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Additional file 3 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 3: Figure S2. The correlation between LARRPM expression, 5hmC level at LINC00240 promoter, CpG43 methylation level and LINC00240 expression in LUAD tissues. A Correlation between LINC00240 and LARRPM expression analysed using the TCGA LUAD data. r = 0.6164, P < 0.0001 by Spearman correlation analysis. B Correlation between LINC00240 and LARRPM expression analyzed in our LUAD cohort. r = 0.5521, P < 0.0001 by Spearman correlation analysis. C 5hmC levels of CpG43 from...

Additional file 5 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 5: Figure S4. The correlation between LARRPM expression, 5hmC level at CSF1 promoter, CpG82 methylation level and CSF1 expression in LUAD tissues. A Correlation between CSF1 and LARRPM expression analysed using the TCGA LUAD data. r = − 0.3069, P < 0.0001 by Spearman correlation analysis. B Correlation between CSF1 and LARRPM expression analysed in our LUAD cohort. r = − 0.5774, P < 0.0001 by Spearman correlation analysis. C 5hmC levels of...

Additional file 2 of SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases

Yue Li, Xinhua Yang, Weijie Zhu, Yuxia Xu, Jiangjun Ma, Caiyun He & Fang Wang
Additional file 2: Fig. S2 The progression-free survival (PFS) of patients receiving immune checkpoint inhibitor (ICI) treatment based on cancer types. The survival analysis was performed for individual cancer types that contained at least 10 cases in the SWI/SNF-mutant or SWI/SNF-non-mutant groups. The PFS of the SWI/SNF-mutant group was significantly superior to that of the SWI/SNF-non-mutant group in colorectal cancer (a) and gastric cancer (b), the same tendency was significant numerically by not statistically in...

figure s1.pdf

Narges Alipanah-Lechner, Lucile Neyton, Eran Mick, Andrew Willmore, Aleksandra Leligdowicz, Kevin Contrepois, Alejandra Jauregui, Hanjing Zhuo, Carolyn Hendrickson, Antonio Gomez, Pratik Sinha, Kirsten N. Kangelaris, Kathleen D. Liu, Michael A. Matthay, Angela Rogers & Carolyn S. Calfee
Overrepresentation analysis of differentially abundant metabolites between the hyperinflammatory ARDS and hypoinflammatory ARDS phenotype groups. Panel A) Figure represents significant metabolites with associated Human Metabolome Database (HMDB) identifiers based on the unadjusted analysis (n=131). Panel B) Figure represents significant metabolites with HMDB identifiers based on the analysis adjusted for age, sex, dexmedetomidine, propofol, kidney and liver injury (n=58). Panel C) Figure represents significant metabolites with HMDB identifiers based on the analysis adjusted for age, sex,...

Figure S1

Narges Alipanah-Lechner, Lucile Neyton, Eran Mick, Andrew Willmore, Aleksandra Leligdowicz, Kevin Contrepois, Alejandra Jauregui, Hanjing Zhuo, Carolyn Hendrickson, Antonio Gomez, Pratik Sinha, Kirsten N. Kangelaris, Kathleen D. Liu, Michael A. Matthay, Angela Rogers & Carolyn S. Calfee
Overrepresentation analysis of differentially abundant metabolites between the hyperinflammatory ARDS and hypoinflammatory ARDS phenotype groups. Panel A) Figure represents significant metabolites with associated Human Metabolome Database (HMDB) identifiers based on the unadjusted analysis (n=131). Panel B) Figure represents significant metabolites with HMDB identifiers based on the analysis adjusted for age, sex, dexmedetomidine, propofol, kidney and liver injury (n=58). Panel C) Figure represents significant metabolites with HMDB identifiers based on the analysis adjusted for age, sex,...

Figure S2

Narges Alipanah-Lechner, Lucile Neyton, Eran Mick, Andrew Willmore, Aleksandra Leligdowicz, Kevin Contrepois, Alejandra Jauregui, Hanjing Zhuo, Carolyn Hendrickson, Antonio Gomez, Pratik Sinha, Kirsten N. Kangelaris, Kathleen D. Liu, Michael A. Matthay, Angela Rogers & Carolyn S. Calfee
Top 20 differentially abundant metabolites in hyperinflammatory ARDS compared to hypoinflammatory ARDS by FDR adjusted p-value. Panel A) No adjustment for Simplified Acute Physiology Score II (SAPSII). Panel B) Adjusted for SAPSII. ✱Denotes metabolites no longer significant when SAPSII is included as a covariate in the model.

Additional file 5 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 5: Figure S4. The correlation between LARRPM expression, 5hmC level at CSF1 promoter, CpG82 methylation level and CSF1 expression in LUAD tissues. A Correlation between CSF1 and LARRPM expression analysed using the TCGA LUAD data. r = − 0.3069, P < 0.0001 by Spearman correlation analysis. B Correlation between CSF1 and LARRPM expression analysed in our LUAD cohort. r = − 0.5774, P < 0.0001 by Spearman correlation analysis. C 5hmC levels of...

Additional file 7 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 7: Fig. S6. Depletion of LARRPM in LUAD cells enhanced the oncogenic roles of infiltrated M2 macrophages. A–F Conditioned medium (CM) was collected from co-culture of macrophages with HCC827 cells with LARRPM depletion or control HCC827 cells, or collected from only HCC827 cells with LARRPM depletion or control HCC827 cells. A Cell proliferation of HCC827 cells treated with the CM was detected using CCK-8 assays. B Cell proliferation of HCC827 cells treated with...

Additional file 1 of SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases

Yue Li, Xinhua Yang, Weijie Zhu, Yuxia Xu, Jiangjun Ma, Caiyun He & Fang Wang
Additional file 1: Fig. S1 The distributions of variant allele frequencies (VAFs) of ARID1A, ARID1B, ARID2, PBRM1, SMARCA4, and SMARCB1. The median VAFs of the above genes were 16.1%, 13.4%, 13.3%, 17.2%, 15.2%, and 16.7%, respectively. Red solid line, median; black dotted line, quartiles.

Figure S4

Narges Alipanah-Lechner, Lucile Neyton, Eran Mick, Andrew Willmore, Aleksandra Leligdowicz, Kevin Contrepois, Alejandra Jauregui, Hanjing Zhuo, Carolyn Hendrickson, Antonio Gomez, Pratik Sinha, Kirsten N. Kangelaris, Kathleen D. Liu, Michael A Matthay, Angela Rogers & Carolyn S. Calfee
Predicted survival at any time point during the 60-day study period stratified by latent class analysis phenotype designation. Group 3 metabolite group is the reference in all estimates of hazard ratio (HR) for death. Top panel shows predicted survival by metabolite group in those with hyperinflammatory ARDS (n=35): Group 1, HR 7.3 (95%CI 0.9 to 57, p-value 0.06); Group 2, HR 2.8 (95%CI 0.4 to 21, p-value 0.3). Bottom panel shows predicted survival by metabolite...

Additional file 2 of SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases

Yue Li, Xinhua Yang, Weijie Zhu, Yuxia Xu, Jiangjun Ma, Caiyun He & Fang Wang
Additional file 2: Fig. S2 The progression-free survival (PFS) of patients receiving immune checkpoint inhibitor (ICI) treatment based on cancer types. The survival analysis was performed for individual cancer types that contained at least 10 cases in the SWI/SNF-mutant or SWI/SNF-non-mutant groups. The PFS of the SWI/SNF-mutant group was significantly superior to that of the SWI/SNF-non-mutant group in colorectal cancer (a) and gastric cancer (b), the same tendency was significant numerically by not statistically in...

Additional file 3 of SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases

Yue Li, Xinhua Yang, Weijie Zhu, Yuxia Xu, Jiangjun Ma, Caiyun He & Fang Wang
Additional file 3: Fig. S3 The signaling pathway enrichment of the variated genes in the SWI/SNF-mutant tumors by GO analysis. The GO analysis was performed on all the mutated genes in 1001 SWI/SNF-mutant samples.

Additional file 4 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 4: Figure S3. LINC00240 repressed proliferation, induced apoptosis and inhibited migration and invasion of LUAD cells. A LINC00240 expression in A549 cells with LINC00240 stable overexpression or control was detected by qRT-PCR. B Cell proliferation of A549 cells with LINC00240 stable overexpression or control was detected using CCK-8 assays. C Cell proliferation of A549 cells with LINC00240 stable overexpression or control was detected using EdU incorporation assays. Scale bar: 100 µm. Red color...

Additional file 7 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 7: Fig. S6. Depletion of LARRPM in LUAD cells enhanced the oncogenic roles of infiltrated M2 macrophages. A–F Conditioned medium (CM) was collected from co-culture of macrophages with HCC827 cells with LARRPM depletion or control HCC827 cells, or collected from only HCC827 cells with LARRPM depletion or control HCC827 cells. A Cell proliferation of HCC827 cells treated with the CM was detected using CCK-8 assays. B Cell proliferation of HCC827 cells treated with...

Additional file 2 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 2: Figure S1. Depletion of LARRPM promoted proliferation, repressed apoptosis and promoted migration and invasion of LUAD cells. A LARRPM expression in HCC827 cells with LARRPM stable depletion or control was detected by qRT-PCR. B Cell proliferation of HCC827 cells with LARRPM stable depletion or control was detected using CCK-8 assays. C Cell proliferation of HCC827 cells with LARRPM stable overexpression or control was detected using EdU incorporation assays. Scale bar: 100 µm....

Additional file 3 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 3: Figure S2. The correlation between LARRPM expression, 5hmC level at LINC00240 promoter, CpG43 methylation level and LINC00240 expression in LUAD tissues. A Correlation between LINC00240 and LARRPM expression analysed using the TCGA LUAD data. r = 0.6164, P < 0.0001 by Spearman correlation analysis. B Correlation between LINC00240 and LARRPM expression analyzed in our LUAD cohort. r = 0.5521, P < 0.0001 by Spearman correlation analysis. C 5hmC levels of CpG43 from...

Additional file 4 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 4: Figure S3. LINC00240 repressed proliferation, induced apoptosis and inhibited migration and invasion of LUAD cells. A LINC00240 expression in A549 cells with LINC00240 stable overexpression or control was detected by qRT-PCR. B Cell proliferation of A549 cells with LINC00240 stable overexpression or control was detected using CCK-8 assays. C Cell proliferation of A549 cells with LINC00240 stable overexpression or control was detected using EdU incorporation assays. Scale bar: 100 µm. Red color...

Additional file 6 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 6: Fig. S5. Anti-CSF1 antibody abolished the effects of LARRPM on M2 macrophage infiltration. A THP-1 cells were subjected to transwell migration assays towards A549 cells with LARRPM overexpression or A549 control cells treated with anti-CSF1. Scale bar: 100 µm. B THP-1 cells were subjected to transwell migration assays towards HCC827 cells with LARRPM depletion or HCC827 control treated with anti-CSF1. Scale bar: 100 µm. C M1 and M2 polarization markers expression in...

Figure S1.pdf

Narges Alipanah-Lechner, Lucile Neyton, Eran Mick, Andrew Willmore, Aleksandra Leligdowicz, Kevin Contrepois, Alejandra Jauregui, Hanjing Zhuo, Carolyn Hendrickson, Antonio Gomez, Pratik Sinha, Kirsten N. Kangelaris, Kathleen D. Liu, Michael A. Matthay, Angela Rogers & Carolyn S. Calfee
Overrepresentation analysis of differentially abundant metabolites between the hyperinflammatory ARDS and hypoinflammatory ARDS phenotype groups. Panel A) Figure represents significant metabolites with associated Human Metabolome Database (HMDB) identifiers based on the unadjusted analysis (n=131). Panel B) Figure represents significant metabolites with HMDB identifiers based on the analysis adjusted for age, sex, dexmedetomidine, propofol, kidney and liver injury (n=58). Panel C) Figure represents significant metabolites with HMDB identifiers based on the analysis adjusted for age, sex,...

Figure S2

Narges Alipanah-Lechner, Lucile Neyton, Eran Mick, Andrew Willmore, Aleksandra Leligdowicz, Kevin Contrepois, Alejandra Jauregui, Hanjing Zhuo, Carolyn Hendrickson, Antonio Gomez, Pratik Sinha, Kirsten N. Kangelaris, Kathleen D. Liu, Michael A. Matthay, Angela Rogers & Carolyn S. Calfee
Top 20 differentially abundant metabolites in hyperinflammatory ARDS compared to hypoinflammatory ARDS by FDR adjusted p-value. Panel A) No adjustment for Simplified Acute Physiology Score II (SAPSII). Panel B) Adjusted for SAPSII. ✱Denotes metabolites no longer significant when SAPSII is included as a covariate in the model.

Figure S1

Narges Alipanah-Lechner, Lucile Neyton, Eran Mick, Andrew Willmore, Aleksandra Leligdowicz, Kevin Contrepois, Alejandra Jauregui, Hanjing Zhuo, Carolyn Hendrickson, Antonio Gomez, Pratik Sinha, Kirsten N. Kangelaris, Kathleen D. Liu, Michael A. Matthay, Angela Rogers & Carolyn S. Calfee
Overrepresentation analysis of differentially abundant metabolites between the hyperinflammatory ARDS and hypoinflammatory ARDS phenotype groups. Panel A) Figure represents significant metabolites with associated Human Metabolome Database (HMDB) identifiers based on the unadjusted analysis (n=131). Panel B) Figure represents significant metabolites with HMDB identifiers based on the analysis adjusted for age, sex, dexmedetomidine, propofol, kidney and liver injury (n=58). Panel C) Figure represents significant metabolites with HMDB identifiers based on the analysis adjusted for age, sex,...

Additional file 1 of SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases

Yue Li, Xinhua Yang, Weijie Zhu, Yuxia Xu, Jiangjun Ma, Caiyun He & Fang Wang
Additional file 1: Fig. S1 The distributions of variant allele frequencies (VAFs) of ARID1A, ARID1B, ARID2, PBRM1, SMARCA4, and SMARCB1. The median VAFs of the above genes were 16.1%, 13.4%, 13.3%, 17.2%, 15.2%, and 16.7%, respectively. Red solid line, median; black dotted line, quartiles.

Additional file 3 of SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases

Yue Li, Xinhua Yang, Weijie Zhu, Yuxia Xu, Jiangjun Ma, Caiyun He & Fang Wang
Additional file 3: Fig. S3 The signaling pathway enrichment of the variated genes in the SWI/SNF-mutant tumors by GO analysis. The GO analysis was performed on all the mutated genes in 1001 SWI/SNF-mutant samples.

Figure S3

Narges Alipanah-Lechner, Lucile Neyton, Eran Mick, Andrew Willmore, Aleksandra Leligdowicz, Kevin Contrepois, Alejandra Jauregui, Hanjing Zhuo, Carolyn Hendrickson, Antonio Gomez, Pratik Sinha, Kirsten N. Kangelaris, Kathleen D. Liu, Michael A. Matthay, Angela Rogers & Carolyn S. Calfee
Predicted survival at any time point during the 60-day study period stratified by metabolite group designation. Top panel shows predicted survival in the hyperinflammatory group compared to the hypoinflammatory group in patients with a Group 1 metabolite group designation (n=28): hazard ratio (HR) for death 3.7 (95%CI 1.4 to 10.1, p-value 0.01). Middle panel shows predicted survival in the hyperinflammatory group compared to the hypoinflammatory group in patients with a Group 2 metabolite group designation...

Additional file 2 of LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1

Yue Li, Chen Chen, Hai-lin Liu, Zhen-fa Zhang & Chang-li Wang
Additional file 2: Figure S1. Depletion of LARRPM promoted proliferation, repressed apoptosis and promoted migration and invasion of LUAD cells. A LARRPM expression in HCC827 cells with LARRPM stable depletion or control was detected by qRT-PCR. B Cell proliferation of HCC827 cells with LARRPM stable depletion or control was detected using CCK-8 assays. C Cell proliferation of HCC827 cells with LARRPM stable overexpression or control was detected using EdU incorporation assays. Scale bar: 100 µm....

Registration Year

  • 2022
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Resource Types

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Affiliations

  • Western University
    28
  • Tianjin Medical University General Hospital
    18
  • Sixth Affiliated Hospital of Sun Yat-sen University
    18
  • Sun Yat-sen University
    18
  • Northwest University
    18
  • Tianjin Medical University Cancer Institute and Hospital
    18
  • Henry Ford Hospital
    18
  • Guangzhou Women and Children Medical Center
    18
  • McGill University
    18
  • National University Heart Centre Singapore
    18