1
|
Unlu I, Maguire S, Guan S, Sun Z. Induro-RT mediated circRNA-sequencing (IMCR-seq) enables comprehensive profiling of full-length and long circular RNAs from low input total RNA. Nucleic Acids Res 2024:gkae465. [PMID: 38850158 DOI: 10.1093/nar/gkae465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/23/2024] [Accepted: 05/17/2024] [Indexed: 06/10/2024] Open
Abstract
Circular RNA (circRNA) has recently gained attention for its emerging biological activities, relevance to disease, potential as biomarkers, and promising an alternative modality for RNA vaccines. Nevertheless, sequencing circRNAs has presented challenges. In this context, we introduce a novel circRNA sequencing method called Induro-RT mediated circRNA-sequencing (IMCR-seq), which relies on a group II intron reverse transcriptase with robust rolling circle reverse transcription activity. The IMCR-seq protocol eliminates the need for conventional circRNA enrichment methods such as rRNA depletion and RNaseR digestion yet achieved the highest circRNA enrichment and detected 6-1000 times more circRNAs for the benchmarked human samples compared to other methods. IMCR-seq is applicable to any organism, capable of detecting circRNAs of longer than 7000 nucleotides, and is effective on samples as small as 10 ng of total RNA. These enhancements render IMCR-seq suitable for clinical samples, including disease tissues and liquid biopsies. We demonstrated the clinical relevance of IMCR-seq by detecting cancer-specific circRNAs as potential biomarkers from IMCR-seq results on lung tumor tissues together with blood plasma samples from both a healthy individual and a lung cancer patient. In summary, IMCR-seq presents an efficient and versatile circRNA sequencing method with high potential for research and clinical applications.
Collapse
Affiliation(s)
- Irem Unlu
- New England Biolabs Inc., Beverly, MA 01915, USA
| | - Sean Maguire
- New England Biolabs Inc., Beverly, MA 01915, USA
| | - Shengxi Guan
- New England Biolabs Inc., Beverly, MA 01915, USA
| | - Zhiyi Sun
- New England Biolabs Inc., Beverly, MA 01915, USA
| |
Collapse
|
2
|
Holt EA, Tyler A, Lakusta-Wong T, Lahue KG, Hankes KC, Teuscher C, Lynch RM, Ferris MT, Mahoney JM, Krementsov DN. Probing the basis of disease heterogeneity in multiple sclerosis using genetically diverse mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597205. [PMID: 38895248 PMCID: PMC11185616 DOI: 10.1101/2024.06.03.597205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Multiple sclerosis (MS) is a complex disease with significant heterogeneity in disease course and progression. Genetic studies have identified numerous loci associated with MS risk, but the genetic basis of disease progression remains elusive. To address this, we leveraged the Collaborative Cross (CC), a genetically diverse mouse strain panel, and experimental autoimmune encephalomyelitis (EAE). The thirty-two CC strains studied captured a wide spectrum of EAE severity, trajectory, and presentation, including severe-progressive, monophasic, relapsing remitting, and axial rotary (AR)-EAE, accompanied by distinct immunopathology. Sex differences in EAE severity were observed in six strains. Quantitative trait locus analysis revealed distinct genetic linkage patterns for different EAE phenotypes, including EAE severity and incidence of AR-EAE. Machine learning-based approaches prioritized candidate genes for loci underlying EAE severity ( Abcc4 and Gpc6 ) and AR-EAE ( Yap1 and Dync2h1 ). This work expands the EAE phenotypic repertoire and identifies novel loci controlling unique EAE phenotypes, supporting the hypothesis that heterogeneity in MS disease course is driven by genetic variation. Summary The genetic basis of disease heterogeneity in multiple sclerosis (MS) remains elusive. We leveraged the Collaborative Cross to expand the phenotypic repertoire of the experimental autoimmune encephalomyelitis (EAE) model of MS and identify loci controlling EAE severity, trajectory, and presentation.
Collapse
|
3
|
Shishkova D, Lobov A, Repkin E, Markova V, Markova Y, Sinitskaya A, Sinitsky M, Kondratiev E, Torgunakova E, Kutikhin A. Calciprotein Particles Induce Cellular Compartment-Specific Proteome Alterations in Human Arterial Endothelial Cells. J Cardiovasc Dev Dis 2023; 11:5. [PMID: 38248875 PMCID: PMC10816121 DOI: 10.3390/jcdd11010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024] Open
Abstract
Calciprotein particles (CPPs) are indispensable scavengers of excessive Ca2+ and PO43- ions in blood, being internalised and recycled by liver and spleen macrophages, monocytes, and endothelial cells (ECs). Here, we performed a pathway enrichment analysis of cellular compartment-specific proteomes in primary human coronary artery ECs (HCAEC) and human internal thoracic artery ECs (HITAEC) treated with primary (amorphous) or secondary (crystalline) CPPs (CPP-P and CPPs, respectively). Exposure to CPP-P and CPP-S induced notable upregulation of: (1) cytokine- and chemokine-mediated signaling, Ca2+-dependent events, and apoptosis in cytosolic and nuclear proteomes; (2) H+ and Ca2+ transmembrane transport, generation of reactive oxygen species, mitochondrial outer membrane permeabilisation, and intrinsic apoptosis in the mitochondrial proteome; (3) oxidative, calcium, and endoplasmic reticulum (ER) stress, unfolded protein binding, and apoptosis in the ER proteome. In contrast, transcription, post-transcriptional regulation, translation, cell cycle, and cell-cell adhesion pathways were underrepresented in cytosol and nuclear compartments, whilst biosynthesis of amino acids, mitochondrial translation, fatty acid oxidation, pyruvate dehydrogenase activity, and energy generation were downregulated in the mitochondrial proteome of CPP-treated ECs. Differentially expressed organelle-specific pathways were coherent in HCAEC and HITAEC and between ECs treated with CPP-P or CPP-S. Proteomic analysis of mitochondrial and nuclear lysates from CPP-treated ECs confirmed bioinformatic filtration findings.
Collapse
Affiliation(s)
- Daria Shishkova
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, 650002 Kemerovo, Russia; (D.S.); (V.M.); (Y.M.); (A.S.); (M.S.); (E.K.); (E.T.)
| | - Arseniy Lobov
- Laboratory of Regenerative Biomedicine, Institute of Cytology of the RAS, 4 Tikhoretskiy Prospekt, 194064 St. Petersburg, Russia;
| | - Egor Repkin
- Centre for Molecular and Cell Technologies, St. Petersburg State University, Universitetskaya Embankment, 7/9, 199034 St. Petersburg, Russia;
| | - Victoria Markova
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, 650002 Kemerovo, Russia; (D.S.); (V.M.); (Y.M.); (A.S.); (M.S.); (E.K.); (E.T.)
| | - Yulia Markova
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, 650002 Kemerovo, Russia; (D.S.); (V.M.); (Y.M.); (A.S.); (M.S.); (E.K.); (E.T.)
| | - Anna Sinitskaya
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, 650002 Kemerovo, Russia; (D.S.); (V.M.); (Y.M.); (A.S.); (M.S.); (E.K.); (E.T.)
| | - Maxim Sinitsky
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, 650002 Kemerovo, Russia; (D.S.); (V.M.); (Y.M.); (A.S.); (M.S.); (E.K.); (E.T.)
| | - Egor Kondratiev
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, 650002 Kemerovo, Russia; (D.S.); (V.M.); (Y.M.); (A.S.); (M.S.); (E.K.); (E.T.)
| | - Evgenia Torgunakova
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, 650002 Kemerovo, Russia; (D.S.); (V.M.); (Y.M.); (A.S.); (M.S.); (E.K.); (E.T.)
| | - Anton Kutikhin
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Boulevard, 650002 Kemerovo, Russia; (D.S.); (V.M.); (Y.M.); (A.S.); (M.S.); (E.K.); (E.T.)
| |
Collapse
|
4
|
Cheng JC, Meng Q, Zhang Q, Zhang L, Chen J, Song T, Fang L, Sun YP. WNK1 mediates amphiregulin-induced MMP9 expression and cell invasion in human extravillous trophoblast cells. Mol Cell Endocrinol 2023; 576:112038. [PMID: 37544354 DOI: 10.1016/j.mce.2023.112038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/21/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
The invasion of human extravillous trophoblast (EVT) cells is a critical event required for a successful pregnancy. Amphiregulin, a ligand of the epidermal growth factor receptor (EGFR), has been shown to stimulate cell invasion in an immortalized human EVT cell line, HTR-8/SVneo. The with-no-lysine kinase 1 (WNK1) is involved in regulating cell invasion. It is known that WNK1 is expressed in the human placenta, but its role in human EVT cells remains unknown. In the present study, we show that AREG treatment phosphorylated WNK1 at Thr60 in both HTR-8/SVneo and primary human EVT cells. The stimulatory effect of AREG on WNK1 phosphorylation was mediated by the activation of PI3K/AKT, but not the ERK1/2 signaling pathway. AREG upregulated matrix metalloproteinase 9 (MMP9) but not MMP2. In addition, cell invasiveness was increased in response to the treatment of AREG. Using the siRNA-mediated knockdown approach, our results showed that the knockdown of WNK1 attenuated the AREG-induced upregulation of MMP9 expression and cell invasion. Moreover, the expression of WNK1 was downregulated in the placentas with preeclampsia, a disease resulting from insufficiency of EVT cell invasion during pregnancy. This study discovers the physiological function of WNK1 in human EVT cells and provides important insights into the regulation of MMP9 and cell invasion in human EVT cells.
Collapse
Affiliation(s)
- Jung-Chien Cheng
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Qingxue Meng
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qian Zhang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lingling Zhang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaye Chen
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Tinglin Song
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lanlan Fang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ying-Pu Sun
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| |
Collapse
|