhtogarimov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Ivashkin V, Shifrin O, Maslennikov R, Poluektova E, Korolev A, Kudryavtseva A, Krasnov G, Benuni N, Barbara G. Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study. BMC Gastroenterol 2023; 23:82. [PMID: 36959568 PMCID: PMC10037807 DOI: 10.1186/s12876-023-02690-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Rifaximin effectively treats symptomatic uncomplicated diverticular disease (SUDD) and has shown eubiotic potential (i.e., an increase in resident microbial elements with potential beneficial effects) in other diseases. This study investigated changes in the fecal microbiome of patients with SUDD after repeated monthly treatment with rifaximin and the association of these changes with the severity of abdominal pain. METHODS This was a single-center, prospective, observational, uncontrolled cohort study. Patients received rifaximin 400 mg twice a day for 7 days per month for 6 months. Abdominal pain (assessed on a 4-point scale from 0 [no pain] to 3 [severe pain]) and fecal microbiome (assessed using 16 S rRNA gene sequencing) were assessed at inclusion (baseline) and 3 and 6 months. The Spearman's rank test analyzed the relationship between changes in the gut microbiome and the severity of abdominal pain. A p-value ≤ 0.05 was considered statistically significant. RESULTS Of the 23 patients enrolled, 12 patients completed the study and were included in the analysis. Baseline abdominal pain levels decreased significantly after 3 (p = 0.036) and 6 (p = 0.008) months of treatment with rifaximin. The abundance of Akkermansia in the fecal microbiome was significantly higher at 3 (p = 0.017) and 6 (p = 0.015) months versus baseline. The abundance of Ruminococcaceae (p = 0.034), Veillonellaceae (p = 0.028), and Dialister (p = 0.036) were significantly increased at 6 months versus baseline, whereas Anaerostipes (p = 0.049) was significantly decreased. The severity of abdominal pain was negatively correlated with the abundance of Akkermansia (r=-0.482; p = 0.003) and Ruminococcaceae (r=-0.371; p = 0.026) but not with Veillonellaceae, Dialister, or Anaerostipes. After 3 months of rifaximin, abdominal pain was significantly less in patients with Akkermansia in their fecal microbiome than in patients without Akkermansia (p = 0.022). CONCLUSION The eubiotic effect of rifaximin was associated with decreased abdominal pain in patients with SUDD.
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Affiliation(s)
- Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
- Scientific Community for the Human Microbiome Research, Moscow, Russian Federation
| | - Oleg Shifrin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
| | - Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation.
- Scientific Community for the Human Microbiome Research, Moscow, Russian Federation.
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
- Scientific Community for the Human Microbiome Research, Moscow, Russian Federation
| | - Alexander Korolev
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
| | - Anna Kudryavtseva
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nona Benuni
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow, Russian Federation
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences, University of Bologna, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy
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Snezhkina A, Fedorova M, Kobelyatskaya A, Markova D, Lantsova M, Ikonnikova A, Emelyanova M, Kalinin D, Pudova E, Melnikova N, Dmitriev A, Krasnov G, Pavlov V, Kudryavtseva A. The SDHD:p.H102R Variant Is Frequent in Russian Patients with Head and Neck Paragangliomas and Associated with Loss of 11p15.5 Region and Hypermethylation of H19-DMR. Int J Mol Sci 2022; 24:ijms24010628. [PMID: 36614070 PMCID: PMC9820527 DOI: 10.3390/ijms24010628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Head and neck paragangliomas (HNPGLs) are rare neuroendocrine neoplasms derived from the parasympathetic paraganglia of the head and neck. At least 30% of HNPGLs are linked to germline mutations, predominantly in SDHx genes. In this study, we analyzed an extended cohort of Russian patients with HNPGLs using whole-exome sequencing and found a highly frequent missense variant p.H102R in the SDHD gene. We determined this variant in 34% of the SDHD mutation carriers. This variant was associated with somatic loss of the gene wild-type allele. Data from the B allele frequency method and microsatellite and microdeletion analysis indicated evident LOH at the 11p15.5 region and potential loss of the whole of chromosome 11. We found hypermethylation of H19-DMR in all tumors, whereas differential methylation of KvDMR was mostly retained. These findings do not support the paternal transmission of SDHD:p.H102R but are in agreement with the Hensen model. Using targeted sequencing, we also studied the variant frequency in a control cohort; we found SDHD:p.H102R in 1.9% of cases, allowing us to classify this variant as pathogenic. The immunohistochemistry of SDHB showed that the SDHD:p.H102R mutation, even in combination with wild-type allele loss, does not always lead to SDH deficiency. The obtained results demonstrate the frequent variant associated with HNPGLs in a Russian population and support its pathogenicity. Our findings help with understanding the mechanism of tumorigenesis and are also important for the development of cost-effective genetic screening programs.
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Affiliation(s)
- Anastasiya Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Correspondence:
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Daria Markova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Margarita Lantsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna Ikonnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Marina Emelyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Dmitry Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, Moscow 117997, Russia
| | - Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Vladislav Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Pudova E, Kobelyatskaya A, Katunina I, Snezhkina A, Nyushko K, Fedorova M, Pavlov V, Bulavkina E, Dalina A, Tkachev S, Alekseev B, Krasnov G, Volodin V, Kudryavtseva A. Docetaxel Resistance in Castration-Resistant Prostate Cancer: Transcriptomic Determinants and the Effect of Inhibiting Wnt/β-Catenin Signaling by XAV939. Int J Mol Sci 2022; 23:ijms232112837. [PMID: 36361635 PMCID: PMC9658696 DOI: 10.3390/ijms232112837] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 10/23/2022] [Indexed: 12/01/2022] Open
Abstract
Castration-resistant prostate cancer (CRPC) is a common form of prostate cancer in which docetaxel-based chemotherapy is used as the first line. The present study is devoted to the analysis of transcriptome profiles of tumor cells in the development of resistance to docetaxel as well as to the assessment of the combined effect with the XAV939 tankyrase inhibitor on maintaining the sensitivity of tumor cells to chemotherapy. RNA-Seq was performed for experimental PC3 cell lines as well as for plasma exosome samples from patients with CRPC. We have identified key biological processes and identified a signature based on the expression of 17 mRNA isoforms associated with the development of docetaxel resistance in PC3 cells. Transcripts were found in exosome samples, the increased expression of which was associated with the onset of progression of CRPC during therapy. The suppression of pathways associated with the participation of cellular microtubules has also been shown when cells are treated with docetaxel in the presence of XAV939. These results highlight the importance of further research into XAV939 as a therapeutic agent in the treatment of CRPC; moreover, we have proposed a number of mRNA isoforms with high predictive potential, which can be considered as promising markers of response to docetaxel.
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Affiliation(s)
- Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence:
| | | | - Irina Katunina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anastasiya Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Kirill Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, 125284 Moscow, Russia
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladislav Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta Bulavkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexandra Dalina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey Tkachev
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Boris Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, 125284 Moscow, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vsevolod Volodin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Maslennikov R, Ivashkin V, Alieva A, Poluektova E, Kudryavtseva A, Krasnov G, Zharkova M, Zharikov Y. Gut dysbiosis and body composition in cirrhosis. World J Hepatol 2022; 14:1210-1225. [PMID: 35978666 PMCID: PMC9258262 DOI: 10.4254/wjh.v14.i6.1210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/09/2021] [Accepted: 05/14/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gut dysbiosis and changes in body composition (i.e., a decrease in the proportion of muscle mass and an increase in extracellular fluid) are common in cirrhosis.
AIM To study the relationship between the gut microbiota and body composition in cirrhosis.
METHODS This observational study included 46 patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. Multifrequency bioelectrical impedance analysis was performed to assess body composition in these patients.
RESULTS An increase in fat mass and a decrease in body cell mass were noted in 23/46 (50.0%) and 15/46 (32.6%) patients, respectively. Changes in the gut microbiome were not independently associated with the fat mass percentage in cirrhosis. The abundance of Bacteroidaceae (P = 0.041) and Eggerthella (P = 0.001) increased, whereas that of Erysipelatoclostridiaceae (P = 0.006), Catenibacterium (P = 0.021), Coprococcus (P = 0.033), Desulfovibrio (P = 0.043), Intestinimonas (P = 0.028), and Senegalimassilia (P = 0.015) decreased in the gut microbiome of patients with body cell mass deficiency. The amount of extracellular fluid increased in 22/46 (47.6%) patients. Proteobacteria abundance (P < 0.001) increased, whereas Firmicutes (P = 0.023), Actinobacteria (P = 0.026), Bacilli (P = 0.008), Anaerovoraceceae (P = 0.027), Christensenellaceae (P = 0.038), Eggerthellaceae (P = 0.047), Erysipelatoclostridiaceae (P = 0.015), Erysipelotrichaceae (P = 0.003), Oscillospiraceae (P = 0.024), Rikenellaceae (P = 0.002), Collinsella (P = 0.030), Hungatella (P = 0.040), Peptococcaceae (P = 0.023), Slackia (P = 0.008), and Senegalimassilia (P = 0.024) abundance decreased in these patients. Patients with clinically significant ascites (n = 9) had a higher abundance of Proteobacteria (P = 0.031) and a lower abundance of Actinobacteria (P = 0.019) and Bacteroidetes (P = 0.046) than patients without clinically significant ascites (n = 37).
CONCLUSION Changes in the amount of body cell mass and extracellular fluid are associated with changes in the gut microbiome in cirrhosis patients.
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Affiliation(s)
- Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Department of Internal Medicine, Сonsultative and Diagnostic Center No. 2, Moscow City Health Department, Moscow 107564, Russia
| | - Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Aliya Alieva
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Anna Kudryavtseva
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George Krasnov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Zharkova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
| | - Yuri Zharikov
- Department of Anatomy, Sechenov University, Moscow 119435, Russia
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Savvateeva M, Kudryavtseva A, Lukyanova E, Kobelyatskaya A, Pavlov V, Fedorova M, Pudova E, Guvatova Z, Kalinin D, Golovyuk A, Bulavkina E, Katunina I, Krasnov G, Snezhkina A. Somatic Mutation Profiling in Head and Neck Paragangliomas. J Clin Endocrinol Metab 2022; 107:1833-1842. [PMID: 35460558 PMCID: PMC9202733 DOI: 10.1210/clinem/dgac250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Head and neck paragangliomas (HNPGLs) are rare neoplasms with a high degree of heritability. Paragangliomas present as polygenic diseases caused by combined alterations in multiple genes; however, many driver changes remain unknown. OBJECTIVE The objective of the study was to analyze somatic mutation profiles in HNPGLs. METHODS Whole-exome sequencing of 42 tumors and matched normal tissues obtained from Russian patients with HNPGLs was carried out. Somatic mutation profiling included variant calling and utilizing MutSig and SigProfiler packages. RESULTS 57% of patients harbored germline and somatic variants in paraganglioma (PGL) susceptibility genes or potentially related genes. Somatic variants in novel genes were found in 17% of patients without mutations in any known PGL-related genes. The studied cohort was characterized by 6 significantly mutated genes: SDHD, BCAS4, SLC25A14, RBM3, TP53, and ASCC1, as well as 4 COSMIC single base substitutions (SBS)-96 mutational signatures (SBS5, SBS29, SBS1, and SBS7b). Tumors with germline variants specifically displayed SBS11 and SBS19, when an SBS33-specific mutational signature was identified for cases without those. Beta allele frequency analysis of copy number variations revealed loss of heterozygosity of the wild-type allele in 1 patient with germline mutation c.287-2A>G in the SDHB gene. In patients with germline mutation c.A305G in the SDHD gene, frequent potential loss of chromosome 11 was observed. CONCLUSION These results give an understanding of somatic changes and the mutational landscape associated with HNPGLs and are important for the identification of molecular mechanisms involved in tumor development.
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Affiliation(s)
- Maria Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna Kudryavtseva
- Anna Kudryavtseva, P.I., Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Elena Lukyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Vladislav Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Zulfiya Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitry Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Alexander Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Elizaveta Bulavkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Irina Katunina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anastasiya Snezhkina
- Correspondence: Anastasiya Snezhkina, PhD, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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Astaykina A, Streletskii R, Maslov M, Krasnov G, Gorbatov V. Effects of Three Pesticides on the Earthworm Lumbricus terrestris Gut Microbiota. Front Microbiol 2022; 13:853535. [PMID: 35422770 PMCID: PMC9004718 DOI: 10.3389/fmicb.2022.853535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/03/2022] [Indexed: 12/26/2022] Open
Abstract
Earthworms play a vital role in the terrestrial ecosystem functioning and maintenance of soil fertility. However, many pesticides, for example, imidacloprid, benomyl, and metribuzin that are world-widely used in agriculture, may be potentially dangerous to earthworms. At the same time, standard tests for pesticides acute and chronic toxicity do not reflect all aspects of their negative impact and might not be enough sensitive for effective assessment. In this paper, we studied the effects of non-lethal concentrations of imidacloprid, benomyl, and metribuzin on the gut bacterial community of Lumbricus terrestris using high-throughput sequencing approach. We found that pesticides reduced the total bacterial diversity in the earthworm's gut even at the recommended application rate. Under the applied pesticides, the structure of the gut prokaryotic community underwent changes in the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Planctomyces, Verrucomicrobia, and Cyanobacteria, as well as the genera Haliangium, Gaiella, Paenisporosarcina, Oryzihumus, Candidatus Udaeobacter, and Aquisphaera. Moreover, the pesticides affected the abundance of Verminephrobacter-the earthworms' nephridia specific symbionts. In general, the negative impact of pesticides on bacterial biodiversity was significant even under pesticides content, which was much lower than their acute and chronic toxicity values for the earthworms. These results highlighted the fact that the earthworm's gut microbial community is highly sensitive to soil contamination with pesticides. Therefore, such examination should be considered in the pesticide risk assessment protocols.
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Affiliation(s)
| | | | - Mikhail Maslov
- Soil Science Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Emelyanova M, Pudova E, Khomich D, Krasnov G, Popova A, Abramov I, Mikhailovich V, Filipenko M, Menshikova S, Tjulandin S, Pokataev I. Platinum-based chemotherapy for pancreatic cancer: impact of mutations in the homologous recombination repair and Fanconi anemia genes. Ther Adv Med Oncol 2022; 14:17588359221083050. [PMID: 35309086 PMCID: PMC8928350 DOI: 10.1177/17588359221083050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background Mutations in homologous recombination (HR) and Fanconi anemia (FA) genes may predispose to pancreatic cancer (PC) and enable the prediction of sensitivity to platinum-based chemotherapy. FOLFIRINOX is a standard treatment option for non-selected PC patients and could be effective due to undiagnosed DNA repair deficiency. Here, we aimed to determine the frequency of mutations in genes involved in the HR and FA pathways, evaluate their clinical implications, and determine the objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) of PC patients treated with platinum. Methods We performed targeted DNA sequencing of 30 genes (ABRAXAS1, ATM, ATR, BARD1, BLM, BRCA1, BRCA2, BRIP1, CDKN2A, CHEK1, CHEK2, FANCC, FANCF, FANCG, FANCI, FANCL, FANCM, MRE11A, NBN, PALB2, PTEN, RAD50, RAD51C, RAD51D, RAD52, RAD54B, RBBP8, RINT1, SLX4, and XRCC2) for 543 PC patients. Results In BRCA/PALB2-mutated patients with advanced PC (33 patients, 6.1%), the PFS and OS were higher for first-line platinum therapy than for non-platinum therapy [PFS: HR = 0.28, 95% confidence interval (CI) = 0.10-0.81, p = 0.02; OS: HR = 0.31, 95% CI = 0.08-1.16, p = 0.08]. Among 93 patients (17.1%) with mutations in other HR/FA genes, no statistically significant difference in PFS and OS was observed between first-line platinum therapy and non-platinum therapy (PFS: HR = 0.83, 95% CI = 0.43-1.62, p = 0.59; OS: HR = 0.58, 95% CI = 0.28-1.22, p = 0.15). For patients with early PC, no prognostic value was observed for BRCA1/2, PALB2, or other HR/FA genes mutations. Moreover, a personal history of breast, ovarian, pancreatic, or prostate cancer was identified as the only independent predictor of the risk of BRCA/PALB2 mutations (HR = 5.83, 95% CI = 2.16-15.73, p < 0.01). Conclusion Mutations in the BRCA1/2 and PALB2 genes increase the sensitivity of PC to platinum agents. Thus, alterations in these genes in PC patients must be determined prior to anticancer therapy.
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Affiliation(s)
- Marina Emelyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Darya Khomich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Anna Popova
- N.N. Blokhin National Medical Research Center for Oncology, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Ivan Abramov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir Mikhailovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | - Sergey Tjulandin
- N.N. Blokhin National Medical Research Center for Oncology, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Ilya Pokataev
- N.N. Blokhin National Medical Research Center for Oncology, Ministry of Health of the Russian Federation, Moscow, Russian Federation
- City Clinical Cancer Hospital No. 1, Moscow Department of Health, Moscow, Russian Federation
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Maslennikov R, Ivashkin V, Efremova I, Poluektova E, Kudryavtseva A, Krasnov G. Gut dysbiosis and small intestinal bacterial overgrowth as independent forms of gut microbiota disorders in cirrhosis. World J Gastroenterol 2022; 28:1067-1077. [PMID: 35431497 PMCID: PMC8968519 DOI: 10.3748/wjg.v28.i10.1067] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/29/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gut dysbiosis and small intestinal bacterial overgrowth (SIBO) are commonly observed in patients with cirrhosis. Despite the substantial number of articles describing the relations between disorders of gut microbiota and various manifestations of cirrhosis, dysbiosis and SIBO were always studied separately.
AIM To study the relationship of gut dysbiosis and SIBO in cirrhosis.
METHODS This observational study included 47 in-patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. SIBO was assessed using the lactulose hydrogen breath test.
RESULTS SIBO was found in 24/47 (51.1%) patients. Patients with SIBO had a higher abundance of Firmicutes (P = 0.017) and Fusobacteria (P = 0.011), and a lower abundance of Bacteroidetes (P = 0.013) than patients without SIBO. This increase in the abundance of Firmicutes occurred mainly due to an increase in the abundance of bacteria from the genus Blautia (P = 0.020) of the Lachnospiraceae family (P = 0.047), while the abundance of other major families of this phylum [Ruminococcaceae (P = 0.856), Peptostreptococcaceae (P = 0.066), Clostridiaceae (P = 0.463), Eubacteriaceae (P = 0.463), Lactobacillaceae (P = 0.413), and Veillonellaceae (P = 0.632)] did not differ significantly between the patients with and without SIBO. Reduced level of Bacteroidetes in samples from patients with SIBO was a result of the decrease in bacterial numbers from all the major families of this phylum [Bacteroidaceae (P = 0.014), Porphyromonadaceae (P = 0.002), and Rikenellaceae (P = 0.047)], with the exception of Prevotellaceae (P = 0.941). There were no significant differences in the abundance of taxa that were the main biomarkers of cirrhosis-associated gut dysbiosis [Proteobacteria (P = 0.790), Bacilli (P = 0.573), Enterobacteriaceae (P = 0.632), Streptococcaceae (P = 0.170), Staphylococcaceae (P = 0.450), and Enterococcaceae (P = 0.873)] between patients with and without SIBO.
CONCLUSION Despite the differences observed in the gut microbiome between patients with and without SIBO, gut dysbiosis and SIBO are most likely independent disorders of gut microbiota in cirrhosis.
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Affiliation(s)
- Roman Maslennikov
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Department of Internal Medicine 1, Сonsultative and Diagnostic Center 2 of the Moscow City Health Department, Moscow 107564, Russia
| | - Vladimir Ivashkin
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Irina Efremova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
| | - Elena Poluektova
- Department of Internal Medicine, Gastroenterology and Hepatology, Sechenov University, Moscow 119435, Russia
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
| | - Anna Kudryavtseva
- Scientific Community for Human Microbiome Research, Moscow 119435, Russia
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Chirkov SN, Sheveleva A, Snezhkina A, Kudryavtseva A, Krasnov G, Zakubanskiy A, Mitrofanova I. Highly divergent isolates of chrysanthemum virus B and chrysanthemum virus R infecting chrysanthemum in Russia. PeerJ 2022; 10:e12607. [PMID: 35036085 PMCID: PMC8742542 DOI: 10.7717/peerj.12607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/16/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Chrysanthemum is a popular ornamental and medicinal plant that suffers from many viruses and viroids. Among them, chrysanthemum virus B (CVB, genus Carlavirus, family Betaflexiviridae) is widespread in all chrysanthemum-growing regions. Another carlavirus, chrysanthemum virus R (CVR), has been recently discovered in China. Information about chrysanthemum viruses in Russia is very scarce. The objective of this work was to study the prevalence and genetic diversity of CVB and CVR in Russia. METHODS We surveyed the chrysanthemum (Chrysanthemum morifolium Ramat.) germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. To detect CVB and CVR, we used RT-PCR with virus-specific primers. To reveal the complete genome sequences of CVB and CVR isolates, metatransciptomic analysis of the cultivars Ribonette, Fiji Yellow, and Golden Standard plants, naturally co-infected with CVB and CVR, was performed using Illumina high-throughput sequencing. The recombination detection tool (RDP4) was employed to search for recombination in assembled genomes. RESULTS A total of 90 plants of 23 local and introduced chrysanthemum cultivars were surveyed. From these, 58 and 43% plants tested positive for CVB and CVR, respectively. RNA-Seq analysis confirmed the presence of CVB and CVR, and revealed tomato aspermy virus in each of the three transcriptomes. Six near complete genomes of CVB and CVR were assembled from the RNA-Seq reads. The CVR isolate X21 from the cultivar Golden Standard was 92% identical to the Chinese isolate BJ. In contrast, genomes of the CVR isolates X6 and X13 (from the cultivars Ribonette and Fiji Yellow, respectively), were only 76% to 77% identical to the X21 and BJ, and shared 95% identity to one another and appear to represent a divergent group of the CVR. Two distantly related CVB isolates, GS1 and GS2, were found in a plant of the cultivar Golden Standard. Their genomes shared from 82% to 87% identity to each other and the CVB genome from the cultivar Fiji Yellow (isolate FY), as well as to CVB isolates from Japan and China. A recombination event of 3,720 nucleotides long was predicted in the replicase gene of the FY genome. It was supported by seven algorithms implemented in RDP4 with statistically significant P-values. The inferred major parent was the Indian isolate Uttar Pradesh (AM765837), and minor parent was unknown. CONCLUSION We found a wide distribution of CVB and CVR in the chrysanthemum germplasm collection of the Nikita Botanical Gardens, which is the largest in Russia. Six near complete genomes of CVR and CVB isolates from Russia were assembled and characterized for the first time. This is the first report of CVR in Russia and outside of China thus expanding the information on the geographical distribution of the virus. Highly divergent CVB and CVR isolates have been identified that contributes the better understanding the genetic diversity of these viruses.
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Affiliation(s)
- Sergei N. Chirkov
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia,Kurchatov Genomic Center-NBG-NSC, Yalta, Russia
| | - Anna Sheveleva
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasiya Snezhkina
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kudryavtseva
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George Krasnov
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zakubanskiy
- Department of Medical Genomics, Centre for Strategic Planning of FMBA of Russia, Moscow, Russia
| | - Irina Mitrofanova
- Kurchatov Genomic Center-NBG-NSC, Yalta, Russia,Plant Developmental Biology, Biotechnology and Biosafety Department, Nikita Botanical Gardens, Yalta, Russia
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15
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Lipatova A, Krasnov G, Vorobyov P, Melnikov P, Alekseeva O, Vershinina Y, Brzhozovskiy A, Goliusova D, Maganova F, Zakirova N, Kudryavtseva A, Moskalev A. Effects of Siberian fir terpenes extract Abisil on antioxidant activity, autophagy, transcriptome and proteome of human fibroblasts. Aging (Albany NY) 2021; 13:20050-20080. [PMID: 34428743 PMCID: PMC8436938 DOI: 10.18632/aging.203448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/23/2021] [Indexed: 11/25/2022]
Abstract
Background: Abisil is an extract of Siberian fir terpenes with antimicrobial and wound healing activities. Previous studies revealed that Abisil has geroprotective, anti-tumorigenic, and anti-angiogenic effects. Abisil decreased the expression of cyclin D1, E1, A2, and increased the phosphorylation rate of AMPK. Objective: In the present study, we analyzed the effect of Abisil on autophagy, the mitochondrial potential of embryonic human lung fibroblasts. We evaluated its antioxidant activity and analyzed the transcriptomic and proteomic effects of Abisil treatment. Results: Abisil treatment resulted in activation of autophagy, reversal of rotenone-induced elevation of reactive oxygen species (ROS) levels and several-fold decrease of mitochondrial potential. Lower doses of Abisil (25 μg/ml) showed a better oxidative effect than high doses (50 or 125 μg/ml). Estimation of metabolic changes after treatment with 50 μg/ml has not shown any changes in oxygen consumption rate, but extracellular acidification rate decreased significantly. Abisil treatment (5 and 50 μg/ml) of MRC5-SV40 cells induced a strong transcriptomic shift spanning several thousand genes (predominantly, expression decrease). Among down-regulated genes, we noticed an over-representation of genes involved in cell cycle progression, oxidative phosphorylation, and fatty acid biosynthesis. Additionally, we observed predominant downregulation of genes encoding for kinases. Proteome profiling also revealed that the content of hundreds of proteins is altered after Abisil treatment (mainly, decreased). These proteins were involved in cell cycle regulation, intracellular transport, RNA processing, translation, mitochondrial organization. Conclusions: Abisil demonstrated antioxidant and autophagy stimulating activity. Treatment with Abisil results in the predominant downregulation of genes involved in the cell cycle and oxidative phosphorylation.
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Affiliation(s)
- Anastasiya Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Pavel Vorobyov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Pavel Melnikov
- V. Serbsky National Research Center for Psychiatry and Narcology, Moscow 119034, Russia
| | - Olga Alekseeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Yulia Vershinina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Daria Goliusova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Natalia Zakirova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Biology of Federal Research Center "Komi Science Center" of Ural Branch of RAS, Syktyvkar 167982, Russia.,Russian Clinical and Research Center of Gerontology, Moscow 129226, Russia
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16
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Ivashkin V, Poluektov Y, Kogan E, Shifrin O, Sheptulin A, Kovaleva A, Kurbatova A, Krasnov G, Poluektova E. Disruption of the pro-inflammatory, anti-inflammatory cytokines and tight junction proteins expression, associated with changes of the composition of the gut microbiota in patients with irritable bowel syndrome. PLoS One 2021; 16:e0252930. [PMID: 34115808 PMCID: PMC8195381 DOI: 10.1371/journal.pone.0252930] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a pathologic condition characterized by changes in gut microbiome composition, low-grade inflammation, and disruption of intestinal wall permeability. The interaction between the gut microbiome and the disease manifestation remains unclear. The changing of tight junction proteins and cytokines expression throughout the gastrointestinal tract in IBS patients has not been studied yet. AIM OF THE STUDY To assess the changes of gut microbiome composition, tight junction proteins, and cytokines expression of intestinal mucosa from the duodenum to the distal part of the colon in IBS patients and healthy volunteers. METHODS In 31 IBS patients (16 patients with IBS-D; 15 patients with IBS-C) and 10 healthy volunteers the expression of CLD-2, CLD-3, CLD-5, IL-2, IL-10, and TNF-α in mucosal biopsy specimens was determined by morphological and immune-histochemical methods. The qualitative and quantitative composition of the intestinal microbiota was assessed based on 16S rRNA gene sequencing in both groups of patients. RESULTS The expression of IL-2 and TNF-α was significantly increased in IBS patients compared with the controls (p<0.001), with a gradual increase from the duodenum to the sigmoid colon. The expression of IL-10, CLD-3, and CLD-5 in mucosal biopsy specimens of these patients was lower than in the control group (p<0.001). Increased ratios of Bacteroidetes and decreased ratios of Firmicutes were noted in IBS patients compared to healthy volunteers (p<0.05). CONCLUSION IBS patients have impaired gut permeability and persisting low-grade inflammation throughout the gastrointestinal tract. Changes in the gut microbiota may support or exacerbate these changes.
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Affiliation(s)
- V. Ivashkin
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
| | - Y. Poluektov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E. Kogan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
| | - O. Shifrin
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
| | - A. Sheptulin
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
| | - A. Kovaleva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
| | - A. Kurbatova
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
| | - G. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E. Poluektova
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation
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17
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Krasnov G, Shkrigunov T, Radko S, Ptitsyn K, Shapovalova V, Timoshenko O, Khmeleva S, Kurbatov L, Kiseleva Y, Ilgisonis E, Kiseleva O, Vakhrushev I, Tsvetkova A, Buromski I, Markin S, Archakov A, Lisitsa A, Ponomarenko E. Human Chr18 transcriptome dataset combined from the Illumina HiSeq, ONT MinION, and qPCR data. Data Brief 2021; 36:107130. [PMID: 34095379 PMCID: PMC8166769 DOI: 10.1016/j.dib.2021.107130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 11/01/2022] Open
Abstract
The chromosome-centric dataset was created by applying several technologies of transcriptome profiling. The described dataset is available at NCBI repository (BioProject ID PRJNA635536). The dataset referred to the same type of tissue, cell lines, transcriptome sequencing technologies, and was accomplished in a period of 8 years (the first data were obtained in 2013 while the last ones - in 2020). The high-throughput sequencing technologies were employed along with the quantitative PCR (qPCR) approach, for data generation using the gene expression level assessment. qPCR was performed for a limited group of genes, encoded on human chromosome 18, for the Russian part of the Chromosome-Centric Human Proteome Project. The data of high-throughput sequencing are provided as Excel spreadsheets, where the data on FPKM and TMP values were evaluated for the whole transcriptome with both Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing.
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Affiliation(s)
- George Krasnov
- Institute of Biomedical Chemistry, Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | | | - Sergey Radko
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - Valeriya Shapovalova
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, Moscow, Russia
| | | | | | | | - Yana Kiseleva
- Russian Scientific Center of Roentgen Radiology, Moscow, Russia
| | | | | | | | | | - Ivan Buromski
- Department of Forensic Medicine, Faculty of General Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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18
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Kobelyatskaya A, Pudova E, Fedorova M, Nyushko K, Alekseev B, Kaprin A, Trofimov D, Sukhikh G, Snezhkina A, Krasnov G, Razin S, Kudryavtseva A. Differentially methylated CpG sites associated with the high-risk group of prostate cancer. J Integr Bioinform 2020. [PMCID: PMC7790183 DOI: 10.1515/jib-2020-0031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Prostate cancer (PC) is one of the most common and socially significant oncological diseases among men. Bioinformatic analysis of omics data allows identifying molecular genetic changes associated with the disease development, as well as markers of prognosis and response to therapy. Alterations in DNA methylation and histone modification profiles widely occur in malignant tumors. In this study, we analyzed changes in DNA methylation in three groups of PC patients based on data from The Cancer Genome Atlas project (TCGA, https://portal.gdc.cancer.gov): (1) high- and intermediate-risk of the tumor progression, (2) favorable and unfavorable prognoses within the high-risk group, and (3) TMPRSS2-ERG-positive (tumors with TMPRSS2-ERG fusion transcript) and TMPRSS2-ERG-free cases within the high-risk group. We found eight CpG sites (cg07548607, cg13533340, cg16643088, cg18467168, cg23324953, cg23753247, cg25773620, and cg27148952) hypermethylated in the high-risk group compared with the intermediate-risk group of PC. Seven differentially methylated CpG sites (cg00063748, cg06834698, cg18607127, cg25273707, cg01704198, cg02067712, and cg02157224) were associated with unfavorable prognosis within the high-risk group. Six CpG sites (cg01138171, cg14060519, cg19570244, cg24492886, cg25605277, and cg26228280) were hypomethylated in TMPRSS2-ERG-positive PC compared to TMPRSS2-ERG-negative tumors within the high-risk group. The CpG sites were localized, predominantly, in regulatory genome regions belonging to promoters of the following genes: ARHGEF4, C6orf141, C8orf86, CLASP2, CSRNP1, GDA, GSX1, IQSEC1, MYOF, OR10A3, PLCD1, PLEC1, PRDM16, PTAFR, RP11-844P9.2, SCYL3, VPS13D, WT1, and ZSWIM2. For these genes, analysis of differential expression and its correlation with CpG site methylation (β-value level) was also performed. In addition, STK33 and PLCD1 had similar changes in colorectal cancer. As for the CSRNP1, the ARHGEF4, and the WT1 genes, misregulated expression levels were mentioned in lung, liver, pancreatic and androgen-independent prostate cancer. The potential impact of changed methylation on the mRNA level was determined for the CSRNP1, STK33, PLCD1, ARHGEF4, WT1, SCYL3, and VPS13D genes. The above CpG sites could be considered as potential prognostic markers of the high-risk group of PC.
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Affiliation(s)
- Anastasiya Kobelyatskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, http://www.genebiology.ru/
| | - Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
| | - Kirill Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia, https://nmicr.ru/
| | - Boris Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia, https://nmicr.ru/
| | - Andrey Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia, https://nmicr.ru/
| | - Dmitry Trofimov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov, Ministry of Health of the Russian Federation, Moscow, Russia, https://en.ncagp.ru/
| | - Gennady Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov, Ministry of Health of the Russian Federation, Moscow, Russia, https://en.ncagp.ru/
| | - Anastasia Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
| | - Sergey Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, http://www.genebiology.ru/
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
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19
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Guvatova Z, Dalina A, Marusich E, Pudova E, Snezhkina A, Krasnov G, Kudryavtseva A, Leonov S, Moskalev A. Protective effects of carotenoid fucoxanthin in fibroblasts cellular senescence. Mech Ageing Dev 2020; 189:111260. [DOI: 10.1016/j.mad.2020.111260] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/27/2022]
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20
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Evgen'ev M, Bobkova N, Krasnov G, Garbuz D, Funikov S, Kudryavtseva A, Kulikov A, Samokhin A, Maltsev A, Nesterova I. The Effect of Human HSP70 Administration on a Mouse Model of Alzheimer's Disease Strongly Depends on Transgenicity and Age. J Alzheimers Dis 2020; 67:1391-1404. [PMID: 30714962 DOI: 10.3233/jad-180987] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In humans, heat shock protein 70 is a key component of the machinery that protects neuronal cells from various stress conditions and whose production significantly declines during aging. Herein, we investigated the protective effect of sub-chronic intranasal administration of human Hsp70 on the state of neurons in the temporal cortex and areas of the hippocampus of old transgenic (Tg) 5XFAD mice (11-13 months), representing a late-onset model of hereditary Alzheimer's disease. Quantitative analysis of the various neuronal pathologies between the two groups (Tg versus nTg) revealed maximal levels of abnormalities in the brains of aged Tg mice. Importantly, intranasal application of HSP70 had profound beneficial effects on neuron morphology in the temporal cortex and hippocampal regions when applied to the aged Tg mice but not in the case of age-matched, non-transgenic, littermate animals. Furthermore, the effect of HSP70 administration on neurons in the hippocampus and temporal cortex differed characteristically between the groups. Using RNA-Seq, we identified a lot of differentially expressed genes in the hippocampus of old Tg mice compared with those of nTg mice. Most importantly, we observed HSP70-induced upregulation of multiple genes participating in antigen processing and presentation especially the members of major histocompatibility complex (class I and II) in the brains of old 5XFAD Tg animals, suggesting that Hsp70 executes its beneficial role via activation of adaptive immunity. Overall, our data enable to conclude that Hsp70 treatment may be a safe and effective therapeutic application against Alzheimer-type neuropathologies manifested at the late stages of the disease.
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Affiliation(s)
| | - Natalia Bobkova
- Institute of Cell Biophysics, RAS, Pushchino, Moscow region, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - David Garbuz
- Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Sergei Funikov
- Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | | | | | | | - Andrey Maltsev
- Institute of Physiologically Active Compounds, RAS, Chernogolovka, Russia
| | - Inna Nesterova
- Institute of Cell Biophysics, RAS, Pushchino, Moscow region, Russia
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21
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Moskalev A, Guvatova Z, Shaposhnikov M, Lashmanova E, Proshkina E, Koval L, Zhavoronkov A, Krasnov G, Kudryavtseva A. The Neuronal Overexpression of Gclc in Drosophila melanogaster Induces Life Extension With Longevity-Associated Transcriptomic Changes in the Thorax. Front Genet 2019; 10:149. [PMID: 30891062 PMCID: PMC6411687 DOI: 10.3389/fgene.2019.00149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 02/12/2019] [Indexed: 01/24/2023] Open
Abstract
Some effects of aging in animals are tissue-specific. In D. melanogaster neuronal overexpression of Gclc increases lifespan and improves certain physiological parameters associated with health benefits such as locomotor activity, circadian rhythmicity, and stress resistance. Our previous transcriptomic analyses of Drosophila heads, primarily composed of neuronal tissue, revealed significant changes in expression levels of genes involved in aging-related signaling pathways (Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta), translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity, and transmission. Considering that various tissues age differently and age-related gene expression changes are tissue-specific, we investigated the effects of neuronal Gclc overexpression on gene expression levels in the imago thorax, which is primarily composed of muscles. A total of 58 genes were found to be differentially expressed between thoraces of control and Gclc overexpressing flies. The Gclc level demonstrated associations with expression of genes involved in the circadian rhythmicity, the genes in categories related to the muscle system process and the downregulation of genes involved in proteolysis. Most of the functional categories altered by Gclc overexpression related to metabolism including Drug metabolism, Metabolism of xenobiotics by cytochrome P450, Glutathione metabolism, Starch and sucrose metabolism, Citrate cycle (TCA cycle), One carbon pool by folate. Thus, the transcriptomic changes caused by neuron-specific Gclc overexpression in the thorax were less pronounced than in the head and affected pathways also differed from previous results. Although these pathways don't belong to the canonical longevity pathways, we suggest that they could participate in the delay of aging of Gclc overexpressing flies.
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Affiliation(s)
- Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Zulfiya Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | - Ekaterina Lashmanova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ekaterina Proshkina
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | - Liubov Koval
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | | | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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22
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Kudryavtseva A, Krasnov G, Lipatova A, Alekseev B, Maganova F, Shaposhnikov M, Fedorova M, Snezhkina A, Moskalev A. Effects of Abies sibirica terpenes on cancer- and aging-associated pathways in human cells. Oncotarget 2018; 7:83744-83754. [PMID: 27888805 PMCID: PMC5347801 DOI: 10.18632/oncotarget.13467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/19/2016] [Indexed: 12/31/2022] Open
Abstract
A large number of terpenoids exhibit potential geroprotector and anti-cancer properties. Here, we studied whole transcriptomic effects of Abisil, the extract of fir (Abies sibirica) terpenes, on normal and cancer cell lines. We used early passaged and senescent none-immortalized fibroblasts as cellular aging models. It was revealed that in normal fibroblasts, terpenes induced genes of stress response, apoptosis regulation and tissue regeneration. The restoration of the expression level of some prolongevity genes after fir extract treatment was shown in old cells. In Caco-2 and AsPC-1 cancer cell lines, Abisil induced expression of both onco-suppressors (members of GADD45, DUSP, and DDIT gene families), and proto-oncogenes (c-Myc, c-Jun, EGR and others). Thus, the study demonstrates the potential anti-aging and anti-cancer effects of Abisil on senescent and cancer cell lines.
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Affiliation(s)
- Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasiya Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Boris Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, 125284, Russia
| | | | - Mikhail Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russia
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasiya Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.,Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
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Moskalev A, Shaposhnikov M, Proshkina E, Belyi A, Fedintsev A, Zhikrivetskaya S, Guvatova Z, Sadritdinova A, Snezhkina A, Krasnov G, Kudryavtseva A. The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions. BMC Genomics 2016; 17:1046. [PMID: 28105938 PMCID: PMC5249042 DOI: 10.1186/s12864-016-3356-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Transcriptional changes that contribute to the organism’s longevity and prevent the age-dependent decline of biological functions are not well understood. Here, we overexpressed pro-longevity gene encoding glutamate-cysteine ligase catalytic subunit (Gclc) and analyzed age-dependent changes in transcriptome that associated with the longevity, stress resistance, locomotor activity, circadian rhythmicity, and fertility. Results Here we reproduced the life extension effect of neuronal overexpression of the Gclc gene and investigated its influence on the age-depended dynamics of transcriptome and biological functions such as fecundity, spontaneous locomotor activity and circadian rhythmicity, as well as on the resistance to oxidative, proteotoxic and osmotic stresses. It was shown that Gclc overexpression reduces locomotor activity in the young and middle ages compared to control flies. Gclc overexpression slowed down the age-dependent decline of locomotor activity and circadian rhythmicity, and resistance to stress treatments. Gclc level demonstrated associations with the expression of genes involved in a variety of cellular processes including Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta signaling pathways, translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity and transmission. Conclusions Our study revealed that Gclc overexpression induces transcriptional changes associated with the lifespan extension and uncovered pathways that may be associated with the age-dependent decline of biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3356-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. .,Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, Russia. .,Syktyvkar State University, Syktyvkar, Russia.
| | - Mikhail Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia.,Syktyvkar State University, Syktyvkar, Russia
| | - Ekaterina Proshkina
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia.,Syktyvkar State University, Syktyvkar, Russia
| | - Alexey Belyi
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia.,Syktyvkar State University, Syktyvkar, Russia
| | | | | | - Zulfiya Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Asiya Sadritdinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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Moskalev A, Zhikrivetskaya S, Krasnov G, Shaposhnikov M, Proshkina E, Borisoglebsky D, Danilov A, Peregudova D, Sharapova I, Dobrovolskaya E, Solovev I, Zemskaya N, Shilova L, Snezhkina A, Kudryavtseva A. A comparison of the transcriptome of Drosophila melanogaster in response to entomopathogenic fungus, ionizing radiation, starvation and cold shock. BMC Genomics 2015; 16 Suppl 13:S8. [PMID: 26694630 PMCID: PMC4686790 DOI: 10.1186/1471-2164-16-s13-s8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The molecular mechanisms that determine the organism's response to a variety of doses and modalities of stress factors are not well understood. Results We studied effects of ionizing radiation (144, 360 and 864 Gy), entomopathogenic fungus (10 and 100 CFU), starvation (16 h), and cold shock (+4, 0 and -4°C) on an organism's viability indicators (survival and locomotor activity) and transcriptome changes in the Drosophila melanogaster model. All stress factors but cold shock resulted in a decrease of lifespan proportional to the dose of treatment. However, stress-factors affected locomotor activity without correlation with lifespan. Our data revealed both significant similarities and differences in differential gene expression and the activity of biological processes under the influence of stress factors. Conclusions Studied doses of stress treatments deleteriously affect the organism's viability and lead to different changes of both general and specific cellular stress response mechanisms.
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Volkomorov V, Grigoryeva E, Krasnov G, Litviakov N, Tsyganov M, Karbyshev M, Zavyalova M, Afanasуev S, Cherdyntseva N, Lisitsyn N, Beresten S. Search for potential gastric cancer markers using miRNA databases and gene expression analysis. Exp Oncol 2013; 35:2-7. [PMID: 23528308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
AIM The aim of this study was to identify genes that are differentially expressed in gastric tumors and to analyze the association of their expression level with tumor clinicopathologic features. METHODS In the present research, we used bioinformatic-driven search to identify miRNA that are down-regulated in gastric tumors and to find their potential targets. Then, the expression levels of some of the target mRNAs were investigated using reverse transcription polymerase chain reaction (RT-PCR) analysis. RESULTS As a result of the bioinformatics analysis, fifteen genes were found to be potentially differentially expressed between the tumors and normal gastric tissue. Five of them were chosen for the further analysis (WNT4, FGF12, EFEMP1, CTGF, and HSPG2) due to their important role in cell proliferation and differentiation. Expression levels of these genes were evaluated in our collection of frozen tissue samples of gastric tumor and paired normal stomach epithelia. Increased FGF12 expression was observed in diffuse type of gastric cancer while WNT4 mRNA was found to be down-regulated in intestinal type of gastric cancer. Besides, CTGF gene overexpression was revealed in diffuse type of stomach cancer in comparison with that in intestinal type. Up-regulation of CTGF was also associated with lymph node metastasis. CONCLUSIONS The findings show its expedient to perform further investigations in order to clarify diagnostic and prognostic value of CTGF, FGF12, and WNT4's in stomach cancer as well as the role of these genes in carcinogenesis.
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Affiliation(s)
- V Volkomorov
- Cancer Research Institute of Siberian Вranch of the Russian Academy of Medical Sciences, Tomsk 634050, Russian Federation.
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Anedchenko E, Oparina N, Dmitriev A, Krasnov G, Pavlova L, Alexandrova N, Kisseljov F, Senchenko V. Activation of the hTERT expression in squamous cell cervical carcinoma is not associated with gene amplification. Oncol Rep 2008; 20:469-474. [PMID: 18636213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
The hTERT gene encodes the telomerase catalytic subunit that plays a key role in cancer cell immortalization. Earlier, hTERT amplification was detected in squamous cell cervical carcinomas (SCC), however possible relations between elevated hTERT mRNA level and gene amplification was not studied. Here, we compared the hTERT expression and copy number in the same tumors by quantitative real-time PCR. The hTERT DNA copy number was virtually unchanged in all 33 studied tumors, when compared to normal tissues. This result was confirmed using two reference genes beta-actin and beta-D-glucuronidase. Nevertheless, the activation of hTERT expression was found in 80% of cases (37/46, p<0.001). There was no correlation between the degree of mRNA increase and the tumor size and/or presence of metastases. No hTERT gene expression was observed in 20% of cases (9/46), while the control GADPH expression was unchanged. The detected elevation of the hTERT mRNA level was found using primers specific to functionally active full-length isoform of mRNA. Similar results were obtained with SCC cell lines carrying human papilloma virus (HPV) genomes. We conclude that frequent activation of hTERT expression in SCC is not associated with gene amplification.
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MESH Headings
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cervix Uteri/metabolism
- Cervix Uteri/pathology
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Enzyme Activation
- Female
- Gene Amplification
- Gene Dosage
- Humans
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Telomerase/genetics
- Telomerase/metabolism
- Tumor Cells, Cultured
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Neoplasms/metabolism
- Uterine Cervical Neoplasms/virology
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Affiliation(s)
- Ekaterina Anedchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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