Научная статья на тему 'ROLE OF ACE2/TMPRSS2 GENES REGULATION BY INTESTINAL microRNA ISOFORMS IN THE COVID-19 PATHOGENESIS'

ROLE OF ACE2/TMPRSS2 GENES REGULATION BY INTESTINAL microRNA ISOFORMS IN THE COVID-19 PATHOGENESIS Текст научной статьи по специальности «Биологические науки»

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Ключевые слова
COVID-19 / SARS-CoV-2 / ACE2 / TMPRSS2 / miRNA / isomiR / acute respiratory distress syndrome / coronavirus / COVID-19 / SARS-CoV-2 / AПФ2 / TMPRSS2 / микроРНК / изоформа микроРНК / острый респираторный дистресс-синдром / коронавирус

Аннотация научной статьи по биологическим наукам, автор научной работы — Stepan A. Nersisyan, Shkurnikov Myu, Osipyants Ai, Vechorko Vi

Coronavirus SARS-CoV-2, the cause of the COVID-19 pandemic, enters the cell by binding the cell surface proteins: angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). The expression of these proteins varies significantly in individual organs and tissues of the human body. One of the proteins’ expression regulation mechanisms is based on the activity of the microRNA (miRNA) molecules, small non-coding RNAs, the most important function of which is the post-transcriptional negative regulation of gene expression. The study was aimed to investigate the mechanisms of the interactions between miRNA isoforms and ACE2/TMPRSS2 genes in the colon tissues known for the high level of expression of the described enzymes. The search for interactions was performed using the correlation analysis applied to the publicly available paired mRNA/miRNA sequencing data of colon tissues. Among the others, such miRNAs as miR-30c and miR-200c were identified known for their involvement in the coronavirus infection and acute respiratory distress syndrome pathogenesis. Thus, new potential mechanisms for the ACE2 and TMPRSS2 enzymes regulation were ascertained, as well as their possible functional activity in a cell infected with coronavirus.

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РОЛЬ РЕГУЛЯЦИИ ГЕНОВ AПФ2/TMPRSS2 ИЗОФОРМАМИ микроРНК КИШЕЧНИКА В ПАТОГЕНЕЗЕ COVID-19

Коронавирус SARS-CoV-2, вызвавший пандемию COVID-19, проникает в клетку, связываясь с поверхностными белками: ангиотензин-превращающим ферментом 2 (AПФ2) и сериновой протеазой 2 (TMPRSS2). Экспрессия данных белков значительно различается в отдельных органах и тканях организма человека. Одним из механизмов регуляции их экспрессии является активность молекул микроРНК — коротких некодирующих РНК, важнейшей функцией которых является посттранскрипционная негативная регуляция экспрессии генов. Целью работы было выявить механизмы взаимодействия изоформ микроРНК и генов AПФ2 / TMPRSS2 в тканях толстого кишечника, известных высоким уровнем экспрессии указанных ферментов. Поиск взаимодействий был осуществлен средствами корреляционного анализа на публично доступной выборке данных парного мРНК / микроРНК-секвенирования тканей кишечника. В числе находок оказались такие микроРНК, как miR-30c и miR-200c, известные своей ролью в патогенезе коронавирусной инфекции и острого респираторного дистресс-синдрома. Таким образом, были установлены новые потенциальные механизмы регуляции ферментов AПФ2 и TMPRSS2 и их возможная функциональная активность в клетке, инфицированной коронавирусом.

Текст научной работы на тему «ROLE OF ACE2/TMPRSS2 GENES REGULATION BY INTESTINAL microRNA ISOFORMS IN THE COVID-19 PATHOGENESIS»

ROLE OF ACE2/TMPRSS2 GENES REGULATION BY INTESTINAL microRNA ISOFORMS IN THE COVID-19 PATHOGENESIS

Nersisyan SA1-2 ^ Shkurnikov MYu3, Osipyants AI3,4, Vechorko VI5

1 National Research University Higher School of Economics, Moscow, Russia

2 Lomonosov Moscow State University, Moscow, Russia

3 P. A. Hertsen Moscow Oncology Research Center, branch of the National Medical Research Radiology Center, Moscow, Russia

4 Far Eastern Federal University, Vladivostok, Russia

5 City Clinical Hospital № 15 named after O. M. Filatov, Moscow, Russia

Coronavirus SARS-CoV-2, the cause of the COVID-19 pandemic, enters the cell by binding the cell surface proteins: angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). The expression of these proteins varies significantly in individual organs and tissues of the human body. One of the proteins' expression regulation mechanisms is based on the activity of the microRNA (miRNA) molecules, small non-coding RNAs, the most important function of which is the post-transcriptional negative regulation of gene expression. The study was aimed to investigate the mechanisms of the interactions between miRNA isoforms and ACE2/TMPRSS2 genes in the colon tissues known for the high level of expression of the described enzymes. The search for interactions was performed using the correlation analysis applied to the publicly available paired mRNA/miRNA sequencing data of colon tissues. Among the others, such miRNAs as miR-30c and miR-200c were identified known for their involvement in the coronavirus infection and acute respiratory distress syndrome pathogenesis. Thus, new potential mechanisms for the ACE2 and TMPRSS2 enzymes regulation were ascertained, as well as their possible functional activity in a cell infected with coronavirus.

Keywords: COVID-19, SARS-CoV-2, ACE2, TMPRSS2, miRNA, isomiR, acute respiratory distress syndrome, coronavirus

Funding: the study was supported by the Ministry of Science and Higher Education of the Russian Federation grant (project RFMEFI61618X0092).

Author contribution: Nersisyan SA, Shkurnikov MYu, Osipyants AI, Vechorko VI — study concept; Nersisyan SA, Shkurnikov MYu — bioinformatics analysis; Nersisyan SA, Shkurnikov MYu, Osipyants AI, Vechorko VI — interpretation of results; Nersisyan SA — manuscript writing.

[>3 Correspondence should be addressed: Stepan A. Nersisyan Vavilova, 7, Moscow, 117312; s.a.nersisyan@gmail.com

Received: 17.04.2020 Accepted: 28.04.2020 Published online: 29.04.2020

DOI: 10.24075/brsmu.2020.024

РОЛЬ РЕГУЛЯЦИИ ГЕНОВ AПФ2/TMPRSS2 ИЗОФОРМАМИ микроРНК КИШЕЧНИКА В ПАТОГЕНЕЗЕ COVID-19

С. А. Нерсисян1,2 М. Ю. Шкурников3, А. И. Осипьянц3,4, В. И. Вечорко5

1 Национальный исследовательский университет «Высшая школа экономики», Москва, Россия

2 Московский государственный университет имени М. В. Ломоносова, Москва, Россия

3 Московский научно-исследовательский онкологический институт имени П. А. Герцена — филиал Национального медицинского исследовательского центра радиологии, Москва, Россия

4 Дальневосточный федеральный университет, Владивосток, Россия

5 Городская клиническая больница № 15 имени О. М. Филатова, Москва, Россия

Коронавирус SARS-CoV-2, вызвавший пандемию COVID-19, проникает в клетку, связываясь с поверхностными белками: ангиотензин-превращающим ферментом 2 ^ПФ2) и сериновой протеазой 2 (TMPRSS2). Экспрессия данных белков значительно различается в отдельных органах и тканях организма человека. Одним из механизмов регуляции их экспрессии является активность молекул микроРНК — коротких некодирующих РНК, важнейшей функцией которых является посттранскрипционная негативная регуляция экспрессии генов. Целью работы было выявить механизмы взаимодействия изоформ микроРНК и генов AПФ2 / TMPRSS2 в тканях толстого кишечника, известных высоким уровнем экспрессии указанных ферментов. Поиск взаимодействий был осуществлен средствами корреляционного анализа на публично доступной выборке данных парного мРНК / микроРНК-секвенирования тканей кишечника. В числе находок оказались такие микроРНК, как miR-30c и miR-200c, известные своей ролью в патогенезе коронавирусной инфекции и острого респираторного дистресс-синдрома. Таким образом, были установлены новые потенциальные механизмы регуляции ферментов AПФ2 и TMPRSS2 и их возможная функциональная активность в клетке, инфицированной коронавирусом.

Ключевые слова: COVID-19, SARS-CoV-2, AПФ2, TMPRSS2, микроРНК, изоформа микроРНК, острый респираторный дистресс-синдром, коронавирус

Финансирование: работа выполнена при поддержке гранта Министерства образования и науки Российской Федерации (проект RFMEFI61618X0092).

Вклад авторов: С. А. Нерсисян, М. Ю. Шкурников, А. И. Осипьянц, В. И. Вечорко — разработка концепции; С. А. Нерсисян, М. Ю. Шкурников — биоинформатический анализ; С. А. Нерсисян, М. Ю. Шкурников, А. И. Осипьянц, В. И. Вечорко — интерпретация результатов; С. А. Нерсисян — написание статьи.

[>3 Для корреспонденции: Степан Ашотович Нерсисян

ул. Вавилова, д. 7, г. Москва, 117312; s.a.nersisyan@gmail.com

Статья получена: 17.04.2020 Статья принята к печати: 28.04.2020 Опубликована онлайн: 29.04.2020 DOI: 10.24075/vrgmu.2020.024

The rapid and progressive spread of the COVID-19 infection caused by the SARS-CoV-2 coronavirus deeply affected the health of hundreds of thousands of people, which became a serious challenge to healthcare systems and global economic

stability. The characteristics of SARS-CoV-2, especially distinguishing the disease from influenza, are the higher infection rate combined with the increased risk of severe course and mortality, mainly due to the acute respiratory

ОРИГИНАЛЬНОЕ ИССЛЕДОВАНИЕ I ВИРУСОЛОГИЯ

distress syndrome (ARDS) [1]. The mechanism of the cells infection is actively studied in many laboratories. In particular, it is known that the SARS-CoV-2 viral envelope expresses the spike protein (S protein) containing the receptor binding domain with high affinity for the extracellular domain of angiotensin-converting enzyme 2 (ACE2). The further S protein cleavage by the transmembrane serine protease 2 (TMPRSS2) aimed to produce the S1 and S2 subunits is a crucial stage for membrane fusion and virus internalization by endocytosis with ACE2 in pulmonary epithelium. It is assumed that the greater virulence of SARS-CoV-2 compared to other coronaviruses can be explained by the S1 protein's significantly higher affinity for ACE2. This mechanism of the SARS-CoV-2 entering the cell leads to the loss of ACE2 on the cell surface, thereby contributing to chronic lung function impairment and severe tissue fibrosis [2].

MicroRNAs (miRNAs) are the small non-coding single stranded RNAs containing an average of 22 nucleotides. One of the most important intracellular functions of miRNA is the negative regulation of gene expression due to complementary miRNA binding with the target mRNA, leading to mRNA degradation or translational inhibition [3]. MicroRNAs are formed from the longer hairpin molecules of pre-miRNA as a result of the hairpin cleaving Drosha and Dicer enzymes' activity [4]. The cleaving site inaccuracy leads to the emergence of various microRNA isoforms that differ in several nucleotides at the ends of the molecule. It is reported that many miRNAs of canonical types are expressed much weaker than some alternative isoforms [5]. It is of key importance that different isoforms of the same miRNA may have completely different target genes. This is because the most important role in binding to the target mRNA is played by the miRNA region between the 5' nucleotides 2-7 (seed region) [6].

It is reported that the functional impairment of miRNAs and their isoforms is associated with a large number of pathological conditions, including cancer, neurological and cardiovascular diseases [7]. A large number of papers is devoted to the study of the role of miRNAs in the pathogenesis of viral infections: some of them are aimed to study the therapeutic potential of the direct miRNA interaction with the virus [8], and the others are aimed to investigate the potential interactions of miRNAs and proteins playing a key role in the viral vital processes [9]. However, the ACE2 and TMPRSS2 expression regulation by miRNA in subjects with COVID-19 remains poorly understood. The study was aimed to reveal the mechanisms of the interactions between miRNA isoforms and ACE2/TMPRSS2 genes in the colon tissues known for the high level of expression of the described enzymes.

METHODS

To search for miRNA isoforms interacting with ACE2 and TMPRSS2 enzymes, we performed the integrated analysis of the paired mRNA and miRNA expression in the normal colon tissues' sample (the enzyme is most intensively expressed in the colon tissues). The tissue selection was also due to the fact that the gut models were often used for in vitro studies of viruses [10, 11]. The available for public access samples from The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) collection were used. The sample analysis was carried out by the next-generation mRNA and miRNA sequencing [12]. The data were expression matrices of thousands of mRNA and miRNA isoforms in eight samples, the unit of expression was the binary logarithm of the corresponding transcript number of reads normalized to the upper quartile of the overall distribution

(FPKM-UQ). To search for potential regulatory interactions between miRNA isoforms and TMPRSS2 the Spearman correlation coefficients between the expressions of 25% of the most highly expressed isoforms with the expressions of the corresponding mRNA were calculated, with subsequent filtering in accordance with the p-value (significance level 0.05).

RESULTS

The ACE2 and TMPRSS2 expression at the mRNA level turned out to be very high: TMPRSS2 was in the list of the most highly expressed genes (1%), and the ACE2 expression was between the 93rd and 94th percentiles, which was fully consistent with published data [13] (see Figure). Correlation analysis allowed us to detect the miR-21 miRNA demonstrating a significant negative correlation with the ACE2 gene expression, as well as the following miRNA families regulating TMPRSS2: let-7a/ let-7d, miR-30a, miR-30c, miR-127, miR-194, miR-200c, miR-361 and miR-423. The let-7a miRNA was represented by the hsa-let-7a-5p isoform, which differed from the canonic type by adenine added at the 5' end of the molecule. The miR-194 was represented by the hsa-miR-194-3p isoform, which lacked the 5' first nucleotide. The absence of the corresponding miRNA canonical forms in the list indicates the importance of taking into account the profiles of all miRNA isoforms, not just canonical isoforms.

DISCUSSION

Some of the discovered miRNAs have already been detected during the virological studies. Thus, it was shown that the miR-30c expression in the lungs of the mouse changed significantly upon infection with SARS-CoV virus [14], which made it possible to put forward a hypothesis about the involvement of that miRNA in the development of a disease caused by the virus. The miR-200c miRNA is also of great interest. In 2017, a paper was published reporting that miR-200c miRNA played a key role in the virus-induced ARDS pathogenesis [15]. The researchers found out that the H5N1 avian influenza virus promoted the miR-200c expression, the target of which was the ACE2 receptor. Moreover, the viral proteins were detected responsible for promoting the miRNA expression. The discovery of the interaction possibility between the described miRNA and

22 -

ACE2 TMPRSS2

Fig. ACE2 and TMPRSS2 expression distribution in the colon tissues. Borders of the boxes correspond to the lower and upper quartiles, vertical segment inside the box represents the median value. Black rhombus shows outlier

ВЕСТНИК РГМУ | 2, 2020 | VESTNIKRGMU.RU

17

the TMPRSS2 enzyme emphasizes the need for studying the role of miR-200c in the COVID-19 pathogenesis.

CONCLUSION

The results obtained indicate the presence of numerous regulatory interactions between miRNA isoforms and ACE2/

TMPRSS2 enzymes. Such Information is extremely important due to the key role of enzymes In the mechanism of cell Infection with SARS-CoV-2 coronavirus. Further research is needed for refining and experimental validation of the findings. In particular, it is possible to discover new treatment options based on the ACE2 and TMPRSS2 expression regulation via microRNAs.

References

1. Munster VJ, Koopmans M, van Doremalen N, van Riel D, de Wit E. A Novel Coronavirus Emerging in China — Key Questions for Impact Assessment. N Engl J Med. 2020 Feb 20; 382 (8): 692-4.

2. Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020 Mar 4. pii: S0092-8674(20)30229-4.

3. Nilsen TW. Mechanisms of microRNA-mediated gene regulation in animal cells. Trends Genet. 2007 May; 23 (5): 243-9.

4. Makarova JA, Shkurnikov MU, Turchinovich AA, Tonevitsky AG, Grigoriev AI. Circulating microRNAs. Biochemistry (Mosc). 2015 Sep; 80 (9): 1117-26.

5. Loher P, Londin ER, Rigoutsos I. IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. Oncotarget. 2014 Sep 30; 5 (18): 8790-802.

6. Maziere P, Enright AJ. Prediction of microRNA targets. Drug Discov Today. 2007 Jun; 12 (11-12): 452-8.

7. Osip'yants AI, Knyazev EN, Galatenko AV Nyushko KM, Galatenko VV Shkurnikov MY, et. al. Changes in the Level of Circulating hsa-miR-297 and hsa-miR-19b-3p miRNA Are Associated with Generalization of Prostate Cancer. Bull Exp Biol Med. 2017 Jan; 162 (3): 379-82.

8. Leon-Icaza SA, Zeng M, Rosas-Taraco AG. microRNAs in viral acute respiratory infections: immune regulation, biomarkers,

therapy, and vaccines. ExRNA. 2019 Feb; 1.

9. Mallick B, Ghosh Z, Chakrabarti J. MicroRNome analysis unravels the molecular basis of SARS infection in bronchoalveolar stem cells. PLoS One. 2009 Nov 13; 4 (11): e7837.

10. Samatov TR, Senyavina NV, Galatenko VV, Trushkin EV, Tonevitskaya SA, Alexandrov DE, et al. Tumour-like druggable gene expression pattern of CaCo2 cells in microfluidic chip. BioChip J. 2016 Jul; 10: 215-20.

11. Sakharov D, Maltseva D, Knyazev E, Nikulin S, Poloznikov A, Shilin S, et. al. Towards embedding Caco-2 model of gut interface in a microfluidic device to enable multi-organ models for systems biology. BMC Syst Biol. 2019 Mar 5; 13 (Suppl 1): 19.

12. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 487 (7407): 330-7.

13. Vaarala MH, Porvari KS, Kellokumpu S, Kyllönen AP, Vihko PT. Expression of transmembrane serine protease TMPRSS2 in mouse and human tissues. J Pathol. 2001 Jan; 193 (1): 134-40.

14. Peng X, Gralinski L, Ferris MT, Frieman MB, Thomas MJ, Proll S, et. al. Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. mBio. 2011 Nov 15; 2 (6).

15. Liu Q, Du J, Yu X, Xu J, Huang F, Li X, Zhang C, Li X, et al. miRNA-200c-3p is crucial in acute respiratory distress syndrome. Cell Discov. 2017 Jun 27; 3: 17021.

Литература

1. Munster VJ, Koopmans M, van Doremalen N, van Riel D, de Wit E. A Novel Coronavirus Emerging in China — Key Questions for Impact Assessment. N Engl J Med. 2020 Feb 20; 382 (8): 692-4.

2. Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020 Mar 4. pii: S0092-8674(20)30229-4.

3. Nilsen TW. Mechanisms of microRNA-mediated gene regulation in animal cells. Trends Genet. 2007 May; 23 (5): 243-9.

4. Makarova JA, Shkurnikov MU, Turchinovich AA, Tonevitsky AG, Grigoriev AI. Circulating microRNAs. Biochemistry (Mosc). 2015 Sep; 80 (9): 1117-26.

5. Loher P, Londin ER, Rigoutsos I. IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. Oncotarget. 2014 Sep 30; 5 (18): 8790-802.

6. Maziere P, Enright AJ. Prediction of microRNA targets. Drug Discov Today. 2007 Jun; 12 (11-12): 452-8.

7. Osip'yants AI, Knyazev EN, Galatenko AV Nyushko KM, Galatenko VV Shkurnikov MY, et. al. Changes in the Level of Circulating hsa-miR-297 and hsa-miR-19b-3p miRNA Are Associated with Generalization of Prostate Cancer. Bull Exp Biol Med. 2017 Jan; 162 (3): 379-82.

8. Leon-Icaza SA, Zeng M, Rosas-Taraco AG. microRNAs in viral acute respiratory infections: immune regulation, biomarkers,

therapy, and vaccines. ExRNA. 2019 Feb; 1.

9. Mallick B, Ghosh Z, Chakrabarti J. MicroRNome analysis unravels the molecular basis of SARS infection in bronchoalveolar stem cells. PLoS One. 2009 Nov 13; 4 (11): e7837.

10. Samatov TR, Senyavina NV, Galatenko VV, Trushkin EV, Tonevitskaya SA, Alexandrov DE, et al. Tumour-like druggable gene expression pattern of CaCo2 cells in microfluidic chip. BioChip J. 2016 Jul; 10: 215-20.

11. Sakharov D, Maltseva D, Knyazev E, Nikulin S, Poloznikov A, Shilin S, et. al. Towards embedding Caco-2 model of gut interface in a microfluidic device to enable multi-organ models for systems biology. BMC Syst Biol. 2019 Mar 5; 13 (Suppl 1): 19.

12. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 487 (7407): 330-7.

13. Vaarala MH, Porvari KS, Kellokumpu S, Kyllönen AP, Vihko PT. Expression of transmembrane serine protease TMPRSS2 in mouse and human tissues. J Pathol. 2001 Jan; 193 (1): 134-40.

14. Peng X, Gralinski L, Ferris MT, Frieman MB, Thomas MJ, Proll S, et. al. Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. mBio. 2011 Nov 15; 2 (6).

15. Liu Q, Du J, Yu X, Xu J, Huang F, Li X, Zhang C, Li X, et al. miRNA-200c-3p is crucial in acute respiratory distress syndrome. Cell Discov. 2017 Jun 27; 3: 17021.

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