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View article: Abstract 2207: Intratumoral bacteria predict survival in clear cell renal cell carcinoma (ccRCC)
Abstract 2207: Intratumoral bacteria predict survival in clear cell renal cell carcinoma (ccRCC) Open
Background: ccRCC is marked by niches of immune evasion in late-stage disease, that are associated with resistance to immune checkpoint inhibitors (CPI). Intratumoral microbes are emerging as key modulators of the tumor immune microenviron…
View article: Supplementary Table 6 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 6 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 6. Differential expression analysis by wGII of genes involved in cGAS-STING pathway.
View article: Supplementary Table 2 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 2 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 2. Changes in ssGSEA scores from normal kidney tissue to primary ccRCC tumor in normal-primary pairs.
View article: Supplementary Table 10 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 10 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 10. Antibody and incubation procedure for immunohistochemistry (IHC) of CD3 and CD68.
View article: Supplementary Note 1 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Note 1 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Inputting information from previous TRACERx Renal studies
View article: Supplementary Table 9 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 9 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 9. Univariate Cox regression results for progression-free survival in the TRACERx Renal cohort based on the expression of each of 613 HERV/LTR elements.
View article: Figure 3 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Figure 3 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Canonical ccRCC subclonal drivers and aneuploidy burden drive specific changes to the tumor transcriptome. A, Illustration of the procedure to analyze the transcriptional association of a subclonal copy number alteration without the…
View article: Supplementary Table 7 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 7 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 7. TCR clones identified applying miXCR to bulk RNA-Sequencing data across 243 ccRCC and kidney-adjacent normal samples in TRACERx Renal.
View article: Figure 1 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Figure 1 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Transcriptional inter- and intratumor heterogeneity is pervasive in TRACERx Renal. A, UMAP visualizing the transcriptional variation across 231 tumor samples (gray points). Samples from patients K390, K243, and K153 are highlighted …
View article: Figure 5 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Figure 5 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Spatial diversity of the TCR repertoire suggests heritable nature of the antigenic source in ccRCC. A, TCR and BCR similarity between pairs of samples across 60 TRACERx Renal patients with at least two regions sampled. Dark purple d…
View article: Figure 2 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Figure 2 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Transcriptional evolution mirrors clonal structure and follows recurrent trends. A, Transcriptional distance between primary tumor samples and other primary tumor samples or adjacent normal kidney samples (12 patients with both avai…
View article: Supplementary Table 3 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 3 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 3. Changes in ssGSEA scores from primary to metastasis in primary-metastasis pairs.
View article: Figure 6 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Figure 6 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Greater overall HERV expression, strongly associated with VHL loss of function, correlates with longer progression-free survival in ccRCC. A, Distribution in TRACERx Renal (n = 243 samples) of the median expression across 615…
View article: Supplementary Table 1 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 1 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 1. Variance in gene expression for 16,716 genes passing expression filtering criteria in the TRACERx Renal study
View article: Supplementary Table 4 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 4 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 4. 50 MSigDB hallmark signatures and corresponding categories.
View article: Supplementary Table 8 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 8 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 8. BCR clones identified applying miXCR to bulk RNA-Sequencing data across 243 ccRCC and kidney-adjacent normal samples in TRACERx Renal.
View article: Supplementary Table 5 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 5 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 5. Changes in ssGSEA scores from early to late clones.
View article: Figure 4 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Figure 4 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Heterogeneity of the TME in ccRCC. A, Association of TME cell abundance estimates from consensus TME and evolutionary trajectory of the tumor from which the sample is taken (in 171 primary tumor samples). Comparisons are one against…
View article: Supplementary Note 2 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Note 2 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Evaluation of the potential to reconstruct TCR repertiore from bulk RNA-Sequencing data
View article: Supplementary Table 11 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Table 11 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Supplementary Table 11. Antibody / Opal combinations, dilutions and positions used for 6 biomarker immunofluorescence panel staining. RTU = Ready to Use.
View article: Supplementary Figures 1-33 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Supplementary Figures 1-33 from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
All Supplementary Figures are provided in PDF format with the corresponding legend after each figure. Supplementary Figure 1. Genetic and clinical composition of the TRACERx Renal cohort Supplementary Figure 2. Comparison between transcrip…
View article: Data from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal
Data from Tracking Nongenetic Evolution from Primary to Metastatic ccRCC: TRACERx Renal Open
Although the key aspects of genetic evolution and their clinical implications in clear-cell renal cell carcinoma (ccRCC) are well documented, how genetic features coevolve with the phenotype and tumor microenvironment (TME) remains elusive…
View article: Chronic Interferon at Baseline is Associated with Acquired Resistance to Immunotherapy in Metastatic Melanoma
Chronic Interferon at Baseline is Associated with Acquired Resistance to Immunotherapy in Metastatic Melanoma Open
View article: 14P Integrated genomic analysis of whole genomes to derive a biomarker of durable response to immunotherapy in melanoma
14P Integrated genomic analysis of whole genomes to derive a biomarker of durable response to immunotherapy in melanoma Open
View article: 173MO Immunological dynamics of HLA-II positive melanoma
173MO Immunological dynamics of HLA-II positive melanoma Open
View article: Supplementary Figures S1-S25 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways
Supplementary Figures S1-S25 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways Open
Supplementary figure 1: Cohort overview. Number of samples sequenced with whole exome, panel or whole RNA sequencing. Supplementary figure 2: Phylogeny and WGD events in CRUKP1047. Supplementary figure 3: Ploidy and SCNA burden. Supplement…
View article: Data from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways
Data from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways Open
Understanding the evolutionary pathways to metastasis and resistance to immune checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here we present the most comprehensive intra-patient metastatic melanoma dataset ass…
View article: Supplementary Tables S1-S8 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways
Supplementary Tables S1-S8 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways Open
S. Table 1: List of PEACE Consortium members. S. Table 2: Sample database used for the study for Panel, Exome and RNASeq samples. S. Table 3: Overview of lines of treatment given to each patient. S. Table 4: Lesions and patients included i…
View article: Supplementary Figures S1-S25 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways
Supplementary Figures S1-S25 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways Open
Supplementary figure 1: Cohort overview. Number of samples sequenced with whole exome, panel or whole RNA sequencing. Supplementary figure 2: Phylogeny and WGD events in CRUKP1047. Supplementary figure 3: Ploidy and SCNA burden. Supplement…
View article: Supplementary Tables S1-S8 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways
Supplementary Tables S1-S8 from Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways Open
S. Table 1: List of PEACE Consortium members. S. Table 2: Sample database used for the study for Panel, Exome and RNASeq samples. S. Table 3: Overview of lines of treatment given to each patient. S. Table 4: Lesions and patients included i…