Identification of Novel Disease Mechanisms and Biomarkers Using High-Throughput Sequencing Techniques

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Medical Research".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 3888

Special Issue Editors

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: high-throughput sequencing technique development and omics data mining for precision medicine; sequencing data analysis tool and database development; identification of novel disease biomarkers
Special Issues, Collections and Topics in MDPI journals
School of Life Sciences, Chongqing University, Chongqing 405200, China
Interests: mechanisms of tumor development; tumor diagnosis and prognosis; tumor-immunotherapy-related biomarker research
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
School of Life Sciences, East China Normal University, Shanghai 200241, China
Interests: multi-omic data integration; tumor-immunotherapy-related biomarker identification; microbiome analysis

E-Mail Website
Guest Editor
Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
Interests: next-generation sequencing data analysis; leukemia minor antigen discovery; biological network modeling

Special Issue Information

Dear Colleagues,

With the rapid development of sequencing techniques, high-throughput sequencing (HTS) is now revolutionizing different aspects of life science and clinical study. The millions of sequencing reads produced by HTS could determine various mutations at the genomic level, accurately quantify gene expression at the transcriptomic level, and identify histone or DNA modification at the epigenomic level. The accumulation of huge multi-omics data has led to the identification of novel disease biomarkers and mechanisms. With HTS, various disease (e.g., cancer, diabetes, and arthritis) markers have been developed at different omics levels, which have been used for disease diagnosis, disease prevention, and the prediction of treatment effects. The quickly acquired multi-omics data, together with newly developed algorithms, provide an excellent chance to reveal novel disease markers and the underlying mechanisms. The aim of this research topic includes:

(1) Developing new disease markers at various omics levels using high-throughput sequencing; and

(2) Using omics data to reveal new mechanisms for disease occurrence or development.

This topic covers a broad spectrum of interests, and studies based on wet lab or dry lab results are all welcomed. In addition, studies successfully uncovering marker-related disease mechanisms are highly preferred.

Dr. Hua Li
Dr. Lei Shi
Dr. Jun Wu
Dr. Shoudan Liang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biomarker identification
  • Disease mechanism investigation
  • Sequencing data analysis
  • Sequencing techniques
  • Multi-omics study

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

18 pages, 3550 KiB  
Article
Upregulation of Spinal miR-155-5p Contributes to Mechanical Hyperalgesia by Promoting Inflammatory Activation of Microglia in Bone Cancer Pain Rats
by Yanping Jian, Zongbin Song, Zhuofeng Ding, Jian Wang, Ruike Wang and Xinran Hou
Life 2022, 12(9), 1349; https://doi.org/10.3390/life12091349 - 30 Aug 2022
Cited by 3 | Viewed by 1625
Abstract
Bone cancer pain (BCP) seriously deteriorates the life quality of patients, but its underlying mechanism is still unclear. Spinal microRNAs might contribute to the development of BCP and the role of microglial activation is controversial. In this study, we established a BCP model [...] Read more.
Bone cancer pain (BCP) seriously deteriorates the life quality of patients, but its underlying mechanism is still unclear. Spinal microRNAs might contribute to the development of BCP and the role of microglial activation is controversial. In this study, we established a BCP model by injecting Walker 256 breast carcinoma cells into the tibial intramedullary cavity of rats and significant hyperalgesia was observed in the BCP rats. The lumbar spinal cords were harvested to perform RNA sequencing (RNA-seq), and 31 differentially expressed miRNAs (26 upregulated and 5 downregulated) were identified in the BCP rats. Among them, miR-155-5p was significantly upregulated in the BCP rats. Spinal microglial activation was observed during BCP development. miR-155-5p could be expressed in spinal microglia and was significantly upregulated in microglia treated with lipopolysaccharide (LPS) in vitro. Serum/glucocorticoid regulated kinase family member 3 (Sgk3) was predicted to be the possible downstream target of miR-155-5p and this was confirmed using a dual-luciferase reporter assay in vitro. The inhibition of miR-155-5p restored Sgk3-expression-attenuated microglial activation and alleviated hyperalgesia in the BCP rats. In conclusion, spinal miR-155-5p/Sgk3/microglial activation might play an important role in BCP pathogenesis. Full article
Show Figures

Graphical abstract

10 pages, 278 KiB  
Article
High-Throughput Sequencing Haplotype Analysis Indicates in LRRK2 Gene a Potential Risk Factor for Endemic Parkinsonism in Southeastern Moravia, Czech Republic
by Kristyna Kolarikova, Radek Vodicka, Radek Vrtel, Julia Stellmachova, Martin Prochazka, Katerina Mensikova, Tereza Bartonikova, Tomas Furst, Petr Kanovsky and Jan Geryk
Life 2022, 12(1), 121; https://doi.org/10.3390/life12010121 - 14 Jan 2022
Cited by 1 | Viewed by 1742
Abstract
Parkinson’s disease and parkinsonism are relatively common neurodegenerative disorders. This study aimed to assess potential genetic risk factors of haplotypes in genes associated with parkinsonism in a population in which endemic parkinsonism and atypical parkinsonism have recently been found. The genes ADH1C, EIF4G1, [...] Read more.
Parkinson’s disease and parkinsonism are relatively common neurodegenerative disorders. This study aimed to assess potential genetic risk factors of haplotypes in genes associated with parkinsonism in a population in which endemic parkinsonism and atypical parkinsonism have recently been found. The genes ADH1C, EIF4G1, FBXO7, GBA, GIGYF2, HTRA2, LRRK2, MAPT, PARK2, PARK7, PINK1 PLA2G6, SNCA, UCHL1, and VPS35 were analyzed in 62 patients (P) and 69 age-matched controls from the researched area (C1). Variants were acquired by high-throughput sequencing using Ion Torrent workflow. As another set of controls, the whole genome sequencing data from 100 healthy non-related individuals from the Czech population were used (C2); the results were also compared with the Genome Project data (C3). We observed shared findings of four intron (rs11564187, rs36220738, rs200829235, and rs3789329) and one exon variant (rs33995883) in the LRRK2 gene in six patients. A comparison of the C1–C3 groups revealed significant differences in haplotype frequencies between ratio of 2.09 for C1, 1.65 for C2, and 6.3 for C3, and odds ratios of 13.15 for C1, 2.58 for C2, and 7.6 for C3 were estimated. The co-occurrence of five variants in the LRRK2 gene (very probably in haplotype) could be an important potential risk factor for the development of parkinsonism, even outside the recently described pedigrees in the researched area where endemic parkinsonism is present. Full article
Back to TopTop