OMIC-04. IDENTIFICATION AND CHARACTERIZATION OF CIRCULATING RNAS (CODING AND NONCODING) AND METABOLITES IN CEREBROSPINAL FLUID IN MEDULLOBLASTOMA PATIENTS

Abstract Medulloblastoma (MB) is the most common malignant brain tumor in children, and monitoring patients for treatment response and recurrence can be challenging with available current technologies in neuro-imaging and performing a biopsy to confirm response or recurrence carries risks, whereas cerebrospinal fluid (CSF) can be obtained with a little invasiveness. MB has altered cellular metabolism due to changes in gene expression, therefore, we hypothesized that any changes in MB cells lead to changes in cell-free transcripts and metabolites in CSF. To test this, we applied RNA-sequencing and mass spectrometry to analyze transcripts and metabolites including lipid in CSF from patients with different sub-groups of MB tumors (i.e., WNT, SHH, G3/4, G4, and unknown) and compared them to non-cancerous CSF. Tumor and sub-group specific transcriptomic and metabolic signatures were shown by unsupervised hierarchical clustering facilitating tumor type differentiation. By comparison with previously published tumor tissue RNA-seq data, we were able to identify a group of upregulated molecular signatures in both tumor tissue and CSF. We also identified a group of lipids that differentiate each MB sub-group from normal CSF, and Pathway analysis confirmed alterations in multiple metabolic pathways. Finally, we attempted to integrate RNA-seq data with lipidomics data, and results depict that the combinatorial analysis of CSF RNAs and metabolites can be useful in diagnosing and monitoring patients with MB tumors. (This research was conducted using samples made available by The Children’s Brain Tumor Network.)

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Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽

10.3390/horticulturae7060149 ◽

2021 ◽

Vol 7 (6) ◽

pp. 149

Author(s):

Chao Gong ◽

Qiangqiang Pang ◽

Zhiliang Li ◽

Zhenxing Li ◽

Riyuan Chen ◽

...

Keyword(s):

Heat Stress ◽

Gene Families ◽

High Temperature Stress ◽

Pcr Analysis ◽

Rna Seq ◽

Genome Wide ◽

Motif Composition ◽

Hsp Genes ◽

Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

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Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

BMC Genomics ◽

10.1186/s12864-018-5205-9 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Omika Thakur ◽

Gursharn Singh Randhawa

Keyword(s):

Molecular Markers ◽

Cyamopsis Tetragonoloba ◽

Rna Seq ◽

Identification And Characterization

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The identification and characterization of novel transcripts from RNA-seq data

Briefings in Bioinformatics ◽

10.1093/bib/bbv067 ◽

2015 ◽

Vol 17 (4) ◽

pp. 678-685 ◽

Cited By ~ 20

Author(s):

Tyler Weirick ◽

Giuseppe Militello ◽

Raphael Müller ◽

David John ◽

Stefanie Dimmeler ◽

...

Keyword(s):

Rna Seq ◽

Novel Transcripts ◽

Identification And Characterization

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Characterization of brain tumor tissue with 1310 nm optical coherence tomography

Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XXV ◽

10.1117/12.2578409 ◽

2021 ◽

Author(s):

Paul Strenge ◽

Birgit Lange ◽

Christin Grill ◽

Wolfgang Draxinger ◽

Veit Danicke ◽

...

Keyword(s):

Optical Coherence Tomography ◽

Brain Tumor ◽

Tumor Tissue ◽

Optical Coherence

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Cerebrospinal Fluid MicroRNA Signatures as Diagnostic Biomarkers in Brain Tumors

Cancers ◽

10.3390/cancers11101546 ◽

2019 ◽

Vol 11 (10) ◽

pp. 1546 ◽

Cited By ~ 8

Author(s):

Alena Kopkova ◽

Jiri Sana ◽

Tana Machackova ◽

Marek Vecera ◽

Lenka Radova ◽

...

Keyword(s):

Cerebrospinal Fluid ◽

Brain Tumor ◽

Brain Tumors ◽

Low Grade ◽

Tumor Type ◽

Tumor Patients ◽

Primary Tumors ◽

Mirna Profiling ◽

Tumor Types ◽

Cns Malignancies

Central nervous system (CNS) malignancies include primary tumors that originate within the CNS as well as secondary tumors that develop as a result of metastatic spread. Circulating microRNAs (miRNAs) were found in almost all human body fluids including cerebrospinal fluid (CSF), and they seem to be highly stable and resistant to even extreme conditions. The overall aim of our study was to identify specific CSF miRNA patterns that could differentiate among brain tumors. These new biomarkers could potentially aid borderline or uncertain imaging results onto diagnosis of CNS malignancies, avoiding most invasive procedures such as stereotactic biopsy or biopsy. In total, 175 brain tumor patients (glioblastomas, low-grade gliomas, meningiomas and brain metastases), and 40 non-tumor patients with hydrocephalus as controls were included in this prospective monocentric study. Firstly, we performed high-throughput miRNA profiling (Illumina small RNA sequencing) on a discovery cohort of 70 patients and 19 controls and identified specific miRNA signatures of all brain tumor types tested. Secondly, validation of 9 candidate miRNAs was carried out on an independent cohort of 105 brain tumor patients and 21 controls using qRT-PCR. Based on the successful results of validation and various combination patterns of only 5 miRNA levels (miR-30e, miR-140, let-7b, mR-10a and miR-21-3p) we proposed CSF-diagnostic scores for each tumor type which enabled to distinguish them from healthy donors and other tumor types tested. In addition to this primary diagnostic tool, we described the prognostic potential of the combination of miR-10b and miR-196b levels in CSF of glioblastoma patients. In conclusion, we performed the largest study so far focused on CSF miRNA profiling in patients with brain tumors, and we believe that this new class of biomarkers have a strong potential as a diagnostic and prognostic tool in these patients.

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Identification and characterization of immune complexes in the cerebrospinal fluid of patients with spinal cord schistosomiasis

Journal of Neuroimmunology ◽

10.1016/j.jneuroim.2010.08.016 ◽

2011 ◽

Vol 230 (1-2) ◽

pp. 188-190 ◽

Cited By ~ 15

Author(s):

Teresa C.A. Ferrari ◽

Luciana C. Faria ◽

Tatiane S. Vilaça ◽

Cristiane R. Correa ◽

Alfredo M. Góes

Keyword(s):

Spinal Cord ◽

Cerebrospinal Fluid ◽

Immune Complexes ◽

Identification And Characterization

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Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines

10.1101/482208 ◽

2018 ◽

Cited By ~ 1

Author(s):

Elsie C. Jacobson ◽

Ralph S. Grand ◽

Jo K. Perry ◽

Mark H. Vickers ◽

Ada L. Olins ◽

...

Keyword(s):

Cell Line ◽

Cell Lines ◽

Myeloid Leukemia ◽

Large Scale ◽

Rna Seq ◽

Structural Variants ◽

The Stability ◽

Different Sources ◽

Identification And Characterization

AbstractCancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used Hi-C and RNA-seq to identify and compare large SVs in HL-60 and HL-60/S4 cell lines. Comparisons with previously published karyotypes identified novel SVs in both cell lines. Hi-C was used to characterize the known expansion centered on the MYC locus. The MYC expansion was integrated into known locations in HL-60/S4, and a novel location (chr4) in HL-60. The HL-60 cell line has more within-line structural variation than the HL-60/S4 derivative cell line. Collectively we demonstrate the usefulness of Hi-C and with RNA-seq data for the identification and characterization of SVs.

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