Systematic prediction of autophagy‐related proteins using <i>Arabidopsis thaliana</i> interactome data

Cheng, Lixin; Zeng, Yonglun; Zhou, Tianjun; Zhang, Ning; Cheung, Katherine; Li, Baiying; Leung, Kwong‐Sak; Jiang, Liwen

doi:10.1111/tpj.15065

Cited by 10 publications

(8 citation statements)

References 53 publications

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“…Following topological network analysis [17,[35][36][37][38], we found that mRNAs have a significantly higher network degree and betweenness, while a lower transitivity than non-coding RNAs (Figure 1G),…”

Section: Identification Of Mrnas That Participate As Cernas In Socmentioning

confidence: 92%

Whole Transcriptome Analyses Identify Pairwise Gene Circuit Motif in Serous Ovarian Cancer

Cheng

Zheng

Ling

et al. 2021

Preprint

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Background: Ovarian cancer is the most lethal gynaecological malignancy, resulting in approximately 14,000 deaths annually in the United States. Transcriptome data are emerging as an effective tool possibly leading to clinical applications for various cancers.Methods: We collected eight serous ovarian carcinomas (SOCs) and eight normal ovary samples, and generated a whole transcriptome profile of human ovarian cancer using microarrays, including mRNAs, lncRNAs, and circRNAs. We constructed a competing endogenous RNA (ceRNA) network involving these three types of RNAs and identified immune-related circRNAs from the network. Moreover, we proposed a gene-pair filtering method to identify significant expression reversals from integrated multi-cohorts, which mitigates the technical variation and improves the statistical power.Results: Three pairs of mRNAs (BIRC5:PRKCQ, PTK2B:OGN, and S100A14:NR2F1) were identified as promising biomarkers and were fused as an indicator (SOC index) for diagnostic prediction. Validation in three independent cohorts demonstrated that the SOC index carries a very high predictive capacity (average ROC, 0.99; sensitivity, 0.98; specificity, 1.00). Additionally, the SOC index exhibited its prognostic potential to discriminate SOC patients between early and late stage disease.Conclusions: Our findings elucidate the repertoire of RNA expressions in SOC and identified three gene pairs for the primary screening of SOC. Further biological experiments of the three gene pairs are warranted in order to investigate the underlying function mechanisms involved in ovarian cancer development.

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Section: Identification Of Mrnas That Participate As Cernas In Socmentioning

confidence: 92%

Whole Transcriptome Analyses Identify Pairwise Gene Circuit Motif in Serous Ovarian Cancer

Cheng

Zheng

Ling

et al. 2021

Preprint

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“…As shown in Figure 7, autophagy is induced by autophagy-related proteins (ATGs) [298,299]. Information on the functions of individual ATGs were summarized in a review by Su et al (2020) [284].…”

Section: Control Of Autophagy By Aba and Ethylene Signalingmentioning

confidence: 99%

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Koyro

Huchzermeyer

2022

Plants

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Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

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“…According to estimates from the American Cancer Society, 1 in 78 women will suffer from ovarian cancer. Furthermore, around 21,750 will be newly diagnosed and 13,940 will die from ovarian cancer in 2020 [2]. Epithelial ovarian carcinomas account for 90% of ovarian cancer cases and serous ovarian carcinoma (SOC) is thus far the most common subtype in epithelial ovarian carcinomas [3, 4].…”

Section: Introductionmentioning

confidence: 99%

Circular RNA’s competing endogenous gene pair as motif in serous ovarian cancer

Cheng

Zheng

Leung

et al. 2022

Preprint

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Understanding the regulatory mechanisms in serous ovarian carcinoma (SOC) is critical for its diagnosis and targeted therapy. However, some critical motifs in the competing endogenous RNA (ceRNA) network in SOC were still undiscovered. We profiled a whole transcriptome of eight human SOCs and eight controls and constructed a ceRNA network including mRNAs, lncRNAs, and circRNAs. We hypothesized the noncoding RNA's competing endogenous gene pairs (ceGPs) relationship for the mRNA-ncRNA-mRNA motifs in the ceRNA network. Then, we proposed the denoised individualized pair analysis of gene expression (deiPAGE) to identify mRNA-ncRNA-mRNA motifs from integrated multi-cohorts. 18 cricRNA's ceGPs (cceGPs) were identified and fused as an indicator (SOC index) for SOC discrimination, which carried a high predictive capacity in independent cohorts. The index was negatively correlated with the CD8+/CD4+ ratio in tumour-infiltration, reflecting the migration and growth of tumour cells in ovarian cancer progression.

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Systematic prediction of autophagy‐related proteins using Arabidopsis thaliana interactome data

Cited by 10 publications

References 53 publications

Whole Transcriptome Analyses Identify Pairwise Gene Circuit Motif in Serous Ovarian Cancer

Whole Transcriptome Analyses Identify Pairwise Gene Circuit Motif in Serous Ovarian Cancer

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Circular RNA’s competing endogenous gene pair as motif in serous ovarian cancer

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