Publications by authors named "Andrey Kaprin"

36 Publications

Unique Combination of Diamond-Blackfan Anemia and Lynch Syndrome in Adult Female: A Case Report.

Front Oncol 2021 16;11:652696. Epub 2021 Apr 16.

Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.

We present an extremely rare clinical case of a 38-year-old Russian patient with multiple malignant neoplasms of the uterus and colon caused by genetically confirmed two hereditary diseases: Diamond-Blackfan anemia and Lynch syndrome. Molecular genetic research carried out by various methods (NGS, Sanger sequencing, aCGH, and MLPA) revealed a pathogenic nonsense variant in the gene: NM_000179.2: c.742C>T, p.(Arg248Ter), as well as a new deletion of the chromosome 15's locus with the capture of 82,662,932-84,816,747 bp interval, including the complete sequence of the gene. The lack of expediency of studying microsatellite instability in endometrial tumors using standard mononucleotide markers NR21, NR24, NR27, BAT25, BAT26 was demonstrated. The estimated prevalence of patients with combination of Diamond-Blackfan anemia and Lynch syndrome in the world is one per 480 million people.
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http://dx.doi.org/10.3389/fonc.2021.652696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085342PMC
April 2021

A Clinical Case of 5 Times Irradiated Recurrent Orbital Hemangiopericytoma.

Case Rep Oncol 2021 Jan-Apr;14(1):78-84. Epub 2021 Feb 25.

National Medical Research Radiological Center, Moscow, Russian Federation.

Orbital hemangiopericytomas (HPCs) are rare mesenchymal tumors with a high tendency to recur. Treatment options are quite limited in case of a relapse, but re-irradiation can be useful. Most of the available data limit the possibility of re-irradiation, while novel techniques (e.g., pencil beam proton therapy [PT]) open new approaches for the safe repeating of treatment. To the best of our knowledge, this is the first well-documented case of multi-times (>3) irradiation of tumors located intracranially. The case reported here describes orbital HPCs with proton irradiation performed two times since 1999 in a 30-year-old woman with a medical history as well as surgery followed by conventional radiotherapy (RT) and chemotherapy, and two times stereotactic RT (in 2009 and 2013). In 2016 the patient came to our hospital with the 3rd relapse of the tumor, located in the left orbit, with an intracranial part, involving cavernous sinus, which was close to the temporal lobe. The 4th course of irradiation was done in May to June 2016 by pencil beam PT. Radiation necrosis occurred after 2 years and was treated with bevacizumab (BVZ). Three years later, another relapse was treated with PT and BVZ. The 9-month follow-up showed complete tumor response without signs of brain toxicity. The patient died due to a brain abscess 1 year after the 5th irradiation. This case shows a possibility of irradiation, applied 5 times to the same location, with promising results and manageable toxicity.
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http://dx.doi.org/10.1159/000513030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7983647PMC
February 2021

Gene Expression Changes and Associated Pathways Involved in the Progression of Prostate Cancer Advanced Stages.

Front Genet 2020 21;11:613162. Epub 2021 Jan 21.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Prostate cancer (PC) is one of the most common cancers among men worldwide, and advanced PCs, such as locally advanced PC (LAPC) and castration-resistant PC (CRPC), present the greatest challenges in clinical management. Current indicators have limited capacity to predict the disease course; therefore, better prognostic markers are greatly needed. In this study, we performed a bioinformatic analysis of The Cancer Genome Atlas (TCGA) datasets, including RNA-Seq data from the prostate adenocarcinoma (PRAD; = 55) and West Coast Dream Team - metastatic CRPC (WCDT-MCRPC; = 84) projects, to evaluate the transcriptome changes associated with progression-free survival (PFS) for LAPC and CRPC, respectively. We identified the genes whose expression was positively/negatively correlated with PFS. In LAPC, the genes with the most significant negative correlations were , , and , and the genes with the most significant positive correlations were , , , , and . In CRPC, the most significant positive correlations were found for , , , and , and the most significant negative correlations were found for , , , , and . In addition, we performed a gene network interaction analysis using STRINGdb, which revealed a significant relationship between genes predominantly involved in the cell cycle and characterized by upregulated expression in early recurrence. Based on the results, we propose several genes that can be used as potential prognostic markers.
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http://dx.doi.org/10.3389/fgene.2020.613162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859645PMC
January 2021

Mutation Frequency in Main Susceptibility Genes Among Patients With Head and Neck Paragangliomas.

Front Genet 2020 18;11:614908. Epub 2020 Dec 18.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Head and neck paragangliomas (HNPGLs) are rare neuroendocrine tumors that have a high degree of heritability and are predominantly associated with mutations in ten genes, such as , and . Elucidating the mutation prevalence is crucial for the development of genetic testing. In this study, we identified pathogenic/likely pathogenic variants in the main susceptibility genes in 102 Russian patients with HNPGLs (82 carotid and 23 vagal paragangliomas) using whole exome sequencing. Pathogenic/likely pathogenic variants were detected in 43% (44/102) of patients. We identified the following variant distribution of the tested genes: (1%), (10%), (5%), (24.5%), and (5%). variants were observed in the majority of the patients with bilateral/multiple paragangliomas. Thus, among Russian patients with HNPGLs the most frequently mutated gene was followed by , and .
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http://dx.doi.org/10.3389/fgene.2020.614908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775293PMC
December 2020

National Association of Biobanks and Biobanking Specialists: New Community for Promoting Biobanking Ideas and Projects in Russia.

Biopreserv Biobank 2021 Feb 15;19(1):73-82. Epub 2020 Oct 15.

National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.

The research biobanking field is developing rapidly in Russia. Over the course of the last decade, numerous biobanks were created or formed from existing collections of human and environmental biospecimens. The Russian National Association of Biobanks and Biobanking Specialists (NASBIO) was established in December 2018, aiming to: (1) unite professionals and research centers to create and develop a network of biobanks in Russia; (2) provide services and expertise in the field of biobanking; (3) execute various research projects utilizing biobanks' infrastructure; and (4) facilitate integration of Russian biomedical research centers into global research activities. The organizational structure, aims, and plans of this newly formed national association are reviewed in this article. The founders of NASBIO hope that the association will promote further development of biobanks and their networking in Russia, which is critically important for the success of national biomedical, pharmaceutical, and biotechnological research, and can facilitate international biobanking projects on a global scale.
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http://dx.doi.org/10.1089/bio.2020.0049DOI Listing
February 2021

Internal doses in experimental mice and rats following exposure to neutron-activated MnO powder: results of an international, multicenter study.

Radiat Environ Biophys 2020 11 29;59(4):683-692. Epub 2020 Sep 29.

The Center for Peace, Hiroshima University, Higashisenda-machi 1-1-89, Naka-ku, Hiroshima, 730-0053, Japan.

The experiment was performed in support of a Japanese initiative to investigate the biological effects of irradiation from residual neutron-activated radioactivity that resulted from the A-bombing. Radionuclide Mn (T = 2.58 h) is one of the main neutron-activated emitters during the first hours after neutron activation of soil dust particles. In our previous studies (2016-2017) related to irradiation of male Wistar rats after dispersion of MnO powder, the internal doses in rats were found to be very inhomogeneous: distribution of doses among different organs ranged from 1.3 Gy in small intestine to less than 0.0015 Gy in some of the other organs. Internal doses in the lungs ranged from 0.03 to 0.1 Gy. The essential pathological changes were found in lung tissue of rats despite a low level of irradiation. In the present study, the dosimetry investigations were extended: internal doses in experimental mice and rats were estimated for various activity levels of dispersed neutron-activated MnO powder. The following findings were noted: (a) internal radiation doses in mice were several times higher in comparison with rats under similar conditions of exposure to MnO powder. (b) When 2.74 × 10 Bq of MnO powder was dispersed over mice, doses of internal irradiation ranged from 0.81 to 4.5 Gy in the gastrointestinal tract (small intestine, stomach, large intestine), from 0.096 to 0.14 Gy in lungs, and doses in skin and eyes ranged from 0.29 to 0.42 Gy and from 0.12 to 0.16 Gy, respectively. Internal radiation doses in other organs of mice were much lower. (c) Internal radiation doses were significantly lower in organs of rats with the same activity of exposure to MnO powder (2.74 × 10 Bq): 0.09, 0.17, 0.29, and 0.025 Gy in stomach, small intestine, large intestine, and lungs, respectively. (d) Doses of internal irradiation in organs of rats and mice were two to four times higher when they were exposed to 8.0 × 10 Bq of MnO (in comparison with exposure to 2.74 × 10 Bq of MnO). (e) Internal radiation doses in organs of mice were 7-14 times lower with the lowest MnO amount (8.0 × 10 Bq) in comparison with the highest amount, 8.0 × 10 Bq, of dispersed MnO powder. The data obtained will be used for interpretation of biological effects in experimental mice and rats that result from dispersion of various levels of neutron-activated MnO powder, which is the subject of separate studies.
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http://dx.doi.org/10.1007/s00411-020-00870-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544755PMC
November 2020

miRNAs expression signature potentially associated with lymphatic dissemination in locally advanced prostate cancer.

BMC Med Genomics 2020 09 18;13(Suppl 8):129. Epub 2020 Sep 18.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: Prostate cancer is one of the most common and socially significant cancers among men. The aim of our study was to reveal changes in miRNA expression profiles associated with lymphatic dissemination in prostate cancer and to identify the most prominent miRNAs as potential prognostic markers for future studies.

Methods: High-throughput miRNA sequencing was performed for 44 prostate cancer specimens taken from Russian patients, with and without lymphatic dissemination (N1 - 20 samples; N0 - 24 samples).

Results: We found at least 18 microRNAs with differential expression between N0 and N1 sample groups: miR-182-5p, miR-183-5p, miR-96-5p, miR-25-3p, miR-93-5p, miR-7-5p, miR-615-3p, miR-10b, miR-1248 (N1-miRs; elevated expression in N1 cohort; p < 0.05); miR-1271-5p, miR-184, miR-222-3p, miR-221-5p, miR-221-3p, miR-455-3p, miR-143-5p, miR-181c-3p and miR-455-5p (N0-miRs; elevated expression in N0; p < 0.05). The expression levels of N1-miRs were highly correlated between each other (the same is applied for N0-miRs) and the expression levels of N0-miRs and N1-miRs were anti-correlated. The tumor samples can be divided into two groups depending on the expression ratio between N0-miRs and N1-miRs.

Conclusions: We found the miRNA expression signature associated with lymphatic dissemination, in particular on the Russian patient cohort. Many of these miRNAs are well-known players in either oncogenic transformation or tumor suppression. Further experimental studies with extended sampling are required to validate these results.
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http://dx.doi.org/10.1186/s12920-020-00788-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7500008PMC
September 2020

Multiple paragangliomas: a case report.

BMC Med Genomics 2020 09 18;13(Suppl 8):125. Epub 2020 Sep 18.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str, Moscow, 119991, Russia.

Background: Carotid and vagal paragangliomas (CPGLs and VPGLs) are rare neoplasms that arise from the paraganglia located at the bifurcation of carotid arteries and vagal trunk, respectively. Both tumors can occur jointly as multiple paragangliomas accounting for approximately 10 to 20% of all head and neck paragangliomas. However, molecular and genetic mechanisms underlying the pathogenesis of multiple paragangliomas remain elusive.

Case Presentation: We report a case of multiple paragangliomas in a patient, manifesting as bilateral CPGL and unilateral VPGL. Tumors were revealed via computed tomography and ultrasound study and were resected in two subsequent surgeries. Both CPGLs and VPGL were subjected to immunostaining for succinate dehydrogenase (SDH) subunits and exome analysis. A likely pathogenic germline variant in the SDHD gene was indicated, while likely pathogenic somatic variants differed among the tumors.

Conclusions: The identified germline variant in the SDHD gene seems to be a driver in the development of multiple paragangliomas. However, different spectra of somatic variants identified in each tumor indicate individual molecular mechanisms underlying their pathogenesis.
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http://dx.doi.org/10.1186/s12920-020-00789-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7500000PMC
September 2020

Disparity between Inter-Patient Molecular Heterogeneity and Repertoires of Target Drugs Used for Different Types of Cancer in Clinical Oncology.

Int J Mol Sci 2020 Feb 26;21(5). Epub 2020 Feb 26.

Oncobox ltd., Moscow 121205, Russia.

Inter-patient molecular heterogeneity is the major declared driver of an expanding variety of anticancer drugs and personalizing their prescriptions. Here, we compared interpatient molecular heterogeneities of tumors and repertoires of drugs or their molecular targets currently in use in clinical oncology. We estimated molecular heterogeneity using genomic (whole exome sequencing) and transcriptomic (RNA sequencing) data for 4890 tumors taken from The Cancer Genome Atlas database. For thirteen major cancer types, we compared heterogeneities at the levels of mutations and gene expression with the repertoires of targeted therapeutics and their molecular targets accepted by the current guidelines in oncology. Totally, 85 drugs were investigated, collectively covering 82 individual molecular targets. For the first time, we showed that the repertoires of molecular targets of accepted drugs did not correlate with molecular heterogeneities of different cancer types. On the other hand, we found that the clinical recommendations for the available cancer drugs were strongly congruent with the gene expression but not gene mutation patterns. We detected the best match among the drugs usage recommendations and molecular patterns for the kidney, stomach, bladder, ovarian and endometrial cancers. In contrast, brain tumors, prostate and colorectal cancers showed the lowest match. These findings provide a theoretical basis for reconsidering usage of targeted therapeutics and intensifying drug repurposing efforts.
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http://dx.doi.org/10.3390/ijms21051580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7084891PMC
February 2020

Detection of Marker miRNAs, Associated with Prostate Cancer, in Plasma Using SOI-NW Biosensor in Direct and Inversion Modes.

Sensors (Basel) 2019 Nov 29;19(23). Epub 2019 Nov 29.

Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia.

Information about the characteristics of measuring chips according to their storage conditions is of great importance for clinical diagnosis. In our present work, we have studied the capability of chips to detect nanowire biosensors when they are either freshly prepared or have been stored for either one or two years in a clean room. Potential to detect DNA oligonucleotides (oDNAs)-synthetic analogues of microRNAs (miRNAs) 198 and 429 that are associated with the development of prostate cancer (PCa)-in buffer solution was demonstrated using a nanowire biosensor based on silicon-on-insulator structures (SOI-NW biosensor). To provide biospecific detection, nanowire surfaces were sensitized with oligonucleotide probes (oDNA probes) complimentary to the known sequences of miRNA 183 and 484. In this study it is demonstrated that freshly prepared SOI-NW biosensor chips with n-type conductance and immobilized oDNA probes exhibit responses to the addition of complimentary oDNAs in buffer, leading to decreases in chips' conductance at a concentration of 3.3 × 10 M. The influence of storage time on the characteristics of SOI-NW biosensor chips is also studied herein. It is shown that a two-year storage of the chips leads to significant changes in their characteristics, resulting in "inverse" sensitivity toward negatively charged oDNA probes (i.e., through an increase in chips' conductance). It is concluded that the surface layer makes the main contribution to conductance of the biosensor chip. Our results indicate that the detection of target nucleic acid molecules can be carried out with high sensitivity using sensor chips after long-term storage, but that changes in their surface properties, which lead to inversed detection signals, must be taken into account. Examples of the applications of such chips for the detection of cancer-associated microRNAs in plasma samples of patients with diagnosed prostate cancer are given. The results obtained herein are useful for the development of highly sensitive nanowire-based diagnostic systems for the revelation of (prostate) cancer-associated microRNAs in human plasma.
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http://dx.doi.org/10.3390/s19235248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6928824PMC
November 2019

Human Platelet Lysate Sustains the Osteogenic/Adipogenic Differentiation Potential of Adipose-Derived Mesenchymal Stromal Cells and Maintains Their DNA Integrity in vitro.

Cells Tissues Organs 2019 8;207(3-4):149-164. Epub 2019 Oct 8.

National Medical Research Centre of Radiology, Moscow, Russian Federation.

Human platelet lysate (HPL) is a promising alternative to fetal calf serum (FCS) for the expansion of adipose tissue mesenchymal stromal cells (AT-MSCs) for translational medicine applications. However, some biological effects of HPL are still to be elucidated. We aimed to compare complex characteristics, such as cell morphology, proliferative activity, differentiation potential, and especially monolayer recovery, DNA integrity, and the gene expression pattern, between AT-MSCs cultured with HPL or FCS. Primary AT-MSC cultures were expanded in medium containing FCS or pooled HPL. Cell growth and proliferation were estimated by cell doubling time and the monolayer formation rate, while migration was assessed by wound-healing assay. The capacity for adipogenic and osteogenic differentiation was evaluated by alkaline phosphatase and Oil Red O staining. DNA integrity was evaluated by comet assay, and analysis of gene expression by real-time PCR. Media supplemented with HPL or FCS provided a similar surface immunophenotype, cell morphology (except some cell dimensions and a bigger colony size in HPL), DNA integrity, and rate of wound healing. Meanwhile, AT-MSC proliferated more intensively in HPL-supplemented media (especially at 5% HPL) and had a reduced doubling population time. AT-MSC in HPL had increased adipogenic potential and similar osteogenic potential in comparison with FCS. Our results indicate the feasibility and evident prospects for the use of pooled HPL as an alternative to FCS and safe non-xenogenic growth supplement for ex vivo expansion of clinical-grade AT-MSCs for regenerative medicine purposes.
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http://dx.doi.org/10.1159/000502813DOI Listing
July 2020

Experience in multicatheter interstitial high-dose-rate breast brachytherapy: dose-volume histogram analysis of the first results.

J Contemp Brachytherapy 2019 Aug 29;11(4):349-355. Epub 2019 Aug 29.

National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia.

Purpose: To report characteristics of our treatment scheme of high-dose-rate (HDR) brachytherapy of breast cancer and to show the first outcomes of dosimetric planning analysis based on dose-volume histogram (DVH).

Material And Methods: Since August 2017, 25 patients diagnosed with T1N0M0 breast cancer have received a treatment in our center. There was lumpectomy and following breast HDR brachytherapy (10 fractions of 3.4 Gy) administered to each patient. A planning target volume (PTV) and organs at risk (OARs) were recorded with DVH analysis.

Results: The study describes the full procedure of breast HDR brachytherapy with the lumpectomy. Twenty-five patients were treated, including 9 with cancer of the left breast and 16 of the right breast. The median age was 65 years. The first analysis of DVH data shows that the main OARs were ribs and skin. Mean value of D (ribs) for all patients was 19.90 Gy (55.88% of prescribed dose) and for the skin 30.88 Gy (90.74% of prescribed dose). During the treatment, there was only one case of toxic effects, which was pigmentation on the skin due to excess of dose limit of 1.4 Gy. Therefore, the limit exceeding of 1 Gy does not give any significant toxic effects.

Conclusions: This study is the first stage of the dosimetric evaluation of a new method. The analysis allows treating complex localizations of the breast cancer, for example, in a close position to the skin or ribs. In order to minimize the toxic effects, it is necessary to consider patient selection, catheter administration, and dose optimization.
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http://dx.doi.org/10.5114/jcb.2019.87024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6737577PMC
August 2019

Differentially Expressed Genes Associated With Prognosis in Locally Advanced Lymph Node-Negative Prostate Cancer.

Front Genet 2019 9;10:730. Epub 2019 Aug 9.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Older age is one of the main risk factors for cancer development. The incidence of prostate cancer, as a multifactorial disease, also depends upon demographic factors, race, and genetic predisposition. Prostate cancer most frequently occurs in men over 60 years of age, indicating a clear association between older age and disease onset. Carcinogenesis is followed by the deregulation of many genes, and some of these changes could serve as biomarkers for diagnosis, prognosis, prediction of drug therapy efficacy, as well as possible therapeutic targets. We have performed a bioinformatic analysis of a The Cancer Genome Atlas (TCGA) data and RNA-Seq profiling of a Russian patient cohort to reveal prognostic markers of locally advanced lymph node-negative prostate cancer (lymph node-negative LAPC). We also aimed to identify markers of the most common molecular subtype of prostate cancer carrying a fusion transcript . We have found several genes that were differently expressed between the favorable and unfavorable prognosis groups and involved in the enriched KEGG pathways based on the TCGA (, , and ) and Russian patient cohort data ( and ). Additionally, we revealed such genes for the prostate cancer molecular subtype (, , , , , , and ). Obtained results contribute to a better understanding of the molecular mechanisms behind prostate cancer progression and could be used for further development of the LAPC prognosis marker panel.
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http://dx.doi.org/10.3389/fgene.2019.00730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697060PMC
August 2019

New Derivatives of Bacteriopurpurin with Thiolated Au (I) Complexes: Dual Darkand Light Activated Antitumor Potency.

Anticancer Agents Med Chem 2020 ;20(1):49-58

National Medical Research Center of Radiology of Ministry of Health of Russia, Moscow, Russian Federation.

Background: Conventional antitumor Photosensitizers (PS) are normally low toxic in the dark whereas light activation triggers massive cell death (photodynamic therapy, PDT).

Objective: To expand the therapeutic potential of PS to dual potency cytocidal agents, taking advantage of the use of bacteriopurpurin for a deeper tissue penetration of light, and suitability of the tetrapyrrolic macrocycle for chemical modifications at its periphery.

Methods: Conjugation of a pro-oxidant thiolate Au (I) moiety to the bacteriopurpurin core and evaluation of cytotoxicity in cell culture and in vivo.

Results: New water-soluble derivatives showed micromolar cytotoxicity for cultured human tumor cell lines in the dark, including the subline with an altered drug response due to p53 inactivation. Cellular PDT with the selected conjugate, thiolate Au (I)-dipropoxybacteriopurpurinimide (compound 6) with two triphenylphosphine Au fragments, triggered rapid (within minutes) cell death. Damage to the plasma membrane (necrosis) was a hallmark of cell death by compound 6 both in the dark and upon light activation. Furthermore, one single i.v. injection of compound 6 caused retardation of transplanted syngeneic tumors at the tolerable dose. Illumination of tumors that accumulated compound 6 significantly synergized with the effect of 6 in the dark.

Conclusion: Complexes of virtually non-toxic, photoactivatable bacteriopurpurin with the gold-containing organic moiety are considered the dual potency antitumor agents, tentatively applicable for intractable tumors.
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http://dx.doi.org/10.2174/1871520619666190801102617DOI Listing
January 2021

Patient-Derived Non-Muscular Invasive Bladder Cancer Xenografts of Main Molecular Subtypes of the Tumor for Anti-Pd-l1 Treatment Assessment.

Cells 2019 05 31;8(6). Epub 2019 May 31.

Department of Oncological urology, Russian National Research Medical Center of Radiology, 3 2nd Botkinsky Proezd, 125284 Moscow, Russia.

Background: Establishment of heterotopic patient-derived xenografts of primary and relapsed non-muscular invasive bladder cancer (NMIBC) to explore the biological property of PD-L1 signaling that may impact bladder tumor growth in humanized animals.

Methods: Tumor cells of luminal, basal, and p53 subtypes of primary and relapsed NMIBC were engrafted to irradiated (3.5 Gy) NOG/SCID female mice along with intraperitoneal transplantation of human lymphocytes (5 × 10 cells/mouse); a role of PD-L1 signaling pathway inhibition for bladder cancer growth was assessed in humanized animals that carried PD-L1-expressing main molecular subtypes of bladder carcinoma patient-derived xenografts (PDX) and provided with selective anti-PD-L1 treatment. We used two-tailed Student's test to explore differences between main and control subgroups. Significance of intergroup comparison was measured with one-way ANOVA followed by the Tukey's or Newman-Keul's criterion. Survival curves were analyzed with the Gehan's criterion with the Yate's correction. The Spearman's correlation was used to assess the link between CD8 expression and sPD-L1 serum level. Differences were considered statistically significant at < 0.05.

Results: Heterotopic primary and relapsed luminal, basal, and p53 subtypes of NMIBC PDXs were established. More than 25% of counted tumor cells of all PDX specimens expressed PD-L1, so the tumors were ranged as PD-L1 positive. Anti-PD-L1 intervention increased survival of the animals that carried both primary and relapsed luminal noninvasive, muscular invasive, and relapsed luminal bladder cancer xenografts. There was significant retardation of tumor volume duplication time in aforementioned subgroups correlated with PD-L1 expression. Bad response of p53 mutant subtypes of NMIBC on specific anti-PD-L1 treatment may be associated with low CD8 cells representation into the tumors tissue.

Conclusions: Established PD-L1-positive NMIBC PDXs differently replied on anti-PD-L1 treatment due to both NMIBC molecular subtype and tumor T-suppressors population. The results may have major implications for further clinical investigations.
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http://dx.doi.org/10.3390/cells8060526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628037PMC
May 2019

Formation of γH2AX and pATM Foci in Human Mesenchymal Stem Cells Exposed to Low Dose-Rate Gamma-Radiation.

Int J Mol Sci 2019 May 29;20(11). Epub 2019 May 29.

State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow 123098, Russia.

DNA double-strand breaks (DSB) are among the most harmful DNA lesions induced by ionizing radiation (IR). Although the induction and repair of radiation-induced DSB is well studied for acute irradiation, responses to DSB produced by chronic IR exposures are poorly understood, especially in human stem cells. The aim of this study was to examine the formation of DSB markers (γH2AX and phosphorylated kinase ATM, pATM, foci) in human mesenchymal stem cells (MSCs) exposed to chronic gamma-radiation (0.1 mGy/min) in comparison with acute irradiation (30 mGy/min) at cumulative doses of 30, 100, 160, 240 and 300 mGy. A linear dose-dependent increase in the number of both γH2AX and pATM foci, as well as co-localized γH2AX/pATM foci ("true" DSB), were observed after an acute radiation exposure. In contrast, the response of MSCs to a chronic low dose-rate IR exposure deviated from linearity towards a threshold model, for γH2AX, pATM foci and γH2AX/pATM foci, with an indication of a "plateau". The state of equilibrium between newly formed DSB at a low rate during the protracted exposure time and the elimination of a fraction of DSB is proposed as a mechanistic explanation of the non-linear DSB responses following a low dose-rate irradiation. This notion is supported by the observation of the elimination of a substantial fraction of DSB 6 h after the cessation of the exposures. Our results demonstrate non-linear dose responses for γH2AX and pATM foci in human MSCs exposed to low dose-rate IR and showed the existence of a threshold, which may have implications for radiation protection in humans.
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http://dx.doi.org/10.3390/ijms20112645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600277PMC
May 2019

The CIMP-high phenotype is associated with energy metabolism alterations in colon adenocarcinoma.

BMC Med Genet 2019 04 9;20(Suppl 1):52. Epub 2019 Apr 9.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: CpG island methylator phenotype (CIMP) is found in 15-20% of malignant colorectal tumors and is characterized by strong CpG hypermethylation over the genome. The molecular mechanisms of this phenomenon are not still fully understood. The development of CIMP is followed by global gene expression alterations and metabolic changes. In particular, CIMP-low colon adenocarcinoma (COAD), predominantly corresponded to consensus molecular subtype 3 (CMS3, "Metabolic") subgroup according to COAD molecular classification, is associated with elevated expression of genes participating in metabolic pathways.

Methods: We performed bioinformatics analysis of RNA-Seq data from The Cancer Genome Atlas (TCGA) project for CIMP-high and non-CIMP COAD samples with DESeq2, clusterProfiler, and topGO R packages. Obtained results were validated on a set of fourteen COAD samples with matched morphologically normal tissues using quantitative PCR (qPCR).

Results: Upregulation of multiple genes involved in glycolysis and related processes (ENO2, PFKP, HK3, PKM, ENO1, HK2, PGAM1, GAPDH, ALDOA, GPI, TPI1, and HK1) was revealed in CIMP-high tumors compared to non-CIMP ones. Most remarkably, the expression of the PKLR gene, encoding for pyruvate kinase participating in gluconeogenesis, was decreased approximately 20-fold. Up to 8-fold decrease in the expression of OGDHL gene involved in tricarboxylic acid (TCA) cycle was observed in CIMP-high tumors. Using qPCR, we confirmed the increase (4-fold) in the ENO2 expression and decrease (2-fold) in the OGDHL mRNA level on a set of COAD samples.

Conclusions: We demonstrated the association between CIMP-high status and the energy metabolism changes at the transcriptomic level in colorectal adenocarcinoma against the background of immune pathway activation. Differential methylation of at least nine CpG sites in OGDHL promoter region as well as decreased OGDHL mRNA level can potentially serve as an additional biomarker of the CIMP-high status in COAD.
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http://dx.doi.org/10.1186/s12881-019-0771-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454590PMC
April 2019

Novel potential causative genes in carotid paragangliomas.

BMC Med Genet 2019 04 9;20(Suppl 1):48. Epub 2019 Apr 9.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: Carotid paragangliomas (CPGLs) are rare neuroendocrine tumors that arise from the paraganglion at the bifurcation of the carotid artery and are responsible for approximately 65% of all head and neck paragangliomas. CPGLs can occur sporadically or along with different hereditary tumor syndromes. Approximately 30 genes are known to be associated with CPGLs. However, the genetic basis behind the development of these tumors is not fully elucidated, and the molecular mechanisms underlying CPGL pathogenesis remain unclear.

Methods: Whole exome and transcriptome high-throughput sequencing of CPGLs was performed on an Illumina platform. Exome libraries were prepared using a Nextera Rapid Capture Exome Kit (Illumina) and were sequenced under 75 bp paired-end model. For cDNA library preparation, a TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) was used; transcriptome sequencing was carried out with 100 bp paired-end read length. Obtained data were analyzed using xseq which estimates the influence of mutations on gene expression profiles allowing to identify potential causative genes.

Results: We identified a total of 16 candidate genes (MYH15, CSP1, MYH3, PTGES3L, CSGALNACT2, NMD3, IFI44, GMCL1, LSP1, PPFIBP2, RBL2, MAGED1, CNIH3, STRA6, SLC6A13, and ATM) whose variants potentially influence their expression (cis-effect). The strongest cis-effect of loss-of-function variants was found in MYH15, CSP1, and MYH3, and several likely pathogenic variants in these genes associated with CPGLs were predicted.

Conclusions: Using the xseq probabilistic model, three novel potential causative genes, namely MYH15, CSP1, and MYH3, were identified in carotid paragangliomas.
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http://dx.doi.org/10.1186/s12881-019-0770-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454587PMC
April 2019

Mutational load in carotid body tumor.

BMC Med Genomics 2019 03 13;12(Suppl 2):39. Epub 2019 Mar 13.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: Carotid body tumor (CBT) is a rare neoplasm arising from paraganglion located near the bifurcation of the carotid artery. There is great intra-tumor heterogeneity, and CBT development could be associated with both germline and somatic allelic variants. Studies on the molecular genetics of CBT are limited, and the molecular mechanisms of its pathogenesis are not fully understood. This work is focused on the estimation of mutational load (ML) in CBT.

Methods: Using the NextSeq 500 platform, we performed exome sequencing of tumors with matched lymph node tissues and peripheral blood obtained from six patients with CBT. To obtain reliable results in tumors with low ML, we developed and successfully applied a complex approach for the analysis of sequencing data. ML was evaluated as the number of somatic variants per megabase (Mb) of the target regions covered by the Illumina TruSeq Exome Library Prep Kit.

Results: The ML in CBT varied in the range of 0.09-0.28/Mb. Additionally, we identified several pathogenic/likely pathogenic somatic and germline allelic variants across six patients studied (including TP53 variants).

Conclusions: Using the developed approach, we estimated the ML in CBT, which is much lower than in common malignant tumors. Identified variants in known paraganglioma/pheochromocytoma-causative genes and novel genes could be associated with the pathogenesis of CBT. The obtained results expand our knowledge of the mutation process in CBT as well as the biology of tumor development.
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http://dx.doi.org/10.1186/s12920-019-0483-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416835PMC
March 2019

Bioinformatic identification of differentially expressed genes associated with prognosis of locally advanced lymph node-positive prostate cancer.

J Bioinform Comput Biol 2019 02;17(1):1950003

* Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russian Federation.

Prostate cancer (PCa) is one of the primary causes of cancer-related mortality in men worldwide. Patients with locally advanced PCa with metastases in regional lymph nodes are usually marked as a high-risk group. One of the chief concerns for this group is to make an informed decision about the necessity of conducting adjuvant androgen deprivation therapy after radical surgical treatment. During the oncogenic transformation and progression of the disease, the expression of many genes is altered. Some of these genes can serve as markers for diagnosis, predicting the prognosis or effectiveness of drug therapy, as well as possible therapeutic targets. We undertook bioinformatic analysis of the RNA-seq data deposited in The Cancer Genome Atlas consortium database to identify possible prognostic markers. We compared the groups with favorable and unfavorable prognosis for the cohort of patients with PCa showing lymph node metastasis (pT2N1M0, pT3N1M0, and pT4N1M0) and for the most common molecular type carrying the fusion transcript TMPRSS2-ERG. For the entire cohort, we revealed at least six potential markers (IDO1, UGT2B15, IFNG, MUC6, CXCL11, and GBP1). Most of these genes are involved in the positive regulation of immune response. For the TMPRSS2-ERG subtype, we also identified six genes, the expression of which may be associated with prognosis: TOB1, GALNT7, INAFM1, APELA, RAC3, and NNMT. The identified genes, after additional studies and validation in the extended cohort, could serve as a prognostic marker of locally advanced lymph node-positive PCa.
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http://dx.doi.org/10.1142/S0219720019500033DOI Listing
February 2019

Autoantibody against arrestin-1 as a potential biomarker of renal cell carcinoma.

Biochimie 2019 Feb 30;157:26-37. Epub 2018 Oct 30.

Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia. Electronic address:

Renal cell carcinoma (RCC) is the second-most common uronephrological cancer. In the absence of specific symptoms, early diagnosis of RCC is challenging. Monitoring of the aberrant expression of tumour-associated antigens (TAAs) and related autoantibody response is considered as a novel approach of RCC diagnostics. The aim of this study was to examine the aberrant expression of arrestin-1 in renal tumours, to investigate the possible epigenetic mechanism underlying arrestin-1 expression, and to assess the frequency of anti-arrestin-1 autoantibody response. Immunohistochemistry was used to assess the presence of arrestin-1 in primary tumours and metastases of 39 patients with RCC and renal oncocytoma. Bisulfite sequencing was employed to analyse the methylation status of the promoter of the SAG gene encoding arrestin-1. Western blot analysis was performed to detect autoantibodies against arrestin-1 in serum samples of 36 RCC and oncocytoma patients. Arrestin-1 was found to be expressed in RCC (58.7% of cases) and renal oncocytoma (90% of cases) cells, while being absent in healthy kidney. The expression of arrestin-1 in RCC metastases was more prominent than in primary tumours. Hypomethylation of the SAG gene promoter is unlikely to be the mechanism for the aberrant expression of arrestin-1. Autoantibodies against arrestin-1 were detected in sera of 75% of RCC patients. Taken together, our findings suggest employment of autoantibody against arrestin-1 as biomarker of RCC.
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http://dx.doi.org/10.1016/j.biochi.2018.10.019DOI Listing
February 2019

Exome analysis of carotid body tumor.

BMC Med Genomics 2018 02 13;11(Suppl 1):17. Epub 2018 Feb 13.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: Carotid body tumor (CBT) is a form of head and neck paragangliomas (HNPGLs) arising at the bifurcation of carotid arteries. Paragangliomas are commonly associated with germline and somatic mutations involving at least one of more than thirty causative genes. However, the specific functionality of a number of these genes involved in the formation of paragangliomas has not yet been fully investigated.

Methods: Exome library preparation was carried out using Nextera® Rapid Capture Exome Kit (Illumina, USA). Sequencing was performed on NextSeq 500 System (Illumina).

Results: Exome analysis of 52 CBTs revealed potential driver mutations (PDMs) in 21 genes: ARNT, BAP1, BRAF, BRCA1, BRCA2, CDKN2A, CSDE1, FGFR3, IDH1, KIF1B, KMT2D, MEN1, RET, SDHA, SDHB, SDHC, SDHD, SETD2, TP53BP1, TP53BP2, and TP53I13. In many samples, more than one PDM was identified. There are also 41% of samples in which we did not identify any PDM; in these cases, the formation of CBT was probably caused by the cumulative effect of several not highly pathogenic mutations. Estimation of average mutation load demonstrated 6-8 mutations per megabase (Mb). Genes with the highest mutation rate were identified.

Conclusions: Exome analysis of 52 CBTs for the first time revealed the average mutation load for these tumors and also identified potential driver mutations as well as their frequencies and co-occurrence with the other PDMs.
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http://dx.doi.org/10.1186/s12920-018-0327-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836820PMC
February 2018

HK3 overexpression associated with epithelial-mesenchymal transition in colorectal cancer.

BMC Genomics 2018 02 9;19(Suppl 3):113. Epub 2018 Feb 9.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: Colorectal cancer (CRC) is a common cancer worldwide. The main cause of death in CRC includes tumor progression and metastasis. At molecular level, these processes may be triggered by epithelial-mesenchymal transition (EMT) and necessitates specific alterations in cell metabolism. Although several EMT-related metabolic changes have been described in CRC, the mechanism is still poorly understood.

Results: Using CrossHub software, we analyzed RNA-Seq expression profile data of CRC derived from The Cancer Genome Atlas (TCGA) project. Correlation analysis between the change in the expression of genes involved in glycolysis and EMT was performed. We obtained the set of genes with significant correlation coefficients, which included 21 EMT-related genes and a single glycolytic gene, HK3. The mRNA level of these genes was measured in 78 paired colorectal cancer samples by quantitative polymerase chain reaction (qPCR). Upregulation of HK3 and deregulation of 11 genes (COL1A1, TWIST1, NFATC1, GLIPR2, SFPR1, FLNA, GREM1, SFRP2, ZEB2, SPP1, and RARRES1) involved in EMT were found. The results of correlation study showed that the expression of HK3 demonstrated a strong correlation with 7 of the 21 examined genes (ZEB2, GREM1, TGFB3, TGFB1, SNAI2, TWIST1, and COL1A1) in CRC.

Conclusions: Upregulation of HK3 is associated with EMT in CRC and may be a crucial metabolic adaptation for rapid proliferation, survival, and metastases of CRC cells.
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http://dx.doi.org/10.1186/s12864-018-4477-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836836PMC
February 2018

Upregulation of NETO2 gene in colorectal cancer.

BMC Genet 2017 12 28;18(Suppl 1):117. Epub 2017 Dec 28.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: Neuropilin and tolloid-like 2 (NETO2) is a single-pass transmembrane protein that has been shown primarily implicated in neuron-specific processes. Upregulation of NETO2 gene was also detected in several cancer types. In colorectal cancer (CRC), it was associated with tumor progression, invasion, and metastasis, and seems to be involved in epithelial-mesenchymal transition (EMT). However, the mechanism of NETO2 action is still poorly understood.

Results: We have revealed significant increase in the expression of NETO2 gene and deregulation of eight EMT-related genes in CRC. Four of them were upregulated (TWIST1, SNAIL1, LEF1, and FOXA2); the mRNA levels of other genes (FOXA1, BMP2, BMP5, and SMAD7) were decreased. Expression of NETO2 gene was weakly correlated with that of genes involved in the EMT process.

Conclusions: We found considerable NETO2 upregulation, but no significant correlation between the expression of NETO2 and EMT-related genes in CRC. Thus, NETO2 may be involved in CRC progression, but is not directly associated with EMT.
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http://dx.doi.org/10.1186/s12863-017-0581-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751543PMC
December 2017

Morbidity dynamics in proton-photon or photon radiation therapy for locally advanced prostate cancer.

Rep Pract Oncol Radiother 2018 Jan-Feb;23(1):21-27. Epub 2017 Nov 24.

P.A. Herzen Moscow Scientific and Research Oncological Institute, Health Ministry of the Russian Federation, 2 Botkinsky Pr., 125284 Moscow, Russian Federation.

Aim: This study evaluated the frequency and long-term dynamics of early and late post irradiation damage after proton-photon or photon therapy for locally advanced prostate cancer.

Background: The results of a randomized study of proton-photon or photon therapy using several fractionation regimes were analyzed in 272 patients with high and intermediate risk of progression.

Materials And Methods: Three variants of proton boost fractionation were studied sequentially: 3.0 (8 daily fractions), 4.0 (5 fractions, 3 or 5 fractions/week), and 5.5 (3 fractions, 3 fractions/week) Gy(RBE).

Results: A significant decrease in the severity of both acute and late gastrointestinal injuries is achievable with a proton beam. The dynamics of late gastrointestinal and genitourinary toxicity over a 10-year period were generally characterized by a decrease in severity of morbidity by 30% and 15%, respectively.

Conclusions: Local irradiation with a fractional dose of 3.0-5.5 Gy(RBE) and a cumulative dose of 28.0-28.8 Gy(RBE) for protons significantly reduces the early and late rectitis severity, but does not reduce the risk of lower urinary tract injuries. Fractionation regimens do not significantly differ in toxicity levels.
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http://dx.doi.org/10.1016/j.rpor.2017.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709285PMC
November 2017

Internal exposure to neutron-activated Mn dioxide powder in Wistar rats: part 1: dosimetry.

Radiat Environ Biophys 2017 03 10;56(1):47-54. Epub 2017 Feb 10.

Medical Radiological Research Center (MRRC) named after A.F. Tsyb - National Medical Research Radiological Center of the Health Ministry of the Russian Federation, Koroliova Str. 4, Obninsk, Kaluga Region, 249036, Russian Federation.

There were two sources of ionizing irradiation after the atomic bombings of Hiroshima and Nagasaki: (1) initial gamma-neutron irradiation at the moment of detonation and (2) residual radioactivity. Residual radioactivity consisted of two components: radioactive fallout containing fission products, including radioactive fissile materials from nuclear device, and neutron-activated radioisotopes from materials on the ground. The dosimetry systems DS86 and DS02 were mainly devoted to the assessment of initial radiation exposure to neutrons and gamma rays, while only brief considerations were given for the estimation of doses caused by residual radiation exposure. Currently, estimation of internal exposure of atomic bomb survivors due to dispersed radioactivity and neutron-activated radioisotopes from materials on the ground is a matter of some interest, in Japan. The main neutron-activated radionuclides in soil dust were Na, Al, Si, P, Cl, K, Ca, Sc, Mn, Fe, Co, and Cs. The radionuclide Mn (T = 2.58 h) is known as one of the dominant beta- and gamma emitters during the first few hours after neutron irradiation of soil and other materials on ground, dispersed in the form of dust after a nuclear explosion in the atmosphere. To investigate the peculiarities of biological effects of internal exposure to Mn in comparison with external gamma irradiation, a dedicated experiment with Wistar rats exposed to neutron-activated Mn dioxide powder was performed recently by Shichijo and coworkers. The dosimetry required for this experiment is described here. Assessment of internal radiation doses was performed on the basis of measured Mn activity in the organs and tissues of the rats and of absorbed fractions of internal exposure to photons and electrons calculated with the MCNP-4C Monte Carlo using a mathematical rat phantom. The first results of this international multicenter study show that the internal irradiation due to incorporated Mn powder is highly inhomogeneous, and that the most irradiated organs of the experimental animals are: large intestine, small intestine, stomach, and lungs. Accumulated absorbed organ doses were 1.65, 1.33, 0.24, 0.10 Gy for large intestine, small intestine, stomach, and lungs, respectively. Other organs were irradiated at lower dose levels. These results will be useful for interpretation of the biological effects of internal exposure of experimental rats to powdered Mn as observed by Shichijo and coworkers.
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http://dx.doi.org/10.1007/s00411-016-0678-xDOI Listing
March 2017

Effect of lentivirus-mediated shRNA inactivation of HK1, HK2, and HK3 genes in colorectal cancer and melanoma cells.

BMC Genet 2016 12 22;17(Suppl 3):156. Epub 2016 Dec 22.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: The switch from oxidative phosphorylation to glycolysis in proliferating cancer cells, even under aerobic conditions, has been shown first in 1926 by Otto Warburg. Today this phenomenon is known as the "Warburg effect" and recognized as a hallmark of cancer. The metabolic shift to glycolysis is associated with the alterations in signaling pathways involved in energy metabolism, including glucose uptake and fermentation, and regulation of mitochondrial functions. Hexokinases (HKs), which catalyze the first step of glycolysis, have been identified to play a role in tumorigenesis of human colorectal cancer (CRC) and melanoma. However, the mechanism of action of HKs in the promotion of tumor growth remains unclear.

Results: The purpose of the present study was to investigate the effect of silencing of hexokinase genes (HK1, HK2, and HK3) in colorectal cancer (HT-29, SW 480, HCT-15, RKO, and HCT 116) and melanoma (MDA-MB-435S and SK-MEL-28) cell lines using short hairpin RNA (shRNA) lentiviral vectors. shRNA lentiviral plasmid vectors pLSLP-HK1, pLSLP-HK2, and pLSLP-HK3 were constructed and then transfected separately or co-transfected into the cells. HK2 inactivation was associated with increased expression of HK1 in colorectal cancer cell lines pointing to the compensation effect. Simultaneous attenuation of HK1 and HK2 levels led to decreased cell viability. Co-transfection with shRNA vectors against HK1, HK2, and HK3 mRNAs resulted in a rapid cell death via apoptosis.

Conclusions: We have demonstrated that simultaneous inactivation of HK1 and HK2 was sufficient to decrease proliferation and viability of melanoma and colorectal cancer cells. Our results suggest that HK1 and HK2 could be the key therapeutic targets for reducing aerobic glycolysis in examined cancers.
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http://dx.doi.org/10.1186/s12863-016-0459-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5249010PMC
December 2016

Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer.

BMC Genomics 2016 12 28;17(Suppl 14):1011. Epub 2016 Dec 28.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Background: Colorectal cancer (CRC) is one of the most common malignant tumors worldwide. CRC molecular pathogenesis is heterogeneous and may be followed by mutations in oncogenes and tumor suppressor genes, chromosomal and microsatellite instability, alternative splicing alterations, hypermethylation of CpG islands, oxidative stress, impairment of different signaling pathways and energy metabolism. In the present work, we have studied the alterations of alternative splicing patterns of genes related to energy metabolism in CRC.

Results: Using CrossHub software, we analyzed The Cancer Genome Atlas (TCGA) RNA-Seq datasets derived from colon tumor and matched normal tissues. The expression of 1014 alternative mRNA isoforms involved in cell energy metabolism was examined. We found 7 genes with differentially expressed alternative transcripts whereas overall expression of these genes was not significantly altered in CRC. A set of 8 differentially expressed transcripts of interest has been validated by qPCR. These eight isoforms encoded by OGDH, COL6A3, ICAM1, PHPT1, PPP2R5D, SLC29A1, and TRIB3 genes were up-regulated in colorectal tumors, and this is in concordance with the bioinformatics data. The alternative transcript NM_057167 of COL6A3 was also strongly up-regulated in breast, lung, prostate, and kidney tumors. Alternative transcript of SLC29A1 (NM_001078177) was up-regulated only in CRC samples, but not in the other tested tumor types.

Conclusions: We identified tumor-specific expression of alternative spliced transcripts of seven genes involved in energy metabolism in CRC. Our results bring new knowledge on alternative splicing in colorectal cancer and suggest a set of mRNA isoforms that could be used for cancer diagnosis and development of treatment methods.
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http://dx.doi.org/10.1186/s12864-016-3351-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5249009PMC
December 2016

Bidirectional chemotherapy in gastric cancer with peritoneal metastasis combining intravenous XELOX with intraperitoneal chemotherapy with low-dose cisplatin and Doxorubicin administered as a pressurized aerosol: an open-label, Phase-2 study (PIPAC-GA2).

Pleura Peritoneum 2016 Sep 20;1(3):159-166. Epub 2016 Sep 20.

Moscow Research Oncological Institute n.a. P.A. Herzen, Director General.

: Peritoneal metastasis (PM) develop in more than 50 % of gastric cancer (GC) patients. Median survival without treatment is not more than 3-7 months, and 8-12 months after modern combination chemotherapy. Innovative therapeutic approaches are urgently needed. : Phase-2, open label prospective clinical trial assessing safety and efficacy of bidirectional chemotherapy for treating peritoneal metastasis of gastric cancer (PMGC). Treatment protocol included initial staging laparoscopy or laparotomy, 3-4 courses of systemic chemotherapy (XELOX) followed by Pressurized IntraPeritoneal Aerosol Chemotherapy (PIPAC) procedures every 6 weeks until progression of disease or death. Primary endpoints were overall survival and histological peritoneal regression grading score after rebiopsy. : 31 patients were included (9 men, 22 women, mean age 52 years), 24 with synchronous PM at diagnosis, 7 with metachronous PM after previous chemotherapy. Mean PCI was 13.8 (min-max 6-34). XELOX was administered in all patients and combined with 56 PIPAC procedures. Complete and partial pathological response was found in 60 % of the 15 patients eligible for tumor response assessment (4 and 5 patients, respectively). Median survival was 13 months. : Bidirectional chemotherapy combining XELOX with PIPAC with cisplatin and doxororubicin is well tolerated, can induce objective tumor regression and is associated with a promising survival in PMGC.
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http://dx.doi.org/10.1515/pp-2016-0017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386494PMC
September 2016

The Dysregulation of Polyamine Metabolism in Colorectal Cancer Is Associated with Overexpression of c-Myc and C/EBPβ rather than Enterotoxigenic Bacteroides fragilis Infection.

Oxid Med Cell Longev 2016 28;2016:2353560. Epub 2016 Jun 28.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; National Medical Research Center of Radiology, Ministry of Healthcare of the Russian Federation, Moscow 125284, Russia.

Colorectal cancer is one of the most common cancers in the world. It is well known that the chronic inflammation can promote the progression of colorectal cancer (CRC). Recently, a number of studies revealed a potential association between colorectal inflammation, cancer progression, and infection caused by enterotoxigenic Bacteroides fragilis (ETBF). Bacterial enterotoxin activates spermine oxidase (SMO), which produces spermidine and H2O2 as byproducts of polyamine catabolism, which, in turn, enhances inflammation and tissue injury. Using qPCR analysis, we estimated the expression of SMOX gene and ETBF colonization in CRC patients. We found no statistically significant associations between them. Then we selected genes involved in polyamine metabolism, metabolic reprogramming, and inflammation regulation and estimated their expression in CRC. We observed overexpression of SMOX, ODC1, SRM, SMS, MTAP, c-Myc, C/EBPβ (CREBP), and other genes. We found that two mediators of metabolic reprogramming, inflammation, and cell proliferation c-Myc and C/EBPβ may serve as regulators of polyamine metabolism genes (SMOX, AZIN1, MTAP, SRM, ODC1, AMD1, and AGMAT) as they are overexpressed in tumors, have binding site according to ENCODE ChIP-Seq data, and demonstrate strong coexpression with their targets. Thus, increased polyamine metabolism in CRC could be driven by c-Myc and C/EBPβ rather than ETBF infection.
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http://dx.doi.org/10.1155/2016/2353560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940579PMC
July 2017