Formalin-Fixed Paraffin-Embedded (FFPE) Sample Preparation ...
An Integrated Multiplexing Approach for the ......Multiplexing Assay Workflow. Two adjacent sections...
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Background and Results Anna Juncker-Jensen 1 • Tyvette S Hilliard 2 • Nicholas Stavrou1 1 • Erinn Parnell 1 • Judy Kuo 1 • Eric Leones 1 • Sharon Stack 2 1 NeoGenomics Laboratories, Aliso Viejo, CA – 2 University of Notre Dame, South Bend, IN Figure 1. Multiplexing Assay Workflow. Two adjacent sections were cut from each FFPE tumor sample. A. MultiOmyx multiplexing IF staining protocol. For each round of staining, conjugated fluorescent antibodies were applied to a 4 μm section, followed by image acquisition of stained slides. The dye was erased, enabling a subsequent round of staining with another pair of fluorescent antibodies. Proprietary cell segmentation algorithms generate unique IDs for every cell allowing them to be tracked through multiple rounds of staining. B. Nanostring nCounter assay. RNA was extracted from the adjacent 10 μm section and then proceeded with hybridization, purification and immobilization and count based on manufacturer’s protocol. Figure 3. MultiOmyx Multiplexed Images & Quantitation. A-F. Multiplexed overlay images of PanCK, S100, vimentin, CD34, CD3, CD68, Ki67, CD68, HLA-DR, and CD163. A+C+E = HGSOC and B+D+F = GCT. G+F. Quantitation of protein density (cell #/mm 2 ) of single markers (G), and co-expressions for T helper cells (CD3+CD4+), T regulatory cells (CD3+CD4+FoxP3+), cytotoxic lymphocytes/CTLs (CD3+CD8+), tumor-associated macrophages/TAMs (CD3-CD68+), and M2-type TAMs (CD3- CD68+HLADR-CD163+). Table 1. Antibody Staining Sequence for MultiOmyx multiplexing staining. Table 2. Phenotyping of human tumor-associated lymphocytes and myeloid cells. Cell surface markers associated with cell subsets analyzed in the tumor samples. TAM: tumor- associated macrophage. PanCK: pan cytokeratin. Background : Granulosa cell tumors (GCTs) are rare tumor in ovaries accounting for 2-5% of all ovarian cancers. GCT malignancies are often low-grade with a five-year survival rate up to 90%, however a clinical characteristic of these tumors is a tendency for late recurrence and a high recurrent rate is the most critical factor for GCT death. As GCTs are rare tumors and tissue availability is very limited, we used a dual multiplexing approach in order to maximize the data output from a total of 14 FFPE rare GCT tumor samples. Gene and protein levels in these 14 GCT samples were compared to levels in 5 high- grade serous ovarian cancer (HGSOC) FFPE samples. Methods : For protein multiplexing we have used MultiOmyx™, an immunofluorescence (IF) multiplexing assay utilizing a pair of directly conjugated Cyanine dye-labeled (Cy3, Cy5) antibodies per round of staining. Each round of staining is imaged and followed by dye inactivation, and deep learning based cell classification algorithms identify positive cells for each. Gene expression analysis was done using the Nanostring PanCancer Immune 770 gene panel assay. RNA was extracted from the adjacent 10 μm section and then proceeded with hybridization, purification and immobilization and count based on manufacturer’s protocol. Results: On protein level we confirmed previous findings that ovarian tumors are so-called “cold” tumors, with a very low density of T cell infiltration which is even further reduced in GCT samples compared to HGSOC samples. This is also reflected by a significant decrease in the gene score for cytotoxic cells. When analyzing tumor markers S100, vimentin, and pan-cytokeratin in GCT samples we observed an almost complete loss of cytokeratin, but increases in vimentin and S100 (protein level), and a highly significant mRNA decrease in MUC1 which codes for EMA, a negative marker for adult GCT. On both mRNA and protein level we found a reduction in macrophages in GCT samples, and on protein level we also observed a reduction in proliferation marker Ki67. Density of angiogenic vessels in the GCT microenvironment was increased, possibly linked to a highly significant increase in NOS2A mRNA which codes for the protein nitric oxide synthase (NOS2), a known modulator of angiogenesis. © 2018 NeoGenomics Laboratories, Inc. All Rights Reserved. MultiOmyx is a trademark of NeoGenomics, Inc, which holds a license from GE HealthCare BioSciences Corp. Rev.112018 An Integrated Multiplexing Approach for the Immunoprofiling of the Tumor Microenvironment of Ovarian Granulosa Cell Tumors Multiplexing Setup – MultiOmyx™ (protein) & NanoString nCounter® (mRNA) Panel Specifications [email protected] A. A. LB-C18 + 2. Stain Slide 3. Acquire immunofluorescence Cy3-Ab A Cy5-Ab B Staining Round 1 Staining Round 2 1. Acquire Background 5. Acquire New Background Staining Round (n) 4. Inactivate Dye 6. Repeat (1..n) Staining Round 3 mRNA expression RNA prep 300ng Co-expression Phenotypes CD3+CD4+ T helper CD3+CD4+FoxP3+ T regulatory CD3+CD4+PD1+ T helper PD-1 CD3+CD4+FoxP3+PD1+ T regulatory PD-1 CD3+CD4+CTLA4+ T helper CTLA-4 CD3+CD4+FoxP3+CTLA4+ Treg CTLA-4 CD3+CD8+ T cytotoxic (CTL) CD3+CD8+PD1+ CTL PD-1 CD3+CD8+CTLA-4+ CTL CTLA-4 CD3-CD20+ B cells CD3-CD68+ TAM CD3-CD68+Ki67+ Proliferating TAM CD3-CD68+HLADR+CD163- M1 TAM CD3-CD68+HLADR-CD163+ M2 TAM PanCK+Ki67+ Tumor proliferation 16-Marker Panel # Cy3 Cy5 1 CTLA-4 CD34 2 PanCK CD163 3 CD4 PD-1 4 CD3 PD-L1 5 CD8 FoxP3 6 CD20 HLA-DR 7 Ki67 CD68 8 Vimentin S100 PanCancer Immune Profiling Panel : • 770 genes from 24 different immune cell types, common checkpoint inhibitors, and CT antigens. • Assesses mechanistic pathway activity. • Identifies TILs in the tumor microenvironment. • 40 reference genes. B. Figure 2. Nanostring Cell Type Profiling & Differential Expression. A+B the gene scores for cytotoxic cells (PRF1, GNLY, GZMA) and macrophages (CD68, CD163, CD84) were significantly reduced in GCT samples compared to HGSOC control samples. C Volcano plot displaying each gene's -log10(p-value) and log2 fold change with the selected covariate. Highly statistically significant genes fall at the top of the plot above the horizontal lines, and highly differentially expressed genes fall to either side. Horizontal lines indicate various False Discovery Rate (FDR) thresholds or p-value thresholds if there is no adjustment to the p-values. NanoString nCounter data – Cell Type Profiling & Differential Expression MultiOmyx Overlay Images – Tumor Markers, TILs, TAMs, & Vessels MultiOmyx Data – Protein Density Quantitation Reduced expression of genes for cytotoxic cells and TAMs in GCT samples Decrease in cytokeratin, CTLs, TAMs, Ki67 in GCT samples, but increase in S100, vimentin & CD34. B. C. Key Findings • We have used a dual multiplexing approach to immunoprofile the tumor microenvironment of rare ovarian Granulosa Cell Tumor FFPE samples on both mRNA level (Nanostring nCounter assay), and protein level (MultiOmyx analysis). • Gene signatures and protein levels for T cytotoxic lymphocytes and tumor-associated macrophages are reduced in GCTs compared to control HGSOC tumors. • Angiogenic vessel protein density is increased in GCTs, possibly linked to a highly significant over-expression of the gene for NOS2 which is a modulator of angiogenesis. EMA (protein) is a negative marker for GCT p-value<0.01 p-value<0.01 -log 10 (p-value) -log 10 (p-value) 3G. 3H. Modulator of angiogenesis
Transcript of An Integrated Multiplexing Approach for the ......Multiplexing Assay Workflow. Two adjacent sections...
Background and Results
Anna Juncker-Jensen1 • Tyvette S Hilliard 2 • Nicholas Stavrou1 1 • Erinn Parnell 1 • Judy Kuo 1 • Eric Leones 1 • Sharon Stack 2
1 NeoGenomics Laboratories, Aliso Viejo, CA – 2University of Notre Dame, South Bend, IN
Figure 1. Multiplexing Assay Workflow. Two adjacent sections were cut from each FFPE tumor sample. A. MultiOmyx multiplexing IF staining protocol. For each round ofstaining, conjugated fluorescent antibodies were applied to a 4 μm section, followed by image acquisition of stained slides. The dye was erased, enabling a subsequentround of staining with another pair of fluorescent antibodies. Proprietary cell segmentation algorithms generate unique IDs for every cell allowing them to be trackedthrough multiple rounds of staining. B. Nanostring nCounter assay. RNA was extracted from the adjacent 10 μm section and then proceeded with hybridization,purification and immobilization and count based on manufacturer’s protocol.
Figure 3. MultiOmyx Multiplexed Images & Quantitation. A-F. Multiplexed overlay images of PanCK, S100, vimentin, CD34, CD3, CD68, Ki67, CD68, HLA-DR, and CD163.A+C+E = HGSOC and B+D+F = GCT. G+F. Quantitation of protein density (cell #/mm2) of single markers (G), and co-expressions for T helper cells (CD3+CD4+), Tregulatory cells (CD3+CD4+FoxP3+), cytotoxic lymphocytes/CTLs (CD3+CD8+), tumor-associated macrophages/TAMs (CD3-CD68+), and M2-type TAMs (CD3-CD68+HLADR-CD163+).
Table 1. Antibody Staining Sequencefor MultiOmyx multiplexing staining.Table 2. Phenotyping of humantumor-associated lymphocytes andmyeloid cells. Cell surface markersassociated with cell subsets analyzedin the tumor samples. TAM: tumor-associated macrophage. PanCK: pancytokeratin.
Background: Granulosa cell tumors (GCTs) are rare tumor in ovaries accounting for 2-5% of all ovariancancers. GCT malignancies are often low-grade with a five-year survival rate up to 90%, however aclinical characteristic of these tumors is a tendency for late recurrence and a high recurrent rate is themost critical factor for GCT death. As GCTs are rare tumors and tissue availability is very limited, weused a dual multiplexing approach in order to maximize the data output from a total of 14 FFPE rare GCTtumor samples. Gene and protein levels in these 14 GCT samples were compared to levels in 5 high-grade serous ovarian cancer (HGSOC) FFPE samples.
Methods: For protein multiplexing we have used MultiOmyx™, an immunofluorescence (IF) multiplexingassay utilizing a pair of directly conjugated Cyanine dye-labeled (Cy3, Cy5) antibodies per round ofstaining. Each round of staining is imaged and followed by dye inactivation, and deep learning based cellclassification algorithms identify positive cells for each. Gene expression analysis was done using theNanostring PanCancer Immune 770 gene panel assay. RNA was extracted from the adjacent 10 μmsection and then proceeded with hybridization, purification and immobilization and count based onmanufacturer’s protocol.
Results: On protein level we confirmed previous findings that ovarian tumors are so-called “cold”tumors, with a very low density of T cell infiltration which is even further reduced in GCT samplescompared to HGSOC samples. This is also reflected by a significant decrease in the gene score forcytotoxic cells. When analyzing tumor markers S100, vimentin, and pan-cytokeratin in GCT samples weobserved an almost complete loss of cytokeratin, but increases in vimentin and S100 (protein level),and a highly significant mRNA decrease in MUC1 which codes for EMA, a negative marker for adult GCT.
On both mRNA and protein level we found a reduction in macrophages in GCT samples, and on proteinlevel we also observed a reduction in proliferation marker Ki67. Density of angiogenic vessels in the GCTmicroenvironment was increased, possibly linked to a highly significant increase in NOS2A mRNA whichcodes for the protein nitric oxide synthase (NOS2), a known modulator of angiogenesis.
© 2018 NeoGenomics Laboratories, Inc. All Rights Reserved. MultiOmyx is a trademark of NeoGenomics, Inc,
which holds a license from GE HealthCare BioSciences Corp. Rev. 112018
An Integrated Multiplexing Approach for the Immunoprofiling of the Tumor Microenvironment of Ovarian Granulosa Cell Tumors
Multiplexing Setup – MultiOmyx™ (protein) & NanoString nCounter® (mRNA) Panel Specifications
A.
A.
LB-C18
+
2. Stain Slide 3. Acquire immunofluorescence
Cy3-Ab A Cy5-Ab B Staining Round 1
Staining Round 2
1. Acquire Background
5. Acquire New Background Staining Round (n)
4. Inactivate Dye6. Repeat (1..n)
Staining Round 3
mRNA expression
RNA prep 300ng
Co-expression Phenotypes
CD3+CD4+ T helper
CD3+CD4+FoxP3+ T regulatory
CD3+CD4+PD1+ T helper PD-1
CD3+CD4+FoxP3+PD1+ T regulatory PD-1
CD3+CD4+CTLA4+ T helper CTLA-4
CD3+CD4+FoxP3+CTLA4+ Treg CTLA-4
CD3+CD8+ T cytotoxic (CTL)
CD3+CD8+PD1+ CTL PD-1
CD3+CD8+CTLA-4+ CTL CTLA-4
CD3-CD20+ B cells
CD3-CD68+ TAM
CD3-CD68+Ki67+ Proliferating TAM
CD3-CD68+HLADR+CD163- M1 TAM
CD3-CD68+HLADR-CD163+ M2 TAM
PanCK+Ki67+ Tumor proliferation
16-Marker Panel
# Cy3 Cy5
1 CTLA-4 CD34
2 PanCK CD163
3 CD4 PD-1
4 CD3 PD-L1
5 CD8 FoxP3
6 CD20 HLA-DR
7 Ki67 CD68
8 Vimentin S100
PanCancer Immune Profiling Panel :
• 770 genes from 24 different immune cell types, common checkpoint inhibitors, and CT antigens.
• Assesses mechanistic pathway activity.
• Identifies TILs in the tumor microenvironment.
• 40 reference genes.
B.
Figure 2. Nanostring Cell Type Profiling & Differential Expression. A+B the gene scores for cytotoxic cells (PRF1, GNLY, GZMA) andmacrophages (CD68, CD163, CD84) were significantly reduced in GCT samples compared to HGSOC control samples. C Volcano plotdisplaying each gene's -log10(p-value) and log2 fold change with the selected covariate. Highly statistically significant genes fall at the top ofthe plot above the horizontal lines, and highly differentially expressed genes fall to either side. Horizontal lines indicate various FalseDiscovery Rate (FDR) thresholds or p-value thresholds if there is no adjustment to the p-values.
NanoString nCounter data – Cell Type Profiling & Differential Expression MultiOmyx Overlay Images – Tumor Markers, TILs, TAMs, & Vessels MultiOmyx Data – Protein Density Quantitation
Reduced expression of genes for cytotoxic cells and TAMs in GCT samples Decrease in cytokeratin, CTLs, TAMs, Ki67 in GCT samples, but increase in S100, vimentin & CD34.
B.
C.
Key Findings
• We have used a dual multiplexing approach to immunoprofile the tumor microenvironment of rare ovarian Granulosa Cell Tumor FFPE samples on both mRNA level (Nanostring nCounter assay), and protein level (MultiOmyx analysis).
• Gene signatures and protein levels for T cytotoxic lymphocytes and tumor-associated macrophages are reduced in GCTs compared to control HGSOC tumors.
• Angiogenic vessel protein density is increased in GCTs, possibly linked to a highly significant over-expression of the gene for NOS2 which is a modulator of angiogenesis.
EMA (protein) is a negative marker for GCTp-value<0.01
p-value<0.01
-lo
g 10
(p-v
alu
e)-l
og 1
0(p
-val
ue)
3G. 3H.
Modulator of angiogenesis
