Systematic Analysis of tRNA-Derived Small RNAs Reveals Novel Potential Therapeutic Targets of Traditional Chinese Medicine (Buyang-Huanwu-Decoction) on Intracerebral Hemorrhage

Although Buyang-Huanwu-Decoction (BYHWD), a famous traditional Chinese medicine, has been utilized to promote the recovery of neurological function in intracerebral hemorrhage (ICH) for centuries, its therapeutic mechanisms remain unclear. tRNA-derived small RNA (tsRNA) is a novel class of short non-coding RNA, possessing potential regulating functions. In the current study, we explored the novel therapeutic targets of BYHWD by tsRNA-sequencing. Rats were randomly divided into three groups: sham, ICH, and BYHWD-treated groups. The modified neurological severity score, corner turn test, foot-fault test, and weight change were used to assess neurological injury. After BYHWD treatment, these behavioral tests were obviously meliorated compared with ICH group in the recovery phase. In the rat brain tissues surrounding the hemorrhagic region, a total of 350 tsRNAs for exact match were identified. 12 of tRNAs (fold change >1.3 and P-value <0.05) were significantly changed in ICH group compared to sham group. Among them, 3 of tRNAs (rno-tRFi-Ser-25a, rno-tRF5-Ala-16a and rno-tRF5-Glu-29a) were markedly regulated by BYHWD treatment and validated with quantitative real-time PCR. Additionally, target prediction and bioinformatics analyses revealed that these tsRNAs could play therapeutic roles through FoxO signaling pathway, positive regulation of long term synaptic depression, autophagy - animal, IL-17 signaling pathway and regulation of cytoskeleton and transforming growth factor beta. In conclusion, tsRNAs are the potential therapeutic targets of BYHWD on ICH treatment. The present study provides novel insights for future investigations to explore the mechanisms, by which BYHWD promotes neurological function recovery after ICH.

[1]  Jian Wang,et al.  Translational Intracerebral Hemorrhage: a Need for Transparent Descriptions of Fresh Tissue Sampling and Preclinical Model Quality , 2015, Translational Stroke Research.

[2]  Yanghao Hou,et al.  Foxo1-mediated inflammatory response after cerebral hemorrhage in rats , 2016, Neuroscience Letters.

[3]  Anindya Dutta,et al.  Global gene repression by Dicer-independent tRNA Fragments , 2017, bioRxiv.

[4]  Yi Zhang,et al.  Simultaneous detection and separation of hyperacute intracerebral hemorrhage and cerebral ischemia using amide proton transfer MRI , 2015, Magnetic resonance in medicine.

[5]  Yu-Chiang Hung,et al.  Chinese Herbal Products for Ischemic Stroke. , 2015, The American journal of Chinese medicine.

[6]  J. Beermann,et al.  Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches. , 2016, Physiological reviews.

[7]  D. Haussecker,et al.  Human tRNA-derived small RNAs in the global regulation of RNA silencing. , 2010, RNA.

[8]  R. Koehler,et al.  Inhibition of tPA-induced hemorrhagic transformation involves adenosine A2b receptor activation after cerebral ischemia , 2017, Neurobiology of Disease.

[9]  Jae Yong Ryu,et al.  A systems approach to traditional oriental medicine , 2015, Nature Biotechnology.

[10]  Qi-dong Yang,et al.  Effect of qi-tonifying and stasis-eliminating therapy (益气活血法) on expression of vascular endothelial growth factor and its receptors Flt-1, Flk-1 in the brain of intracerebral hemorrhagic rats , 2007, Chinese journal of integrative medicine.

[11]  C. Anderson,et al.  Guidelines for the Management of Spontaneous Intracerebral Hemorrhage: A Guideline for Healthcare Professionals From the American Heart Association/American Stroke Association , 2015, Stroke.

[12]  S. Kim,et al.  Neuronal functions of FOXO/DAF-16 , 2016, Nutrition and healthy aging.

[13]  Xiaoning Han,et al.  Modulators of microglial activation and polarization after intracerebral haemorrhage , 2017, Nature Reviews Neurology.

[14]  Yunhui Liu,et al.  Blood–brain barrier permeability change and regulation mechanism after subarachnoid hemorrhage , 2014, Metabolic Brain Disease.

[15]  Suowen Xu.  Transcriptome Profiling in Systems Vascular Medicine , 2017, Front. Pharmacol..

[16]  W. Ziai,et al.  Changes in the cellular immune system and circulating inflammatory markers of stroke patients , 2016, Oncotarget.

[17]  GuoQiuyan,et al.  A Systems Biology Perspective on the Molecular Mechanisms Underlying the Therapeutic Effects of Buyang Huanwu Decoction on Ischemic Stroke , 2015 .

[18]  Anindya Dutta,et al.  tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner , 2018, RNA.

[19]  D. Hanley,et al.  Ultrastructural Characteristics of Neuronal Death and White Matter Injury in Mouse Brain Tissues After Intracerebral Hemorrhage: Coexistence of Ferroptosis, Autophagy, and Necrosis , 2018, Front. Neurol..

[20]  Jian Wang,et al.  Preclinical and clinical research on inflammation after intracerebral hemorrhage , 2010, Progress in Neurobiology.

[21]  Andrey Grigoriev,et al.  Dynamics of tRNA fragments and their targets in aging mammalian brain , 2016, F1000Research.

[22]  Runyue Huang,et al.  Buyang Huanwu decoction facilitates neurorehabilitation through an improvement of synaptic plasticity in cerebral ischemic rats , 2017, BMC Complementary and Alternative Medicine.

[23]  Chenxia Sheng,et al.  Xuefu Zhuyu decoction, a traditional Chinese medicine, provides neuroprotection in a rat model of traumatic brain injury via an anti-inflammatory pathway , 2016, Scientific Reports.

[24]  Hai-bin Qu,et al.  Transcriptome Profiling Analysis Reveals the Potential Mechanisms of Three Bioactive Ingredients of Fufang E’jiao Jiang During Chemotherapy-Induced Myelosuppression in Mice , 2018, Front. Pharmacol..

[25]  Joseph P. Broderick,et al.  Advances in the management of intracerebral hemorrhage , 2010, Nature Reviews Neurology.

[26]  Canan Kuscu,et al.  Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). , 2016, Trends in biochemical sciences.

[27]  E. Ross,et al.  Philosophy of Science Association , 2022 .

[28]  M. Kay,et al.  A tRNA-derived small RNA regulates ribosome biogenesis , 2017, Nature.

[29]  J. Hao,et al.  Interleukin‐23 Secreted by Activated Macrophages Drives γδT Cell Production of Interleukin‐17 to Aggravate Secondary Injury After Intracerebral Hemorrhage , 2016, Journal of the American Heart Association.

[30]  B. Strooper,et al.  Noncoding RNAs in neurodegeneration , 2017, Nature Reviews Neuroscience.

[31]  Yang Wang,et al.  An Intersectional Study of LncRNAs and mRNAs Reveals the Potential Therapeutic Targets of Buyang Huanwu Decoction in Experimental Intracerebral Hemorrhage , 2018, Cellular Physiology and Biochemistry.

[32]  D. Hanley,et al.  Thrombolytic removal of intraventricular haemorrhage in treatment of severe stroke: results of the randomised, multicentre, multiregion, placebo-controlled CLEAR III trial , 2017, The Lancet.

[33]  Pankaj Kumar,et al.  tRFdb: a database for transfer RNA fragments , 2014, Nucleic Acids Res..

[34]  Andrey Grigoriev,et al.  Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets , 2015, Biology Direct.

[35]  Jian Lu,et al.  Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response , 2018, Nucleic acids research.

[36]  Lian Pengfei,et al.  Altered Long Noncoding RNA and Messenger RNA Expression in Experimental Intracerebral Hemorrhage - a Preliminary Study , 2018, Cellular Physiology and Biochemistry.

[37]  Andrea Califano,et al.  tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma , 2013, Proceedings of the National Academy of Sciences.

[38]  Lin Luo,et al.  Buyang Huanwu Decoction Ameliorates Poststroke Depression via Promoting Neurotrophic Pathway Mediated Neuroprotection and Neurogenesis , 2017, Evidence-based complementary and alternative medicine : eCAM.

[39]  Andrew D. Johnson,et al.  Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes , 2018, Nature Genetics.

[40]  R. Ransohoff,et al.  Neutrophil depletion after subarachnoid hemorrhage improves memory via NMDA receptors , 2016, Brain, Behavior, and Immunity.

[41]  Rustam Al-Shahi Salman,et al.  Platelet transfusion versus standard care after acute stroke due to spontaneous cerebral haemorrhage associated with antiplatelet therapy (PATCH): a randomised, open-label, phase 3 trial , 2016, The Lancet.

[42]  Translating the power of TCM into patients’ hope , 2014, Frontiers of Medicine.

[43]  Yang Wang,et al.  Rhubarb attenuates blood-brain barrier disruption via increased zonula occludens-1 expression in a rat model of intracerebral hemorrhage , 2016, Experimental and therapeutic medicine.

[44]  N. Polacek,et al.  tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA in Haloferax volcanii , 2012, Archaea.

[45]  F. Gao,et al.  Buyang Huanwu Decoction (BYHWD) Enhances Angiogenic Effect of Mesenchymal Stem Cell by Upregulating VEGF Expression After Focal Cerebral Ischemia , 2015, Journal of Molecular Neuroscience.

[46]  Lisa Fish,et al.  Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement , 2015, Cell.

[47]  Jiekun Luo,et al.  Buyang huanwu decoction promotes angiogenesis via vascular endothelial growth factor receptor-2 activation through the PI3K/Akt pathway in a mouse model of intracerebral hemorrhage , 2015, BMC Complementary and Alternative Medicine.

[48]  Gwendolyn M. Jang,et al.  Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. , 2015, Cell host & microbe.

[49]  Jian Wang,et al.  Danshen-Chuanxiong-Honghua Ameliorates Cerebral Impairment and Improves Spatial Cognitive Deficits after Transient Focal Ischemia and Identification of Active Compounds , 2017, Front. Pharmacol..

[50]  B. Luo,et al.  A Systematic Review and Meta-Analysis of Buyang Huanwu Decoction in Animal Model of Focal Cerebral Ischemia , 2013, Evidence-based complementary and alternative medicine : eCAM.

[51]  K. Yin,et al.  Noncoding RNAs and Stroke , 2019, The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry.

[52]  E. Chan,et al.  Disposition pathways and pharmacokinetics of herbal medicines in humans. , 2012, Current medicinal chemistry.

[53]  Phillipe Loher,et al.  MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data , 2017, Scientific Reports.

[54]  A. Cayota,et al.  Hints of tRNA-Derived Small RNAs Role in RNA Silencing Mechanisms , 2012, Genes.

[55]  J. Lupski,et al.  Human CLP1 Mutations Alter tRNA Biogenesis, Affecting Both Peripheral and Central Nervous System Function , 2014, Cell.

[56]  Xin Niu,et al.  tRNA-Derived Small Non-Coding RNAs in Response to Ischemia Inhibit Angiogenesis , 2016, Scientific Reports.

[57]  Jordan Anaya,et al.  Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets , 2014, BMC Biology.

[58]  Shuai Zhang,et al.  Analyses of mRNA Profiling through RNA Sequencing on a SAMP8 Mouse Model in Response to Ginsenoside Rg1 and Rb1 Treatment , 2017, Front. Pharmacol..

[59]  Xudong Zhang,et al.  Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder , 2016, Science.

[60]  Hui Zhou,et al.  Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia , 2008, Nucleic acids research.