Journal: Nature Communications

Article Title: Hypoxia induced responses are reflected in the stromal proteome of breast cancer

doi: 10.1038/s41467-023-39287-7

Figure Lengend Snippet: Multivariate survival analysis (proportional hazards regression model) of breast cancer patients (METABRIC-Discovery cohort)

Article Snippet: Of relevance for secretome studies, we found that 40 of the PAM50 signature genes/proteins have been reported in serum or plasma (plasma proteome database; PPD: http://www.plasmaproteomedatabase.org/ ) , and/or the Human Protein Atlas—blood protein (Human Protein Atlas proteinatlas.org) .

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Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: Example Utah high-risk breast cancer pedigree 1817. a. Confirmed and sampled breast cancer cases are indicated in black (55 sampled out of 138 total confirmed UCR cases). Star, triangle and hexagon symbols indicate pedigree branches. b. shows only those cases from (a) with tumor expression data available and indicates PAM50 intrinsic subtype by color. Cases whose tumors are extreme for PC3 are indicated by ‘3’; extreme for PC5 are indicated by ‘5’. c. shows only the PC3-extreme cases from (b). A ‘+’ indicates those cases that share the genomewide significant region at 12q15.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

Techniques: Expressing

Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: Summary of the 11 high-risk Utah pedigrees Tumor count by intrinsic subtype per pedigree.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

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Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: A slice from a three-dimensional scatterplot of PC1, PC2, and PC4 shows that they recapitulate the PAM50 intrinsic subtypes. Reinforcing the constrasts illustrated in Figure 2, PC1 here clearly distinguishes Basal-like from Luminal A tumors. PC2 and PC4 aid in distinguishing HER2-enriched from Luminal B tumors. Combined, these three components define clusters corresponding to the intrinsic subtypes.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

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Journal: Nature genetics

Article Title: A single-cell and spatially resolved atlas of human breast cancers

doi: 10.1038/s41588-021-00911-1

Figure Lengend Snippet: a, Bar and boxplot (inset) of the Pearson correlation for 45 cell-types between the actual cell-fractions captured by scRNA-Seq and the CIBERSORTx predicted fractions from pseudo-bulk expression profiles (*denotes significance p<0.05, two-sided correlation coefficient). Inset box plot depicts the first and third quartiles as the lower and upper bounds, respectively. The whiskers represent 1.5x the interquartile range and the centre depicts the median. b, Barplot comparing the Pearson correlation for cell-types between the actual cell-fractions captured by scRNA-Seq and the CIBERSORTx (red) and DWLS (blue) predicted fractions from pseudo-bulk expression profiles (*denotes significance p<0.05, two-sided correlation coefficient). c, Boxplot comparing the CIBERSORTx predicted scSubtype and Cycling cell-fractions in each METABRIC tumor, stratified by PAM50 subtypes (n = 1,608; 209 Basal, 224 Her2, 700 LumA and 475 LumB). Box plots depicted as described in b. d, Heatmap of ecotypes formed from the common METABRIC tumors (columns) identified from combining ecotypes generated using CIBERSORTx with all 32 significantly correlated cell-types (rows), when using CIBERSORTx on pseudo-bulk samples. e-f, Relative proportion of the PAM50 subtypes (e) and major cell-types (f) in each ecotype, when combining CIBERSORTx consensus clustering results. g-h, Kaplan-Meier (KM) plot of all patients with common tumors in each of the ecotypes (g) and patients with tumors in ecotypes E4 and E7 (h), when combining CIBERSORTx consensus clustering results. p-values calculated using the log-rank test. i-j, Relative proportion of the PAM50 molecular subtypes (i) and major cell-types (j) of the common tumors from combining CIBERSORT and DWLS generated ecotypes. k, KM plot of the patients with tumors in ecotypes E4 and E7, formed from combining CIBERSORT and DWLS generated ecotypes. p-value calculated using the log-rank test. l, Relative proportion of the METABRIC integrative cluster annotations of the tumors in each ecotype, as determined using CIBERSORTx across all cell-types.

Article Snippet: We first identified tumors that shared the same “concordant” subtype from both Allcells-Pseudobulk PAM50 calls and TCGA hierarchical clustering based subtype classifications ( Supplementary Table 3 ).

Techniques: Expressing, Generated

Journal: Nature genetics

Article Title: A single-cell and spatially resolved atlas of human breast cancers

doi: 10.1038/s41588-021-00911-1

Figure Lengend Snippet: a-b, Hierarchical Clustering of Allcells-Pseudobulk (indicated by yellow stars) and Ribozero mRNA-Seq (indicated by blue stars) profiles of the patient samples with TCGA patient mRNA-Seq data. a, View of the basal cluster showing pairing of Allcells-Pseudobulk and Ribozero mRNA-Seq profiles of 2 representative tumors (CID4495 and CID4515) in the present study. b, View of the luminal cluster showing pairing of Allcells-Pseudobulk and Ribozero mRNA-Seq profiles of 4 representative tumors (CID4067, CID4463, CID4290 and CID3948) in the present study. c, Heatmap of scSubtype gene sets across the training and test samples in each individual group. Colored outlined boxes highlighting the top expressed genes per group. d, Barplot representing proportions of scSubtype calls in individual samples. Test dataset samples are highlighted within the golden colored outline. e, Scatterplot of individual cancer cells plotted according to the Proliferation score (x-axis) and Differentiation – DScore (y-axis). Individual cells are colored based on the scSubtype calls. f, Scatterplot of individual TCGA breast tumors plotted according to the Proliferation score (x-axis) and Differentiation – DScore (y-axis). Individual patients are colored based on the PAM50 subtype calls.

Article Snippet: We first identified tumors that shared the same “concordant” subtype from both Allcells-Pseudobulk PAM50 calls and TCGA hierarchical clustering based subtype classifications ( Supplementary Table 3 ).

Techniques:

Journal: Nature genetics

Article Title: A single-cell and spatially resolved atlas of human breast cancers

doi: 10.1038/s41588-021-00911-1

Figure Lengend Snippet: Deconvolution of breast cancer cohorts using single-cell signatures reveals robust ecotypes associated with patient survival and intrinsic subtypes. a, Consensus clustering of all tumors (columns) in METABRIC showing nine robust tumor ecotypes and 4 groups of cell enrichments from 45 cell-types in the breast cancer cell taxonomy. Total 1,985 tumors (E1 = 266, E2= 269, E3 = 205, E4 = 263, E5 = 195, E6 = 215, E7 = 199, E8 = 213, E9 = 160). b, Relative proportion of the PAM50 molecular subtypes of the tumors in each ecotype. c, Relative average proportion of the major cell-types enriched in the tumors in each ecotype. d-f, Kaplan-Meier (KM) plot of the patients with tumors in each of the nine ecotypes (d), patients with tumors in ecotypes E2 and E7 (e), patients with tumors in ecotypes E4 and E7 (f). p-values calculated using the log-rank test. g, Summary of the major epithelial, immune and stromal cell types identified in this study grouped by their major (inner), minor and subset (outer) level classification tiers.

Article Snippet: We first identified tumors that shared the same “concordant” subtype from both Allcells-Pseudobulk PAM50 calls and TCGA hierarchical clustering based subtype classifications ( Supplementary Table 3 ).

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Journal: NPJ Breast Cancer

Article Title: Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

doi: 10.1038/s41523-024-00658-y

Figure Lengend Snippet: Intrinsic breast cancer molecular-subtyping methods in PALOMA-2

Article Snippet: Tumor samples from consenting patients in the PALOMA-2 trial were subtyped using the validated RUO PAM50 assay (ruoProsigna-PAM50); results were compared with published subtype results using AIMS on EdgeSeq Oncology Biomarker Panel (HTG-AIMS; HTG Molecular Diagnostics®, Tucson, AZ, USA; Supplementary Fig. ) .

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Journal: NPJ Breast Cancer

Article Title: Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

doi: 10.1038/s41523-024-00658-y

Figure Lengend Snippet: a Pie charts of subtype distributions by HTG-AIMs, HTG-PAM50.sgPct, and ruoProsigna-PAM50 subtyping methods among total available samples. HTG-AIMS and HTG-PAM50.sgPct were applied on the entire cohort of 455 samples; only 222 samples were available for ruoProsigna-PAM50. b Kaplan–Meier curves of median PFS by subtype and treatment in PALOMA-2 with ruoProsigna-PAM50, the gold standard. c Hazard ratios and 95% CIs for PFS by breast cancer subtype and subtyping method in PALOMA-2; for HGT-AIMS analysis, six patients were not included (four NL and two BL). *Data from Finn et al. . LET letrozole, N number of patients in the analysis group, n number of patients, NA not available, PAL palbociclib, PBO placebo.

Article Snippet: Tumor samples from consenting patients in the PALOMA-2 trial were subtyped using the validated RUO PAM50 assay (ruoProsigna-PAM50); results were compared with published subtype results using AIMS on EdgeSeq Oncology Biomarker Panel (HTG-AIMS; HTG Molecular Diagnostics®, Tucson, AZ, USA; Supplementary Fig. ) .

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Journal: NPJ Breast Cancer

Article Title: Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

doi: 10.1038/s41523-024-00658-y

Figure Lengend Snippet: Intrinsic breast cancer molecular-subtyping methods in PALLET

Article Snippet: Tumor samples from consenting patients in the PALOMA-2 trial were subtyped using the validated RUO PAM50 assay (ruoProsigna-PAM50); results were compared with published subtype results using AIMS on EdgeSeq Oncology Biomarker Panel (HTG-AIMS; HTG Molecular Diagnostics®, Tucson, AZ, USA; Supplementary Fig. ) .

Techniques:

Journal: NPJ Breast Cancer

Article Title: Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

doi: 10.1038/s41523-024-00658-y

Figure Lengend Snippet: a Pie chart of subtype distributions by the RNAseq-AIMS and RNAseq-PAM50.sgMd.TC subtyping methods for PALLET samples. b Odds ratios and 95% CIs for non-CCCA by breast cancer RNAseq-AIMS and RNAseq-PAM50.sgMd.TC subtype in PALLET. LET letrozole, n number of patients in the subtype treatment group, PAL palbociclib.

Article Snippet: Tumor samples from consenting patients in the PALOMA-2 trial were subtyped using the validated RUO PAM50 assay (ruoProsigna-PAM50); results were compared with published subtype results using AIMS on EdgeSeq Oncology Biomarker Panel (HTG-AIMS; HTG Molecular Diagnostics®, Tucson, AZ, USA; Supplementary Fig. ) .

Techniques:

Journal: NPJ Breast Cancer

Article Title: Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

doi: 10.1038/s41523-024-00658-y

Figure Lengend Snippet: a Plot of the largest two correlations between sample expression data and ruoProsigna subtype centroids. The solid line is the equal line, and the dashed line is 0.1 from the equal line. Each symbol is a sample. Symbol “AB” means the largest correlation coefficient is with LumA and the second largest correlation is with LumB. The same pattern follows for the remaining symbol combinations. b PFS in the palbociclib plus letrozole group between patients with clear-defined subtypes (solid lines) versus patients with discord subtypes (dashed lines) based on agreement between the HTG-AIMS and ruoProsigna-PAM50 methods. In the figure on the left, the subtype is based on AIMS; in the figure on the right, the subtype is based on PAM50. LET letrozole, NonLum nonluminal, PAL palbociclib.

Article Snippet: Tumor samples from consenting patients in the PALOMA-2 trial were subtyped using the validated RUO PAM50 assay (ruoProsigna-PAM50); results were compared with published subtype results using AIMS on EdgeSeq Oncology Biomarker Panel (HTG-AIMS; HTG Molecular Diagnostics®, Tucson, AZ, USA; Supplementary Fig. ) .

Techniques: Expressing

Journal: NPJ Breast Cancer

Article Title: Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

doi: 10.1038/s41523-024-00658-y

Figure Lengend Snippet: Heatmap of cross-classification of different breast cancer molecular intrinsic subtypes according to PAM50 bioclassifier centroids and their proposed sensitivities to CDK4/6 inhibitors.

Article Snippet: Tumor samples from consenting patients in the PALOMA-2 trial were subtyped using the validated RUO PAM50 assay (ruoProsigna-PAM50); results were compared with published subtype results using AIMS on EdgeSeq Oncology Biomarker Panel (HTG-AIMS; HTG Molecular Diagnostics®, Tucson, AZ, USA; Supplementary Fig. ) .

Techniques: