The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases

Zhao, Zhongming; Dai, Yulin; Zhang, Chi; Mathé, Ewy A.; Wei, Lai; Wang, Kai

doi:10.1186/s12859-019-3240-4

Cited by 6 publications

(6 citation statements)

References 25 publications

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“…To enable detection of small changes in methylation, we trichotomized the β-value into three categories; un-methylated, semi-methylated, and full-methylated; transforming the β-value into 0, 1, 2, respectively 66 . Using these trichotomized data, we identified a larger number of DMPs, with the number of probes that consistently remained in the DMPs through reprogramming and differentiation ranging from ~ 560–3000 (568 and 564 hypomethylated DMPs maintained through differentiation at day + 4 in 21% and 2% oxygen, respectively; and 2927 and 2614 hypermethylated DMPs maintained through differentiation at day + 4 in 21% and 2% oxygen, respectively).…”

Section: Resultsmentioning

confidence: 99%

“…Cross reacting probes 92 and sex chromosomes were removed from the list of DMPs. Beta values were trichotomized (unmethylated, semi-methylated, and full-methylated) using a probability approach (Bayesian Gaussian Mixture model) using CpGtools (v. 1.0.2) 66 . Trichotomized probes were used for differential methylation analysis where stated.…”

Section: Methodsmentioning

confidence: 99%

“…Trichotomized probes were used for differential methylation analysis where stated. Beta values and the beta_profile_region.py script were used to create average methylation line plots using hg38.RefSeq.union.bed 66 . Functional significance of cis-regulatory regions was performed in GREAT using a 100 kb maximum extension 67 .…”

Section: Methodsmentioning

confidence: 99%

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Modeling preeclampsia using human induced pluripotent stem cells

Horii

Morey

Bui

et al. 2021

Sci Rep

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Preeclampsia (PE) is a pregnancy-specific hypertensive disorder, affecting up to 10% of pregnancies worldwide. The primary etiology is considered to be abnormal development and function of placental cells called trophoblasts. We previously developed a two-step protocol for differentiation of human pluripotent stem cells, first into cytotrophoblast (CTB) progenitor-like cells, and then into both syncytiotrophoblast (STB)- and extravillous trophoblast (EVT)-like cells, and showed that it can model both normal and abnormal trophoblast differentiation. We have now applied this protocol to induced pluripotent stem cells (iPSC) derived from placentas of pregnancies with or without PE. While there were no differences in CTB induction or EVT formation, PE-iPSC-derived trophoblast showed a defect in syncytialization, as well as a blunted response to hypoxia. RNAseq analysis showed defects in STB formation and response to hypoxia; however, DNA methylation changes were minimal, corresponding only to changes in response to hypoxia. Overall, PE-iPSC recapitulated multiple defects associated with placental dysfunction, including a lack of response to decreased oxygen tension. This emphasizes the importance of the maternal microenvironment in normal placentation, and highlights potential pathways that can be targeted for diagnosis or therapy, while absence of marked DNA methylation changes suggests that other regulatory mechanisms mediate these alterations.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Modeling preeclampsia using human induced pluripotent stem cells

Horii

Morey

Bui

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…enrichment pathway analysis and functional network analysis), which is a valuable way to capture meaningful outliers (i.e. the greatest variation between samples with and without submergence) and asymmetrical behavior in the whole genome expression dataset 60 . Our results demonstrated a high degree of skewness (Fig.…”

Section: Discussionmentioning

confidence: 99%

Integrative pathway and network analysis provide insights on flooding-tolerance genes in soybean

Jhan

Yang

Huang

et al. 2023

Sci Rep

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Soybean is highly sensitive to flooding and extreme rainfall. The phenotypic variation of flooding tolerance is a complex quantitative trait controlled by many genes and their interaction with environmental factors. We previously constructed a gene-pool relevant to soybean flooding-tolerant responses from integrated multiple omics and non-omics databases, and selected 144 prioritized flooding tolerance genes (FTgenes). In this study, we proposed a comprehensive framework at the systems level, using competitive (hypergeometric test) and self-contained (sum-statistic, sum-square-statistic) pathway-based approaches to identify biologically enriched pathways through evaluating the joint effects of the FTgenes within annotated pathways. These FTgenes were significantly enriched in 36 pathways in the Gene Ontology database. These pathways were related to plant hormones, defense-related, primary metabolic process, and system development pathways, which plays key roles in soybean flooding-induced responses. We further identified nine key FTgenes from important subnetworks extracted from several gene networks of enriched pathways. The nine key FTgenes were significantly expressed in soybean root under flooding stress in a qRT-PCR analysis. We demonstrated that this systems biology framework is promising to uncover important key genes underlying the molecular mechanisms of flooding-tolerant responses in soybean. This result supplied a good foundation for gene function analysis in further work.

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“…Basic analysis were performed using our in-house pipeline 53 . Raw fastq was aligned to human reference genome GRCh38 with hisat2 v2.1.0 54 .…”

Section: Methodsmentioning

confidence: 99%

Cytokine polarized, alternatively activated bone marrow neutrophils drive axon regeneration

Segal,

Jerome,

Sas

et al. 2023

Preprint

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The adult central nervous system (CNS) possesses a limited capacity for self-repair. Severed CNS axons typically fail to regrow. There is an unmet need for treatments designed to enhance neuronal viability, facilitate axon regeneration, and ultimately restore lost neurological functions to individuals affected by traumatic CNS injury, multiple sclerosis, stroke, and other neurological disorders. Here we demonstrate that both mouse and human bone marrow (BM) neutrophils, when polarized with a combination of recombinant interleukin (IL)-4 and granulocyte-colony stimulating factor (G-CSF), upregulate alternative activation markers and produce an array of growth factors, thereby gaining the capacity to promote neurite outgrowth. Moreover, adoptive transfer of IL-4/G-CSF polarized BM neutrophils into experimental models of CNS injury triggered substantial axon regeneration within the optic nerve and spinal cord. These findings have far-reaching implications for the future development of autologous myeloid cell-based therapies that may bring us closer to effective solutions for reversing CNS damage.

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The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases

Cited by 6 publications

References 25 publications

Modeling preeclampsia using human induced pluripotent stem cells

Modeling preeclampsia using human induced pluripotent stem cells

Integrative pathway and network analysis provide insights on flooding-tolerance genes in soybean

Cytokine polarized, alternatively activated bone marrow neutrophils drive axon regeneration

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