70 research outputs found
ΠΠΈΡΡΡΠ½Π°Ρ ΡΠ΅ΠΊΠ»Π°ΠΌΠ° ΠΊΠ°ΠΊ ΡΡΠ΅Π΄ΡΡΠ²ΠΎ ΠΏΡΠΈΠ²Π»Π΅ΡΠ΅Π½ΠΈΡ Π²Π½ΠΈΠΌΠ°Π½ΠΈΡ ΠΊ ΡΡΠ»ΡΠ³Π°ΠΌ ΠΎΡΠ³Π°Π½ΠΈΠ·Π°ΡΠΈΠΈ
ΠΠΠ ΠΏΠΎΡΠ²ΡΡΠ΅Π½Π° ΠΈΠ·ΡΡΠ΅Π½ΠΈΡ Π²ΠΈΡΡΡΠ½ΠΎΠΉ ΡΠ΅ΠΊΠ»Π°ΠΌΡ ΠΊΠ°ΠΊ ΡΡΠ΅Π΄ΡΡΠ²Π° ΠΏΡΠΈΠ²Π»Π΅ΡΠ΅Π½ΠΈΡ Π²Π½ΠΈΠΌΠ°Π½ΠΈΡ ΠΊ ΡΡΠ»ΡΠ³Π°ΠΌ ΠΎΡΠ³Π°Π½ΠΈΠ·Π°ΡΠΈΠΈ. ΠΠ²ΡΠΎΡΠΎΠΌ Π±ΡΠ» ΡΠ°Π·ΡΠ°Π±ΠΎΡΠ°Π½ ΠΊΠΎΠΌΠΏΠ»Π΅ΠΊΡ Π½Π΅ΠΎΠ±Ρ
ΠΎΠ΄ΠΈΠΌΡΡ
ΡΠ΅ΠΊΠ»Π°ΠΌΠ½ΡΡ
ΠΏΡΠΎΠ΄ΡΠΊΡΠΎΠ² ΠΈ ΠΌΠ΅ΡΠΎΠΏΡΠΈΡΡΠΈΠΉ Π΄Π»Ρ ΠΏΡΠΈΠ²Π»Π΅ΡΠ΅Π½ΠΈΡ Π²Π½ΠΈΠΌΠ°Π½ΠΈΡ ΠΊ ΡΡΠ»ΡΠ³Π°ΠΌ ΠΌΠ°Π³Π°Π·ΠΈΠ½Π° Π΄Π΅ΡΡΠΊΠΈΡ
ΡΠΎΠ²Π°ΡΠΎΠ² Π½ΠΎΠ²ΠΎΠ³ΠΎ ΡΠ΅Π³ΠΌΠ΅Π½ΡΠ° ΡΠ΅Π»Π΅Π²ΠΎΠΉ Π°ΡΠ΄ΠΈΡΠΎΡΠΈΠΈ
Examples of paired PASR (promoter-associated small RNA) and TASR (terminus-associated small RNA) peaks potentially mediating site-specific DNA methylation, and analysis of their biogenesis and action pathways.
<p>Examples of paired PASR (promoter-associated small RNA) and TASR (terminus-associated small RNA) peaks potentially mediating site-specific DNA methylation, and analysis of their biogenesis and action pathways.</p
Sequence characteristics of the PASRs (promoter-associated small RNAs) and the TASRs (terminus-associated small RNAs).
<p>(A) Sequence length distribution of the PASRs identified on the sense strands of the protein-coding genes of <i>Arabidopsis</i>. (B) Sequence length distribution of the PASRs identified on the antisense strands of the protein-coding genes of <i>Arabidopsis</i>. (C) Sequence length distribution of the TASRs identified on the sense strands of the protein-coding genes of <i>Arabidopsis</i>. (D) Sequence length distribution of the TASRs identified on the antisense strands of the protein-coding genes of <i>Arabidopsis</i>. (E) 5β terminal nucleotide compositions of the PASRs identified on the sense strands of the protein-coding genes of <i>Arabidopsis</i>. (F) 5β terminal nucleotide compositions of the PASRs identified on the antisense strands of the protein-coding genes of <i>Arabidopsis</i>. (G) 5β terminal nucleotide compositions of the TASRs identified on the sense strands of the protein-coding genes of <i>Arabidopsis</i>. (H) 5β terminal nucleotide compositions of the antisense strands of the protein-coding genes of <i>Arabidopsis</i>.</p
Examples of site-specific DNA methylation potentially mediated by PASRs (promoter-associated small RNAs) and TASRs (terminus-associated small RNAs) in <i>Arabidopsis</i>.
<p>(A) Site-specific DNA methylation signals were observed within the genomic region surrounding the TSS (transcription start site; marked by a vertical dashed line) of <i>AT1G53265</i>. Accordingly, abundant small RNAs (i.e. PASRs) were mapped onto this region. (B) Site-specific DNA methylation signals were detected within the genomic region surrounding the transcription terminus of <i>AT5G54700</i>. Accordingly, abundant small RNAs (i.e. TASRs) were mapped onto this region. <i>Arabidopsis</i> epigenome maps (neomorph.salk.edu/epigenome/epigenome.html) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0169212#pone.0169212.ref032" target="_blank">32</a>] were employed for this analysis.</p
Examples of the chloroplast genes generating PASRs (promoter-associated small RNAs) or TASRs (terminus-associated small RNAs) dominantly in green organ (leaves) of <i>Arabidopsis</i>.
<p>(A) The PASR peak was identified on the sense strand of <i>ATCG00540</i> (encoding photosynthetic electron transfer A). The <i>x</i> axis measures the genomic positions surrounding the TSS (transcription start site, marked by a black vertical bar) of this gene. The <i>y</i> axis measures the abundance of the small RNAs perfectly mapped onto the genomic region surrounding the TSS, which is also applied to the other figure panels. (B) The PASR peak was identified on both strands of <i>ATCG01120</i> (chloroplast ribosomal protein S15). The <i>x</i> axis measures the genomic positions surrounding the TSS of this gene. (C) The TASR peak was identified on the sense strand of <i>ATCG00270</i> (photosystem II reaction center protein D). The <i>x</i> axis measures the genomic positions surrounding the transcription terminus (marked by a black vertical bar) of this gene.</p
PASRs (promoter-associated small RNAs) identified on both strands of <i>AT5G48000</i>, and small RNA (sRNA) and double-stranded RNA (dsRNA) high-throughput sequencing (HTS)-based evidences showing potential Argonaute (AGO) loading preference and biogenesis pathways of PASRs.
<p>(A) Total: Initially, four sRNA HTS data sets belonging to GEO (Gene Expression Omnibus; <a href="http://www.ncbi.nlm.nih.gov/geo" target="_blank">www.ncbi.nlm.nih.gov/geo</a>) accession ID GSE28591 were utilized to identify PASR peak near the TSS (transcription start site, marked by a red vertical bar) of the gene. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0169212#pone.0169212.g001" target="_blank">Fig 1</a> for the analytical workflow. (B) AGO: Eight sRNA HTS data sets belonging to GSE28591 were divided into AGO1 data group (GSM707682, GSM707683, GSM707684 and GSM707685) and AGO4 data group (GSM707686, GSM707687, GSM707688 and GSM707689). To analyze the AGO loading preference of the PASRs, an accumulation level-based comparison was performed between the two AGO-associated sRNA HTS data groups. The higher accumulation levels of the PASRs were detected in the AGO4 data group, and were denoted by black lines. (C) RDR-, DCL-dependence: sRNA HTS data sets from different mutants (including <i>dcl</i> and <i>rdr</i> mutants) involved in sRNA biogenesis pathways were recruited for this analysis. Prominently repressed abundances of PASRs observed in specific mutants were denoted by black lines. (D) Pol IV-dependence: sRNA HTS data sets from two mutants (<i>nrpd1a</i> and <i>nrpd1b</i>, and both were denoted by black lines) of RNA polymerase (Pol) IV were used to analyze the dependence of PASR biogenesis on Pol IV. For all the figure panels, the dsRNA sequencing read-covered regions (the positions were provided on the top right) were highlighted in semitransparent red (for sense strand) and green (for antisense strand) background color. For the detailed explanation of the HTS data sets, please refer to βData sourcesβ within the βMaterials and Methodsβ section.</p
TASRs (terminus-associated small RNAs) identified on both strands of <i>AT3G41762</i>, and small RNA (sRNA) and double-stranded RNA (dsRNA) high-throughput sequencing (HTS)-based evidences showing potential Argonaute (AGO) loading preference and biogenesis pathways of TASRs.
<p>(A) Total: Initially, four sRNA HTS data sets belonging to GEO (Gene Expression Omnibus; <a href="http://www.ncbi.nlm.nih.gov/geo" target="_blank">www.ncbi.nlm.nih.gov/geo</a>) accession ID GSE28591 were utilized to identify TASR peak near the transcription terminus (marked by a red vertical bar) of the gene. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0169212#pone.0169212.g001" target="_blank">Fig 1</a> for the analytical workflow. (B) AGO: Eight sRNA HTS data sets belonging to GSE28591 were divided into AGO1 data group (GSM707682, GSM707683, GSM707684 and GSM707685) and AGO4 data group (GSM707686, GSM707687, GSM707688 and GSM707689). To analyze the AGO loading preference of the TASRs, an accumulation level-based comparison was performed between the two AGO-associated sRNA HTS data groups. The higher accumulation levels of the TASRs were detected in the AGO4 data group, and were denoted by black lines. (C) RDR-, DCL-dependence: sRNA HTS data sets from different mutants (including <i>dcl</i> and <i>rdr</i> mutants) involved in sRNA biogenesis pathways were recruited for this analysis. Prominently repressed abundances of TASRs observed in specific mutants were denoted by black lines. (D) Pol IV-dependence: sRNA HTS data sets from two mutants (<i>nrpd1a</i> and <i>nrpd1b</i>, and <i>nrpd1a</i> was denoted by black lines) of RNA polymerase (Pol) IV were used to analyze the dependence of TASR biogenesis on Pol IV. For all the figure panels, the dsRNA sequencing read-covered regions (the positions were provided on the top right) were highlighted in semitransparent red (for sense strand) and green (for antisense strand) background color. For the detailed explanation of the HTS data sets, please refer to βData sourcesβ within the βMaterials and Methodsβ section.</p
Inhibition of GRP78 abrogates radioresistance in oropharyngeal carcinoma cells after EGFR inhibition by cetuximab
<div><p>The EGFR-specific mAb cetuximab is one of the most effective treatments for oropharyngeal carcinoma, while patient responses to EGFR inhibitors given alone are modest. Combination treatment with radiation can improve the efficacy of treatment through increasing radiosensitivity, while resistance to radiation after administration of cetuximab limits its efficiency. Radiation and drugs can damage the endoplasmic reticulum (ER) homeostatic state and result in ER stress (ERS), subsequently causing resistance to radiation and drugs. Whether the ERS pathway is involved in radioresistance after administration of cetuximab has not been reported. Herein, we show that cetuximab could increase the radiosensitivity of FaDu cells but not Detroit562 cells. In addition, cetuximab inhibited the radiation-induced activation of the ERS signalling pathway IRE1Ξ±/ATF6-GRP78 in FaDu cells, while this effect was absent in Detroit562 cells. Silencing GRP78 increased the radiosensitivity of oropharyngeal carcinoma cells and inhibited radiation-induced DNA double-strand-break (DSB) repair and autophagy. More interestingly, silencing GRP78 abrogated resistance to cetuximab and radiation in Detroit562 cells and had a synergistic effect with cetuximab in increasing the radiosensitivity of FaDu cells. Immunohistochemistry showed that overexpression of both GRP78 and EGFR was associated with a poor prognosis in oropharyngeal carcinoma patients (P<0.05). Overall, the results of this study show that radioresistance after EGFR inhibition by cetuximab is mediated by the ERS signalling pathway IRE1Ξ±/ATF6-GRP78. This suppression was consequently unable to inhibit radiation-induced DSB repair and autophagy in oropharyngeal carcinoma cells, which conferred resistance to radiotherapy and cetuximab. These results suggest that the cooperative effects of radiotherapy and cetuximab could be further improved by inhibiting GRP78 in non-responsive oropharyngeal carcinoma patients.</p></div
Targeting GRP78 abrogates resistance to cetuximab and radiation.
<p>Oropharyngeal carcinoma cells transfected with siRNA to silence GRP78 or negative siRNA were treated with 50 ΞΌg/mL cetuximab for 12 h and then irradiated. (A) Colony formation experiments showed that cetuximab inhibited the colony formation of FaDu cells, which was further enhanced by silencing GRP78. In contrast, cetuximab alone did not affect the colony formation of Detroit562 cells, which was reversed by the silencing of GRP78. (B) Cetuximab weakened the radiation-mediated inhibition of FaDu cell proliferation, which was further enhanced by the silencing of GRP78. In addition, cetuximab had no significant effects on the radiation-mediated inhibition of Detroit562 cell proliferation, which was reversed by the silencing of GRP78. (C) Cetuximab increased the radiation-induced apoptosis of FaDu cells, which was further enhanced by the silencing of GRP78. The effect of cetuximab on the apoptosis of Detroit562 cells was not obvious, and this changed after GRP78 was silenced. Note: CTX = cetuximab, Neg = negative. *P < 0.05 Compared with Negative siRNA + IR; ΞP < 0.01 Compared with Negative siRNA + IR + CTX; Π€P = 0.05 Compared with Negative siRNA + IR + CTX.</p
GRP78 confers radioresistance by increasing radiation-induced DNA double-strand break repair and cell autophagy and the subsequent inhibition of apoptosis.
<p>(A) Silencing GRP78 inhibited the radiation-induced (5 Gy, 12 h) expression of the DNA double-strand break repair protein DNA-PK and increased the phosphorylation level of ATM. Silencing GRP78 also inhibited the radiation-induced expression of the autophagy-related proteins LC3B (LC3B-II/Ξ²-actin) and Atg16L1 and increased the expression of the apoptosis marker protein cleaved caspase-3 and cleaved PARP. (B) Immunofluorescence studies showed that after oropharyngeal carcinoma cells received 5 Gy radiation for 1 h, the Ξ³-H2AX foci in nucleus increased (the blue background indicates the cell nucleus, and light red dots indicate Ξ³-H2AX foci). In addition, the effect of radiation after GRP78 silencing was more evident than that of simple radiation. (C) Immunofluorescence studies by LC3B staining also showed autophagy regions in the nucleus after 5 Gy radiation for 1 h (the blue background indicates the cell nucleus, and light green dots indicate LC3B foci), which was reversed after GRP78 silencing. The oropharyngeal carcinoma cells were pretreated with 20 ΞΌmol/L Ly294002 or 5 mmol/L 3-MA for 12 h. The cells were then treated with 5 Gy of radiation. Compared with the IR group, *P < 0.05. For (A), bands were quantified using ImageJ software and were normalized to a loading control. Fold changes are shown compared with the negative control lane without radiation. N/A = not applicable.</p
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