Potential role of chimeric genes in pathway-related gene co-expression modules

Li, Piaopiao; Li, Yingxia; Ma, Lei

doi:10.1186/s12957-021-02248-9

Cited by 8 publications

(8 citation statements)

References 33 publications

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“…The collective evidence has demonstrated that targeting abnormal genes in specific signaling pathways is a significant and effective strategy to eliminate cancers [ 18 , 19 ]. In this study, we found that mutations of the EGFR gene in exons E18, E19, and E20 in lung cancer patients were common in adenosquamous carcinoma, while E21 mutations were common in adenocarcinoma.…”

Section: Discussionmentioning

confidence: 99%

Analysis of EGFR, KRAS, and PIK3CA gene mutation rates and clinical distribution in patients with different types of lung cancer

2021

World J Surg Onc

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Background To analyze and evaluate EGFR, KRAS, and PIK3CA gene mutation rates and clinical distribution in patients with different types of lung cancer Method A total of 221 lung cancer patients treated in our hospital between January 2016 and June 2019 were enrolled. Tissue and whole blood samples were collected and analyzed to determine the mutation status of EGFR, KRAS, and PIK3CA genes. The gene exon mutation rates were determined. Relevant clinical data, such as age, gender, tumor sample type, treatment method, pathologic type, and lung cancer stage were recorded and statistically analyzed. Results The EGFR gene mutation rates in exons E18-E21 were 2.3%, 17.6%, 3.6%, and 20.4%, respectively. E18, E19, and E20 mutations were commonly detected in adenosquamous carcinoma, and E21 mutations were commonly detected in adenocarcinoma. Mutations in exons E18-E21 were frequently detected in patients with lung cancer stages IA, IB, IIA, or IIB, respectively. The KRAS gene mutation rate in lung cancer patients in exon E2 was higher in whole blood and tissue samples than other exon mutations, while the KRAS gene mutation rate in exons E2 and E3 was significantly higher in patients with lung cancer stages IIB and IA, respectively. PIK3CA gene mutations in exons E9 and E20 occurred in patients < 60 years of age. Exon E9-positive mutations were more common in men or patients with squamous cell carcinoma, while exon E20-positive mutations were more common in females. Conclusion The EGFR, KRAS, and PIK3CA gene exon mutation rates differ and were shown to be correlated with different clinical indicators, which have significance in clinical treatment.

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Section: Discussionmentioning

confidence: 99%

Analysis of EGFR, KRAS, and PIK3CA gene mutation rates and clinical distribution in patients with different types of lung cancer

2021

World J Surg Onc

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“…But little research is conducted to analyze chimeric genes. Li and colleagues examined chimeric genes for their biological effects as well as related mechanisms by weighted co-expression network analysis ( Li, Li & Ma, 2021a ). Liu et al (2021) firstly reported that the chimeric RNAs related mechanism in modulating skeletal muscle development in pigs.…”

Section: Discussionmentioning

confidence: 99%

Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing

Wang

et al. 2022

PeerJ

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Background In intensive and large-scale farms, abnormal estradiol levels in sows can cause reproductive disorders. The high incidence rate of reproductive disturbance will induce the elimination of productive sows in large quantities, and the poor management will bring great losses to the pig farms. The change in estradiol level has an important effect on follicular development and estrus of sows. To solve this practical problem and improve the productive capacity of sows, it is significant to further clarify the regulatory mechanism of estradiol synthesis in porcine granulosa cells (GCs). The most important function of granulosa cells is to synthesize estradiol. Thus, the studies about the complex transcriptome in porcine GCs are significant. As for precursor-messenger RNAs (pre-mRNAs), their post-transcriptional modification, such as alternative polyadenylation (APA) and alternative splicing (AS), together with long non-coding RNAs (lncRNAs), may regulate the functions of granulosa cells. However, the above modification events and their function are unclear within pig granulosa cells. Methods Combined PacBio long-read isoform sequencing (Iso-Seq) was conducted in this work for generating porcine granulosa cells’ transcriptomic data. We discovered new transcripts and possible gene loci via comparison against reference genome. Later, combined Iso-Seq data were adopted to uncover those post-transcriptional modifications such as APA or AS, together with lncRNA within porcine granulosa cells. For confirming that the Iso-Seq data were reliable, we chose four AS genes and analyzed them through RT-PCR. Results The present article illustrated that pig GCs had a complex transcriptome, which gave rise to 8,793 APA, 3,465 AS events, 703 candidate new gene loci, as well as 92 lncRNAs. The results of this study revealed the complex transcriptome in pig GCs. It provided a basis for the interpretation of the molecular mechanism in GCs.

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“…TNM stage was shown [20]. Many items indicated that some genes or models including PD-1/PD-L1 had a certain correlation with prognosis in severe tumours [21][22][23][24][25]. For PD-1/PD-L1, Peng et al conducted a systematic search to show the PD-L1 might be a predictive biomarker for EGFR-mutant nonsmall cell lung cancer treated with EGFR-TKIs [26].…”

Section: Discussionmentioning

confidence: 99%

The immune checkpoint regulator PD-L1 expression are associated with clinical progression in prostate cancer

et al. 2021

World J Surg Onc

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Background The programmed death 1 (PD-1)/programmed death-ligand 1 (PD-L1) have shown positive efficacy in several solid cancers due to their targeted antitumour effects. However, the frequency and clinical implication value in prostate cancer still remain unclear. Methods The PD-1/PD-L1 expression was detected by immunohistochemical (IHC) analysis in 96 retrospectively collected cases of prostatic cancer and 44 controls of benign prostatic hyperplasia (BPH). Its correlation with clinicopathological features including age, PSA level, Gleason score, lymph node metastasis, clinical T stage and risk factor grade in prostate cancer was also assessed. Results The PD-L1-positive expression was significantly higher in cancer cases compared with benign tissues, whereas no difference in PD-1 positive expression was found. Moreover, the PD-L1 expression in tumour cells or lymphocytes was associated with Gleason score, but not related to age, preoperative PSA level, clinical T-stage, lymph node metastasis and grade of risk factors. In addition, no association between the positive expression of PD-1 and PD-L1 in tumour cells and lymphocytes was found. Conclusions The expression of PD-L1 not PD-1 is highly prevalent in prostate cancer. PD-L1 is closely related to Gleason score and may be a co-factor associated with the progression of prostate cancer.

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Potential role of chimeric genes in pathway-related gene co-expression modules

Cited by 8 publications

References 33 publications

Analysis of EGFR, KRAS, and PIK3CA gene mutation rates and clinical distribution in patients with different types of lung cancer

Analysis of EGFR, KRAS, and PIK3CA gene mutation rates and clinical distribution in patients with different types of lung cancer

Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing

The immune checkpoint regulator PD-L1 expression are associated with clinical progression in prostate cancer

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