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Medical genomics at the Systems Biology and Bioinformatics (SBB-2019) school.
BMC Medical Genomics ( IF 2.7 ) Pub Date : 2020-09-18 , DOI: 10.1186/s12920-020-00786-x
Yuriy L Orlov 1, 2, 3 , Elena N Voropaeva 3 , Ming Chen 4 , Ancha V Baranova 5, 6
Affiliation  

Next-Generation Sequencing-driven analysis and Systems Biology approaches commonly serve as a backdrop for a study of a tumor genome. This issue of BMC Medical Genomics SBB-2019 (“Systems Biology and Bioinformatics”) presents recent works discussed at the 11th Young Scientists School “Systems Biology and Bioinformatics”-2019, held in Novosibirsk, Russia (http://conf.bionet.nsc.ru/sbb2019/en/). Here we collated some cancer gene expression studies, some mutation profiling studies as well as some insightful case reports. The SBB school series on bioinformatics proceeds annually since 2008 under the joint steerage of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences and Novosibirsk State University [1, 2]. We had publications in special topic issues after the Schools before in BMC Genomics, BMC Medical Genomics and related BioMed Central family journals since 2014 [3,4,5]. The SBB Schools in Novosibirsk were initially conceived as satellite event for young scientists held at the same time as BGRS\SB (Bioinformatics of Genome Regulation and Structure \ Systems Biology) conference series, since 1998 taking place biannually. The recent BGRS\SB-2020 event in Novosibirsk was over at the time of the current journal issue publication (https://bgrssb.icgbio.ru/2020/). Other special issues (Supplements) to the BMC journals in the fields of genomics, genetics, bioinformatics, and medical genetics are published at BMC Genomics, BMC Genetics and three other BMC journals. The BGRS\SB-2018 conference highlights were published in 2018 [5,6,7], and continued the BMC Medical Genomics special issues in 2019 [8]. Public discussion of the conference presentations at the open access platforms of BioMed Central and other publishers serve as an international educational resource for young scientists [9, 10].

The articles comprising this issue of BMC Medical Genomics are focused on cancer genomics. Using transcriptomic data, bioinformatic models can be built for patient-oriented ranking of cancer drugs [11]. Nicolas Borisov et al. [12] (this issue) developed the database for cancer gene expression profiles associated with clinical outcomes of the chemotherapy treatments. Authors mined Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and Tumor Alterations Relevant for GEnomics-driven Therapy (TARGET) repositories to pull a database of 2786 gene expression profiles associated with clinical responses on chemotherapy. The cases represented breast cancer, lung cancer, low-grade glioma, endothelial carcinoma, multiple myeloma, adult leukemia, pediatric leukemia and kidney tumors and suitable for Machine Learning analysis of these malignancy.

Alexander Lavrov and co-authors [13] (this issue) review pathogenic variants targetable by single base editing. Single nucleotide variants account for approximately 90% of all known pathogenic variants responsible for human diseases, including thousands of known 6000 monogenic diseases. Recently discovered CRISPR/Cas9 base editors are capable of correcting individual nucleotide positions, thus, providing opportunities for personalized therapy. Unfortunately, none of such editors are perfect in their specificity [14]. Authors summarized all possible pathogenic variants which may be efficiently targeted by each of the known base editors. They analyzed 21 editing system currently reported in 9 publications and showed that C > T base editors are capable of precisely targeting about 3200 mutations, a total of 46% of all pathogenic T > C variants, while A > G editors may precisely target 6900 mutations (34% of all pathogenic G > A variants). Thus, even now the list of mutations which can be targeted with currently available systems is very large, and enough to choose from and embrak on developing new targeted therapies.

Next few papers highlight genomic studies of particular tumors. Anna Kudryavtseva et al. [15] (this issue) discuss mutation profiles of vagal paragangliomas, a group of rare head and neck neuroendocrine tumors, arising from the vagus nerve, and differing from more common carotid paragangliomas dissected by same group of authors earlier [16, 17]. Authors collected vagal paragangliomas from 8 patients, analyzed tumor exomes and discussed their findings in details. In particular, a number of novel and known pathogenic/likely pathogenic variants of the SDHx genes, frequently mutated in paragangliomas/pheochromocytomas were described.

Elena Pudova and colleagues [18] (this issue) analyzed miRNAs expression signatures associated with lymphatic dissemination of the locally advanced prostate tumors. Making an informed decision on PC treatment options after radical prostatectomy (with expanded pelvic lymphadenectomy) is far from being easy and depends on the stratification of patients into risk groups according to tumor stage, Gleason index, PSA level, and regional metastasis. These clinical indicators are clearly in the need of augmenting with some molecular biomarkers. The changes in miRNA expression profiles associated with lymphatic dissemination of the prostate cancer yielded a couple of miRNAs suitable for the development into the prognostic tools. The most prominent condidates, namely, miR-20a-5p, miR-106a-5p, miR-93-5p, and miR-15b-5p are well-known players in oncogenic transformation or tumor suppression [19].

Tatyana Vasilyeva et al. [20] (this issue) present a case study of congenital aniridia caused by pericentric inversion in the chromosome 11. Aniridia is a Mendelian autosomal dominant developmental disorder that can affect all eye structures as well as central nervous system, the endocrine system, and other systems and organs. In the case described, a near-megabase deletion removed a locus with ELP4, PAX6, and RCN1 genes while the coding sequence of the WT1 gene was not affected. The authors conclude that the risk of developing Wilms’ tumor in a probed is similar to that in the general population.

We conclude this special journal issue by the multiple paraganglioma cases report compiled by Vladislav Pavlov et al. [21] (this issue). The authors report a case of multiple paragangliomas, manifesting as bilateral carotid and vagal paragangliomas. After immunostaining for succinate dehydrogenase (SDH) subunits and exome analysis, a likely pathogenic variant in the SDHD gene was found in the germline, with additional likely pathogenic somatic variants founds in some of the tumors. It seems that authors sussessfully pinpointed germline variant in the SDHD gene as a driver of the development of multiple paragangliomas.

Overall, this issue includes reports of recent medical genomics applications in cancer and databases development, as well as case reports, continuing series on BMC Med Genomics special post-conference journal issues [10, 17, 22, 23]. We hope for continuing international exchange and education via the schools and competitions for young scientists. We invite our readers worldwide to attend the systems biology meetings in Russia. Digital Medicine Forum (Digital Medicine Forum) and MGNGS-2020 (Medical Genetics - Next-Generation Sequencing) event postponed to 2021 (http://ngs.med-gen.ru/mgngs20/).

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We are grateful to Professor Academician N.A. Kolchanov for the organization of the “Systems Biology and Bioinformatics”-2019 event and providing platform for international bioinformatics and genomics research. We acknowledge Prof. T.V. Tatarinova for the editorial work on SBB-2019 issues and the organization of the “Centenary of Human Population Genetics” conference in Moscow in 2019 that provided materials to the SBB-2019 special issue series at BioMed Central journals. Thanks to Prof. R.A.Zinchenko and Dr. M.Y.Skoblov for MGNGS-2019 conference organization.

SBB-19 School holding in Novosibirsk was supported by RFBR (grant 19-04-20036). YO (medical genetics study) was supported by RSF (grant 19-15-00219).

The guest editors of the special issue are grateful to the conference committee members and the reviewers who helped in the peer-review and the special issue preparation. We acknowledge Mikhail Ponomarenko (Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia), Hildegard Nikki Hall (University of Edinburgh, UK), Olga Arkova (Institute of Gene Biology RAS, Moscow), Piramanayagam Shanmughavel (Bharatiar University, India), Haiqing Zhao (Columbia University Medical Center, USA), Vitaly Gursky (S.Petersburg Polytech University, Russia), Olga Zolotareva (Bielefeld University, Germany), Elvira Galieva (Novosibirsk State University, Russia), Alexey Kolodkin (University of Luxemburg), Alexander Ratushny (Bristol Myers Squibb, USA), Eric Mjolsness (Irvine University, USA), Paul Jones (AIC Inc., USA), Shuan Li (University of Rhode Island, USA), Mengting Liu (University of Southern California, USA), Lydia Manor (AIC Inc., USA), Guohao Wang (NIH, USA), Nina Oparina (Karolinska Institut, Sweden), Stanislav Rybtsov (University of Edinburgh, UK), Anastasia Efimenko (Moscow State University, Russia), Ed Hollox (University of Leicester, USA), Igor Sharakhov (Virginia Tech, USA), Alexander Konev (NRC «Kurchatov Institute» - PNPI, Gatchina, Russia), Anatoly Ivashchenko (al-Farabi Kazakh National University, Kazakhstan), Ekaterina Marakasova (US FDA, USA), Chris Tyler (Sanger Centre, UK), Dmitry Karpov (Institute of Biomedical Chemistry RAS), Nikolai Barlev (Institute of Cytology RAS, St.-Petersburg, Russia), Elena Leberfarb (Novosibirsk State Medical University, Russia), Lyubov Chuvakova (Moscow State University, Russia), Andrei Krivtsov (Dana Farber Cancer Institute, USA), Olga Tarasova (Sechenov University, Moscow, Russia), Nadezhda Antipova (Moscow State University, Russia), Oleg Gusev (RIKEN, Japan), Konstantin Gunbin (Novosibirsk State University, Russia), Hua Zhong (Fred Hutchinson Cancer Research Center, USA), Elena Zaklyazminskaya (Petrovsky Russian Research Centre of Surgery, Russia), Nataly Bondar (Novosibirsk State University, Russia), Michael Linderman (Icahn School of Medicine at Mount Sinai), Sergei Fedotov (MEPhI, Moscow, Russia), Vadim Efimov (Novosibirsk State University, Russia), Gordon Crippen (University of Michigan, USA), Igor Berezovsky (Bioinformatics Institute, Singapore), Andreas Laner (Medizinisch Genetisches Zentrum, Munich, Germany), Arun Kumar (Shanmugha Arts Science Technology and Research Academy, India), Lars Fehren-Schmitz (University of California Santa Cruz, USA), Mikhail Sadovsky (Siberian Federal University, Krasnoyarsk, Russia), Nataliya Dorogova (Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia), Vasily Ramensky (National Research Institute of Preventive Medicine, Moscow, Russia), Patrick Harrison (University College Cork, Ireland), Irina Medvedeva (Bristol Myers Squibb, USA).

About this supplement

This article has been published as part of BMC Medical Genomics Volume 13 Supplement 8, 2020: Selected Topics in “Systems Biology and Bioinformatics” - 2019: medical genomics. The full contents of the supplement are available online at https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-13-supplement-8.

Publication of this article was not covered by sponsorship.

Affiliations

  1. The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia

    Yuriy L. Orlov

  2. Novosibirsk State University, 630090, Novosibirsk, Russia

    Yuriy L. Orlov

  3. Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630089, Novosibirsk, Russia

    Yuriy L. Orlov & Elena N. Voropaeva

  4. Department of Bioinformatics, College of Life Sciences, First Affiliated Hospital of Medical School, Zhejiang University, Hangzhou, 310058, China

    Ming Chen

  5. George Mason University, Fairfax, VA, 22030, USA

    Ancha V. Baranova

  6. Research Centre for Medical Genetics, 115522, Moscow, Russia

    Ancha V. Baranova

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  1. Yuriy L. OrlovView author publications

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  2. Elena N. VoropaevaView author publications

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  4. Ancha V. BaranovaView author publications

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Contributions

AB and YO are guest editors of the special post-conference issues and Program Committee members of SBB-2019 School. EV and MC are the invited editor and the organizing committee member of the conference. All the authors read, revised, and approved the final manuscript.

Corresponding author

Correspondence to Yuriy L. Orlov.

Competing interests

The authors declare that they have no competing interests.

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Orlov, Y.L., Voropaeva, E.N., Chen, M. et al. Medical genomics at the Systems Biology and Bioinformatics (SBB-2019) school. BMC Med Genomics 13, 127 (2020). https://doi.org/10.1186/s12920-020-00786-x

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  • DOI: https://doi.org/10.1186/s12920-020-00786-x

中文翻译：
系统生物学和生物信息学（SBB-2019）学校的医学基因组学。

下一代测序驱动的分析和系统生物学方法通常作为研究肿瘤基因组的背景。本期BMC医学基因组学SBB-2019（“系统生物学和生物信息学”）介绍了在俄罗斯新西伯利亚举行的第11届青年科学家学校“系统生物学和生物信息学” -2019上讨论的最新研究成果（http：//conf.bionet。 nsc.ru/sbb2019/en/）。在这里，我们整理了一些癌症基因表达研究，一些突变谱研究以及一些有见地的病例报告。SBB关于生物信息学的系列丛书自2008年以来每年在俄罗斯科学院西伯利亚分校细胞与遗传研究所和新西伯利亚国立大学的联合指导下进行[1，2]。在学校毕业后，我们在BMC基因组学领域出版了有关特殊主题的出版物，自2014年以来，BMC Medical Genomics和相关的BioMed Central系列期刊[3,4,5]。自1998年以来，新西伯利亚的SBB学校最初被视为与BGRS \ SB（基因组调控和结构\系统生物学的生物信息学）会议系列同时举行的年轻科学家的卫星活动，自1998年开始每两年举办一次。在本期期刊发行（https://bgrssb.icgbio.ru/2020/）时，新西伯利亚最近的BGRS \ SB-2020事件已结束。BMC基因组学，遗传学，生物信息学和医学遗传学领域的BMC期刊的其他特殊问题（增刊）已在BMC Genomics，BMC Genetics和其他三本BMC期刊上发表。BGRS \ SB-2018会议摘要于2018年发表[5,6,7]，并在2019年继续发表BMC Medical Genomics特刊[8]。

包含本期BMC Medical Genomics的文章重点讨论了癌症基因组学。利用转录组数据，可以建立生物信息学模型，以患者为导向对癌症药物进行排名[11]。Nicolas Borisov等。[12]（本期）开发了与化学疗法的临床结果相关的癌症基因表达谱的数据库。作者挖掘了基因表达综合（GEO），癌症基因组图谱（TCGA）和与基因组驱动疗法（TARGET）存储库相关的肿瘤改变的信息，以提取与化学疗法临床反应相关的2786个基因表达谱的数据库。这些病例代表乳腺癌，肺癌，低度神经胶质瘤，内皮细胞癌，多发性骨髓瘤，成人白血病，小儿白血病和肾脏肿瘤，适合于对这些恶性肿瘤进行机器学习分析。

Alexander Lavrov及其合作者[13]（本期）回顾了可通过单碱基编辑靶向的病原体。单核苷酸变体约占导致人类疾病的所有已知致病变体的90％，包括数千种已知的6000种单基因疾病。最近发现的CRISPR / Cas9碱基编辑器能够校正单个核苷酸的位置，从而为个性化治疗提供了机会。不幸的是，这些编辑者的专业性都不是完美的[14]。作者总结了所有可能的病原体变体，每个已知的基础编辑者都可以有效地靶向这些变体。他们分析了9种出版物中目前报道的21种编辑系统，结果表明C> T碱基编辑者能够精确针对约3200个突变，占所有致病性T> C变体的46％，而A> G编辑者可以精确地靶向6900个突变（占所有致病性G> A变体的34％）。因此，即使是现在，可用当前可用系统靶向的突变列表仍然非常庞大，足以选择并着手开发新的靶向疗法。

接下来的几篇论文重点介绍了特定肿瘤的基因组研究。Anna Kudryavtseva等。[15]（本期）讨论迷走神经节瘤的突变谱，迷走神经节瘤是一组罕见的头颈部神经内分泌肿瘤，起源于迷走神经，与早期由同一组作者解剖的更常见的颈动脉副神经节瘤不同[16，17]。作者从8例患者中收集了迷走神经节旁瘤，分析了肿瘤的外显子组并详细讨论了他们的发现。特别地，描述了SDHx基因的许多新颖的和已知的致病性/可能致病性变体，其经常在副神经节瘤/嗜铬细胞瘤中突变。

Elena Pudova及其同事[18]（本期）分析了与局部晚期前列腺肿瘤的淋巴扩散相关的miRNA表达特征。在根治性前列腺切除术（扩大盆腔淋巴结切除术）后对PC治疗方案做出明智的决定远非易事，而是取决于根据肿瘤分期，格里森指数，PSA水平和区域转移将患者分为危险组。这些临床指标显然需要增加一些分子生物标志物。与前列腺癌的淋巴扩散相关的miRNA表达谱的变化产生了一些适合发展为预后工具的miRNA。最突出的候选对象是miR-20a-5p，miR-106a-5p，miR-93-5p，

Tatyana Vasilyeva等。[20]（本期）提供了一个由11号染色体上的中心点倒置引起的先天性无虹膜的案例研究。无虹膜是一种孟德尔常染色体显性发育异常，可以影响所有眼睛结构以及中枢神经系统，内分泌系统和其他系统和器官。在描述的情况下，近兆碱基的缺失删除了具有ELP4，PAX6和RCN1基因的基因座，而WT1基因的编码序列不受影响。作者得出的结论是，在被调查者中患上威尔姆斯肿瘤的风险与普通人群相似。

我们通过Vladislav Pavlov等人编写的多个副神经节瘤病例报告来结束本期特殊期刊。[21]（本期）。作者报告了一例多发神经节旁瘤，表现为双侧颈和迷走神经节旁瘤。在对琥珀酸脱氢酶（SDH）亚基进行免疫染色并进行外显子组分析后，在种系中发现了SDHD基因中可能的病原体变异，在某些肿瘤中发现了其他可能的病原体变异。似乎作者怀疑地将SDHD基因中的种系变异体定位为多种副神经节瘤发展的驱动力。

总体而言，本期报告包括最近医学基因组学在癌症和数据库开发中的应用报告，以及病例报告，以及有关BMC Med基因组学特别会议后期刊的连续系列文章[10，17，22，23]。我们希望通过学校和青年科学家竞赛继续国际交流和教育。我们邀请世界各地的读者参加在俄罗斯举行的系统生物学会议。数字医学论坛（Digital Medicine Forum）和MGNGS-2020（医学遗传学-下一代测序）活动推迟到2021年（http://ngs.med-gen.ru/mgngs20/）。

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下载参考

我们感谢NA Kolchanov院士组织的“系统生物学和生物信息学” -2019活动，并为国际生物信息学和基因组学研究提供了平台。我们感谢TV Tatarinova教授在SBB-2019问题上的编辑工作以及2019年在莫斯科举办的“人类种群遗传学百年”会议的组织工作，该会议为BioMed Central期刊的SBB-2019特刊系列提供了材料。感谢RAZinchenko教授和MYSkoblov博士组织的MGNGS-2019会议。

RFBR支持了在新西伯利亚举行的SBB-19学校（赠款19-04-20036）。YO（医学遗传学研究）得到RSF（19-15-00219赠款）的支持。

特刊的特邀编辑感谢会议委员会成员和审稿人，他们协助了同行审阅和特刊准备。我们感谢Mikhail Ponomarenko（俄罗斯新西伯利亚SB RAS细胞与遗传研究所），Hildegard Nikki Hall（英国爱丁堡大学），Olga Arkova（莫斯科RAS基因生物学研究所），Piramanayagam Shanmughavel（印度巴拉蒂亚大学），赵海清（美国哥伦比亚大学医学中心），维塔利·古尔斯基（Vitaly Gursky）（俄罗斯圣彼得堡理工大学），奥尔加·佐洛塔雷娃（Olga Zolotareva）（德国比勒费尔德大学），埃尔维拉·加里耶娃（Elvira Galieva）（俄罗斯新西伯利亚国立大学），阿列克谢·科洛金（Alexey Kolodkin）（卢森堡大学），亚历山大·拉图西（Alexander Ratushny）（美国布里斯托尔·迈尔斯·斯奎布（Bristol Myers Squibb）），埃里克·穆尔尼斯（Eric Mjolsness）（美国尔湾大学），保罗·琼斯（Paul Jones）（美国AIC Inc.），李立安（美国罗德岛大学）

关于此补品

本文已作为BMC医学基因组学第13卷增刊2020：《系统生物学和生物信息学》-2019：医学基因组学中的精选主题的一部分发表。该补充剂的全部内容可在https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-13-supplement-8在线获得。

这篇文章的发表不包括在赞助范围内。

隶属关系

  1. IMSechenov第一莫斯科国立医科大学（Sechenov大学）数字健康研究所，119991，俄罗斯莫斯科

    尤里·L·奥尔洛夫（Yuriy L.Orlov）

  2. 新西伯利亚国立大学，630090，俄罗斯新西伯利亚

    尤里·L·奥尔洛夫（Yuriy L.Orlov）

  3. 内科学与预防医学研究所-俄罗斯新西伯利亚细胞遗传学研究所SB RAS 630089

    Yuriy L.Orlov和Elena N.Voropaeva

  4. 浙江大学医学院附属第一医院生命科学学院生物信息学教研室，杭州310058

    陈铭

  5. 乔治梅森大学，弗吉尼亚州费尔法克斯，22030，美国

    安查·巴拉诺娃（Ancha V.Baranova）

  6. 115522，俄罗斯莫斯科，医学遗传学研究中心

    安查·巴拉诺娃（Ancha V.Baranova）

s
  1. Yuriy L. Orlov查看作者出版物

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  2. Elena N. Voropaeva查看作者出版物

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  3. 陈铭查看作者出版物

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  4. Ancha V. Baranova查看作者出版物

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会费

AB和YO是特别会议后议题的客座编辑，也是SBB-2019学校的程序委员会成员。EV和MC是会议的受邀编辑和组委会成员。所有作者都阅读，修订和批准了最终手稿。

通讯作者

与Yuriy L. Orlov的对应。

利益争夺

作者宣称他们没有竞争利益。

发行人须知

对于出版的地图和机构隶属关系中的管辖权主张，Springer Nature保持中立。

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引用本文

Orlov，YL​​，Voropaeva，EN，Chen，M。等。系统生物学和生物信息学（SBB-2019）学校的医学基因组学。BMC基因组学医学 13， 127（2020）。https://doi.org/10.1186/s12920-020-00786-x

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  • DOI ：https ：//doi.org/10.1186/s12920-020-00786-x
更新日期：2020-09-20
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