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van Raay K, Kriner M, Reeves J, Piazza E, Kaplan H, Vivian J, Fernandez F, Hoang M, Beechem J. Abstract 615: Spatially resolved expression of T cell receptors elucidates spatial relationships between T cells, immune infiltration, and cancer-associated pathways. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Spatial distribution of T cells is key in understanding the escape of tumors from immune surveillance via the adaptive immune response, including interactions between immune cells and the surrounding tumor microenvironment. T cells are critical to the adaptive immune response to pathogens and cancers, mediating an antigen-specific response through both specificity and diversity of T cell receptor (TCR) clonotypes. Many methods exist to determine specific clonotypes and overall TCR diversity present from bulk tissues or sorted cell populations; however, nearly all fail to capture spatial orientation and arrangement of T cells engaging with their microenvironment, and most require large amounts of starting material from precious samples. Here, we present a TCR expression profiling panel for the GeoMx® Digital Spatial Profiler that can be combined with the GeoMx Cancer Transcriptome Atlas (CTA) or Human Whole Transcriptome Atlas (WTA) on archival formalin-fixed paraffin embedded (FFPE) tissue specimens. This represents the first commercial spatial expression profiling assay for the simultaneous quantification of TCR constant, variable, and joining segments in situ.
We show reliable sensitivity and specificity (>90%) with respect to orthogonal sequencing and robust detection of TCR chains with evidence of clonal expansion and CD8 infiltration across tumor regions in colorectal cancer tissue. These events also corresponded to increased signatures of exhaustion from the T cells and suggest that the T cells resident in or near the tumor are tumor-specific and poised for activation via checkpoint blockade. Signaling pathways and tumor-specific signatures were also evaluated to look for mechanisms through which tumor cells respond to T cell infiltration. We further validated the performance of the TCR probe pool in cell pellet arrays with orthogonal TCR sequencing, tonsil and colorectal cancer tissues.
Together, the combination of our TCR add-on panel with the CTA or WTA illuminates T cell phenotypes, signaling pathways, population dynamics, and transcriptomic changes, yielding an unparalleled view of the T cell response in any context.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
Citation Format: Katrina van Raay, Michelle Kriner, Jason Reeves, Erin Piazza, Hargita Kaplan, John Vivian, Francis Fernandez, Margaret Hoang, Joseph Beechem. Spatially resolved expression of T cell receptors elucidates spatial relationships between T cells, immune infiltration, and cancer-associated pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 615.
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Sprenger CC, Coleman I, Kriner M, Brady L, Hoang M, Roudier M, Damodarasamy M, Patel R, True L, Nelson P, Haffner M, Plymate S. Abstract 989: Spatial profiling of androgen receptor splice variant 7 transcriptional activity in prostate cancer metastases. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Androgen receptor splice variant 7 (AR-V7) is expressed in metastases from patients with castration resistant prostate cancer (CRPC) and shows a high level of inter- and intra-tumoral variability. However, the downstream activity generated by AR-V7 in tissue has not been shown. Whether AR-V7 is active in tissue or whether AR-V7 is a non-functioning biomarker with full-length AR is not known. To address this question, we constructed a tissue microarray (TMA) of 56 metastases from 27 patients with CRPC to analyze spatial gene expression using the GeoMx Digital Spatial Profiler. Immunostaining was performed to define epithelial, vascular, and stromal compartments. The stained tissues were then hybridized with barcoded tagged oligonucleotides targeting 2093 unique genes, which included those representing AR, AR-V cryptic exons, AR and neuroendocrine activity, and immune cell markers. One 500 um region of interest (ROI) was assessed per tissue core (approximately 1200 cells). A sequential section from the same TMA was then stained with AR-V7 and AR-C-terminal specific antibodies. ROIs for RNA and protein were selected to be similar between slides. In addition to DSP, each metastasis was assessed by RNA-seq on the bulk tissue.
Results: The most differentially expressed genes (FDR<0.05) based on association with AR-V7 staining were known downstream AR regulated genes including KLK2 and 3, FKBP5, NKX3.1, TMPRSS2, FASN, and TARP. Additionally, genes associated with proliferation and stemness, e.g., POLB, KRT1, SOX2, were significantly expressed. Since 93% of patients were on ADT at time of tissue collection and over 80% also had been treated with either abiraterone or enzalutamide, the increase in AR downstream genes would not be expected to occur from ligand activation of AR-FL. We also have previously shown that knock-down of AR-V7 in LNCaP95 cells results in loss of AR binding to AREs. In these metastases, then, activation of AR downstream genes would be a result of AR-V7 nuclear transport of AR-FL through AR-V7/AR-FL heterodimers or transcriptional activation by AR-V7 homodimers. Of further note, AR cryptic exons 1, 2, and 5 were also significantly expressed in AR-V7 positive ROIs (p< 0.0001). RNA-seq intron/exon junction reads were used to demonstrate that additional AR-Vs, most commonly AR-V9, were also expressed in tissues positive for AR-V7, suggesting that AR splicing is a common event in CRPC. Finally, expression of neuroendocrine (NE) genes INSM1 and TUBB2 were not expressed in AR-V7 positive ROIs (negatively correlated, p<0.001), indicating that AR-V7 and NE phenotypes cannot co-exist in the same cell.
Conclusion: AR-V7 continues to drive prostate cancer through activation of the AR-cistrome. Its expression is heterogenous in metastases along with NE cells, suggesting that in the presence of AR-V7 and NE markers, therapy needs to be directed at the N-terminus of AR and NE components.
Citation Format: Cynthia C. Sprenger, Ilsa Coleman, Michelle Kriner, Lauren Brady, Margaret Hoang, Martine Roudier, Mamatha Damodarasamy, Radhika Patel, Lawrence True, Peter Nelson, Michael Haffner, Stephen Plymate. Spatial profiling of androgen receptor splice variant 7 transcriptional activity in prostate cancer metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 989.
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Affiliation(s)
| | - Ilsa Coleman
- 2Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Lauren Brady
- 2Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | - Radhika Patel
- 2Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Peter Nelson
- 2Fred Hutchinson Cancer Research Center, Seattle, WA
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McNamara KL, Caswell-Jin JL, Joshi R, Ma Z, Kotler E, Bean GR, Kriner M, Zhou Z, Hoang M, Beechem J, Zoeller J, Press MF, Slamon DJ, Hurvitz SA, Curtis C. Spatial proteomic characterization of HER2-positive breast tumors through neoadjuvant therapy predicts response. Nat Cancer 2021; 2:400-413. [PMID: 34966897 PMCID: PMC8713949 DOI: 10.1038/s43018-021-00190-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The addition of HER2-targeted agents to neoadjuvant chemotherapy has dramatically improved pathological complete response (pCR) rates in early-stage, HER2-positive breast cancer. Nonetheless, up to 50% of patients have residual disease after treatment, while others are likely overtreated. Here, we performed multiplex spatial proteomic characterization of 122 samples from 57 HER2-positive breast tumors from the neoadjuvant TRIO-US B07 clinical trial sampled pre-treatment, after 14-21 d of HER2-targeted therapy and at surgery. We demonstrated that proteomic changes after a single cycle of HER2-targeted therapy aids the identification of tumors that ultimately undergo pCR, outperforming pre-treatment measures or transcriptomic changes. We further developed and validated a classifier that robustly predicted pCR using a single marker, CD45, measured on treatment, and showed that CD45-positive cell counts measured via conventional immunohistochemistry perform comparably. These results demonstrate robust biomarkers that can be used to enable the stratification of sensitive tumors early during neoadjuvant HER2-targeted therapy, with implications for tailoring subsequent therapy.
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Affiliation(s)
- Katherine L. McNamara
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer L. Caswell-Jin
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rohan Joshi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhicheng Ma
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Eran Kotler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory R. Bean
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Zoey Zhou
- NanoString Technologies, Seattle, WA, USA
| | | | | | - Jason Zoeller
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Michael F. Press
- Department of Pathology Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Dennis J. Slamon
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Sara A. Hurvitz
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to C.C.
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Brady L, Kriner M, Coleman I, Morrissey C, Roudier M, True LD, Gulati R, Plymate SR, Zhou Z, Birditt B, Meredith R, Geiss G, Hoang M, Beechem J, Nelson PS. Inter- and intra-tumor heterogeneity of metastatic prostate cancer determined by digital spatial gene expression profiling. Nat Commun 2021; 12:1426. [PMID: 33658518 PMCID: PMC7930198 DOI: 10.1038/s41467-021-21615-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/04/2021] [Indexed: 02/08/2023] Open
Abstract
Metastatic prostate cancer (mPC) comprises a spectrum of diverse phenotypes. However, the extent of inter- and intra-tumor heterogeneity is not established. Here we use digital spatial profiling (DSP) technology to quantitate transcript and protein abundance in spatially-distinct regions of mPCs. By assessing multiple discrete areas across multiple metastases, we find a high level of intra-patient homogeneity with respect to tumor phenotype. However, there are notable exceptions including tumors comprised of regions with high and low androgen receptor (AR) and neuroendocrine activity. While the vast majority of metastases examined are devoid of significant inflammatory infiltrates and lack PD1, PD-L1 and CTLA4, the B7-H3/CD276 immune checkpoint protein is highly expressed, particularly in mPCs with high AR activity. Our results demonstrate the utility of DSP for accurately classifying tumor phenotype, assessing tumor heterogeneity, and identifying aspects of tumor biology involving the immunological composition of metastases. The inter- and intra-tumor heterogeneity of metastatic prostate cancer (mPC) is underexplored. Here the authors use Digital Spatial Profiling to study gene and protein expression heterogeneity in 27 mPC patients, finding variation in associated pathways and potential immunotherapy targets.
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Affiliation(s)
- Lauren Brady
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Ilsa Coleman
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | - Roman Gulati
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen R Plymate
- University of Washington, Seattle, WA, USA.,VAPSHCS-GRECC, Seattle, WA, USA
| | - Zoey Zhou
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | | | - Gary Geiss
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | | | - Peter S Nelson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,University of Washington, Seattle, WA, USA.
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Hoang ML, Kriner M, Zhou Z, Norgaard Z, Sorg K, Merritt C, Piazza E, Ross M, Fropf R, Saraf N, Danaher P, Rhodes M, Beechem J. Abstract 1364: Spatially-resolved in situ expression profiling using the GeoMx™ Cancer Transcriptome Atlas panel in FFPE tissue. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The emerging field of spatial genomics represents a significant advance for biology. To drive new discoveries in spatial genomics and immuno-oncology, we introduce the GeoMx Cancer Transcriptome Atlas (CTA) Panel for comprehensive spatial analysis of cancer pathways using the Nanostring GeoMx Digital Spatial Profiler (DSP). We demonstrate profiling of 1600+ immuno-oncology targets in the tumor, microenvironment, and immune compartments of archival FFPE tissue sections, coupled to downstream Next Generation Sequencing (NGS) readout to enable high-throughput workflows. High-plex spatial RNA molecular profiling with GeoMx CTA was performed as follows:
1. Photocleavable DNA oligonucleotides tags were coupled to 8000+ in situ hybridization probes targeting 1600+ genes. These reagents were allowed to bind targets directly on slide-mounted FFPE tissue sections.
2. ROIs were identified and selected using GeoMx DSP, and ROI-specific oligonucleotide tags were released using ultraviolet exposure.
3. Released oligonucleotide tags from each ROI were collected and deposited into designated wells on a microtiter plate, allowing well indexing of each ROI during NGS library preparation.
4. After indexing, the entire plate was pooled into a single tube for purification and then sequenced on an Illumina instrument.
5. NGS reads were processed into digital counts and mapped back to each ROI, generating a map of transcript activity within the tissue architecture.
We compared data from experiments in which bulk RNA-seq and GeoMx DSP using the CTA Panel were performed on the same samples. Overall, we found good correlation between pseudo-bulk GeoMx CTA (sum of ROIs) and RNA-seq from the same tissue specimen. Individually, however, each ROI showed a distinct expression pattern from bulk, and ROI expression patterns clustered based on similar tissue morphology. Importantly, GeoMx CTA was able to detect a higher number of genes with low expression within the microenvironment and immune spatial compartment compared to bulk RNA-seq, providing a detailed look at the anti-tumor immune response. Lastly, we profiled similar tissues using a novel 18000+ gene whole transcriptome panel and found further enrichment of low-expressers relative to RNA-seq, revealing novel spatial biology previously masked by bulk assays. Together, these data demonstrate that GeoMx offers high sensitivity for genome-scale expression profiling while preserving critical information about tissue architecture. GeoMx DSP technology is for Research Use Only and not for use in diagnostic procedures.
Citation Format: Margaret L. Hoang, Michelle Kriner, Zoey Zhou, Zach Norgaard, Kristina Sorg, Chris Merritt, Erin Piazza, Marty Ross, Robin Fropf, Nileshi Saraf, Patrick Danaher, Michael Rhodes, Joseph Beechem. Spatially-resolved in situ expression profiling using the GeoMx™ Cancer Transcriptome Atlas panel in FFPE tissue [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1364.
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Affiliation(s)
| | | | - Zoey Zhou
- NanoString Technologies, Inc., Seattle, WA
| | | | | | | | | | - Marty Ross
- NanoString Technologies, Inc., Seattle, WA
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Norgaard Z, Zollinger D, Reeves J, Zhou Z, Kriner M, McKay-Fleisch J, Bahrami A, Warren S, Church S, Merritt C, Hoang M, Beechem J. Abstract 2825: High-plex, spatial RNA profiling of tumor infiltrating leukocytes and the tumor microenvironment of microsatellite instable colorectal cancer using GeoMx™ Digital Spatial Profiler. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immunotherapeutic intervention has revolutionized cancer treatment but improved understanding of immunomodulation in tumors is still necessary to expand the reach of these therapies and identify rational combination approaches. An important aspect of this process will be characterizing the molecular differences between tumor-infiltrating leukocytes (TILs) and stromal leukocytes (non-TILs) surrounding the same tissues. Most studies to date have focused on dissociated tissues, which means identifying the origin of the profiled leukocytes is only possible with post-hoc inference. High-plex profiling that retains spatial orientation has proven difficult in fixed tissues, preventing direct understanding of TIL localization beyond a handful of pre-selected targets. To explore the transcriptional profile of TILs in situ, we leveraged a high-plex (1,400+ gene) mRNA panel for the GeoMxTM Digital Spatial Profiler (DSP) to profile microsatellite instable (MSI) colorectal cancer (CRC) samples noted to have a high abundance of CD3+ TILs by 4-color immunofluorescence (IF).
In this study, more than 5,000 unique probes (3 to 10 probes per target mRNA) with coupled photocleavable oligonucleotide tags were hybridized to formalin-fixed paraffin-embedded (FFPE) tissue sections from these CRC samples. Regions of interest were selected inside (n = 6, per tumor) and outside (n = 6, per tumor) the tumor invasive margin focusing on tumor or stromal regions with high numbers of CD3+ cells. Within each region of interest, we created a custom segmentation strategy to specifically illuminate CD3+ cells, and then sequentially illuminate regions neighboring those cells. These additional custom masks (n = 47) were defined by extending multiple contours around the initially selected TILs and non-TILs to determine differences in the local environment of each population.
Collected photocleaved oligonucleotide tags were sequenced using the GeoMxTM NGS workflow. Targets included in the 1,400+ gene panel represent immune cell markers, checkpoint molecules, cytokines and chemokines, canonical cancer pathways, and biological signatures. We found that regions neighboring TILs express higher levels of known oncogenic pathways and stromal regions neighboring non-TILs were noted to have higher expression of ECM genes, confirming the specificity of the profiling approach. Furthermore, we found that TILs specifically up-regulate expression of cytolytic pathway genes, as well as several coinhibitory and costimulatory checkpoint genes. We also observe dysregulation of members of the adenosine metabolism pathway within the tumor regions profiled and TILs, but not in regions adjacent to the tumor itself. Together, our results demonstrate the feasibility of profiling specific cell populations with a high plex mRNA panel in situ in FFPE tissue, thus enabling pathway level differential expression analyses and exploration of key interactions between neighboring cell types while retaining their spatial context. For research use only. Not for use in diagnostic procedures.
Citation Format: Zachary Norgaard, Dan Zollinger, Jason Reeves, Zoey Zhou, Michelle Kriner, Jill McKay-Fleisch, Arya Bahrami, Sarah Warren, Sarah Church, Chris Merritt, Margaret Hoang, Joseph Beechem. High-plex, spatial RNA profiling of tumor infiltrating leukocytes and the tumor microenvironment of microsatellite instable colorectal cancer using GeoMx™ Digital Spatial Profiler [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2825.
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Kiuru M, Kriner M, Zhu G, Terrell J, Hoang M, Beechem J, McPherson J. 691 Identification of RNA biomarker candidates in melanocytic tumors using digital spatial profiling. J Invest Dermatol 2020. [DOI: 10.1016/j.jid.2020.03.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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McNamara KL, Caswell-Jin JL, Ma Z, Zoeller JJ, Kriner M, Zhou Z, Reeves J, Hoang M, Beechem J, Slamon DJ, Press MF, Brugge J, Hurvitz SA, Curtis C. Abstract P4-10-12: Characterizing the tumor and immune microenvironment through treatment to predict response to neoadjuvant HER2-targeted therapy using the Digital Spatial Profiler. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p4-10-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: While introduction of HER2-targeted therapies has dramatically improved outcomes for patients with HER2-positive disease, even with the addition of HER2-targeted agents, 40-50% of patients do not achieve a pCR (pathologic complete response) following neoadjuvant therapy implying that clinical or molecular differences may be present in responders versus non-responders. While recent bulk expression studies have identified several biomarkers associated with response to HER2-targeted therapies in the neoadjuvant setting, these studies are limited in their ability to assign observed changes to specific geographic or phenotypic cell populations, such as the malignant tumor core or the surrounding microenvironment.
Methods: Here we used the Digital Spatial Profiler (DSP, NanoString Technologies, Inc.) to profile regions-of-interest containing pancytokeratin (panCK)+ tumor cells and infiltrated immune cells that are co-localized with the tumor cells. Using this technology, we assayed archival tissue from 28 patients with HER2-positive breast cancer from the TRIO-B07 (NCT00769470) clinical trial, who were treated with trastuzumab, lapatinib, or both, followed by standard chemotherapy plus HER2-targeted therapy. Tissue specimens were collected from the pre-treatment diagnostic biopsy (Baseline) and after one cycle of targeted therapy (Runin). To study regional heterogeneity, we selected an average of four panCK-enriched tissue regions from each sample. Using DSP, we performed multiplexed quantification of 38 tumor and immune protein markers and 96 RNA markers on the selected tissue regions and compared our findings to bulk mRNA expression data from the same cohort.
Results: Within the panCK-enriched regions, DSP revealed significant treatment-associated decreases in HER2 protein levels and the downstream PI3K-Akt signaling pathway in Runin compared to Baseline samples. In tandem, we observed a significant increase in infiltrating leukocytes, with CD45, a pan-leukocyte marker, and CD8, a marker for T cells that mediate tumor cell killing, showing the most dramatic changes. These changes in Runin compared to Baseline were more significant in the subset of cases that achieved a pCR versus those that do not, independent of ER status. Comparison of Runin samples to matched Baseline samples from the same patient enabled improved prediction of patient outcome (pCR) compared with analysis of a single timepoint alone. We also found that the DSP panCK enrichment strategy captures additional signal not observed in bulk expression data. For instance, using bulk expression, a decrease in HER2 RNA levels between Baseline and Runin was evident but there was no difference in the degree of decrease in HER2 mRNA between pCR and no pCR cases. Using DSP, we observed that the significant decrease in HER2 levels at Runin is more pronounced in cases that achieved a pCR. Across both tumor and immune markers, regional heterogeneity increased at Runin compared to Baseline.
Conclusions: In this study, we used DSP and a panCK enrichment strategy to retrospectively delineate the changes that occurred in tumor cells and co-localized immune cells during HER2-targeted therapy. In comparison to traditional or multiplexed IHC, DSP allows for simultaneous profiling of a large number of markers, enabling the characterization of multiple cancer signaling pathways and immune markers on a single tissue specimen. This study demonstrates the utility of pancytokeratin-enriched spatial proteomic profiling to characterize treatment-associated changes and identify predictive biomarkers.
NanoString’s Digital Spatial Profiler is for Research Use Only. Not to be used for diagnostic procedures.
Citation Format: Katherine Lee McNamara, Jennifer L. Caswell-Jin, Zhicheng Ma, Jason J. Zoeller, Michelle Kriner, Zoey Zhou, Jason Reeves, Margaret Hoang, Joseph Beechem, Dennis J. Slamon, Michael F. Press, Joan Brugge, Sara A. Hurvitz, Christina Curtis. Characterizing the tumor and immune microenvironment through treatment to predict response to neoadjuvant HER2-targeted therapy using the Digital Spatial Profiler [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-12.
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Affiliation(s)
- Katherine Lee McNamara
- 1Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Jennifer L. Caswell-Jin
- 1Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Zhicheng Ma
- 1Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | - Zoey Zhou
- 3NanoString Technologies, Seattle, WA
| | | | | | | | - Dennis J. Slamon
- 4Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Michael F. Press
- 5Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Joan Brugge
- 2Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Sara A. Hurvitz
- 4Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Christina Curtis
- 1Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA
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Hoang M, Zhou Z, Kriner M, Sorg K, Norgaard Z, Piazza E, Merritt C, Kim D, Beechem J. Abstract 753: In situ RNA expression profiling of 1600+ immuno-oncology targets in FFPE tissue using NanoString GeoMx™Digital Spatial Profiler. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Clinical specimens including formalin-fixed, paraffin embedded (FFPE) tumor sections preserve spatial and molecular information of tumor cells and their surrounding microenvironment. This valuable spatial information is loss with bulk RNA-seq, the most prevalent method for gene expression profiling of archival FFPE samples. In contrast, the NanoString GeoMx™ Digital Spatial Profiler (DSP) is a high multiplexing assay that can profile thousands of RNAs from user selectable regions of interest (ROIs) in FFPE sections. Here we introduce a 1600+ gene panel of tumor, stroma, and immune cell-specific content derived from NanoString nCounter® PanCancer series. We compare RNA profiling using our 1600+ immune-oncology panel to the RNA-seq methodology in FFPE samples. DSP RNA in situ probes are photocleavable oligonucleotides tags coupled to hybridization sequences that bind to mRNA transcripts in the FFPE tissue section. We gridded 96 ROIs upon the FFPE section, photocleaved oligonucleotide tags from each ROI were collected and prepared into sequencing libraries with our NGS readout workflow. After sequencing, reads were charted back to each ROI in the tissue section, generating a map of transcript activity within the tissue. We found high concordance between “bulk” DSP RNA (counts from all 96 gridded ROIs) and RNA-seq from the same FFPE block. Individually, however, each ROI showed different expression patterns than bulk and ROI expression patterns clustered based on similar tissue morphology. We further profiled the tumor and microenvironment compartments from multiple FFPE cancer tissues, comparing our 1600+ RNA expression profile to RNA-seq. DSP was able to detect a higher number of genes with low expression within each spatial compartment compared to bulk RNA-seq. These data demonstrate that DSP offers unparalleled sensitivity for large-scale gene expression while preserving critical information about tissue architecture. GeoMx™ DSP technology is for Research Use Only and not for use in diagnostic procedures.
Citation Format: Margaret Hoang, Zoey Zhou, Michelle Kriner, Kristina Sorg, Zach Norgaard, Erin Piazza, Chris Merritt, Dae Kim, Joseph Beechem. In situ RNA expression profiling of 1600+ immuno-oncology targets in FFPE tissue using NanoString GeoMx™Digital Spatial Profiler [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 753.
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Affiliation(s)
| | - Zoey Zhou
- NanoString Technologies, Seattle, WA
| | | | | | | | | | | | - Dae Kim
- NanoString Technologies, Seattle, WA
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Anckaert E, Jank A, Petzold J, Rohsmann F, Paris R, Renggli M, Schönfeld K, Schiettecatte J, Kriner M. Extensive monitoring of the natural menstrual cycle using the serum biomarkers luteinising hormone, estradiol and progesterone. Clin Chim Acta 2019. [DOI: 10.1016/j.cca.2019.03.701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kümmel S, Eggemann H, Lüftner D, Gebauer N, Bühler H, Schaller G, Schmid P, Kreienberg R, Emons G, Kriner M, Elling D, Blohmer JU, Thomas A. Significant Changes in Circulating Plasma Levels of IGF1 and IGFBP3 after Conventional or Dose-Intensified Adjuvant Treatment of Breast Cancer Patients with one to three Positive Lymph Nodes. Int J Biol Markers 2018; 22:186-93. [DOI: 10.1177/172460080702200304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The insulin-like growth factor 1 (IGF1) and its binding protein IGFBP3 (insulin-like growth factor binding protein 3) play a pivotal role during the growth and development of tissues. The purpose of this study was to evaluate the influence of anthracycline- and taxane-containing adjuvant chemotherapy in breast cancer patients on the circulating plasma levels of IGF1 and its main binding protein, IGFBP3. This investigation was part of a prospective randomized phase III study in which breast cancer patients were treated with either conventional or dose-intensified adjuvant chemotherapy. The factors were quantified in the plasma of 151 patients with a commercially available sandwich enzyme immunoassay. Before therapy, both parameters were within the normal range in most patients (n=145 and n=144). After therapy, both factors had increased significantly by 29% (IGF1) and 19% (IGFBP3), with the highest increase being observed in the dose-intensified group. Correlations with patient and tumor characteristics revealed a relatively higher increase in both parameters in premenopausal patients, patients with lower-grade tumors, more positive lymph nodes, larger tumor volume, and positive hormone receptor status. No correlation was found with the HER2 expression of the tumors.
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Affiliation(s)
- S. Kümmel
- Department of Obstetrics and Gynecology, University of Duisburg-Essen, Essen
| | - H. Eggemann
- Department of Obstetrics and Gynecology Otto von Guericke University Magdeburg, Magdeburg
| | - D. Lüftner
- Department of Hematology and Oncology, University Medicine Berlin, Campus Charité Mitte, Berlin
| | - N. Gebauer
- Department of Obstetrics and Gynecology, University of Duisburg-Essen, Essen
| | - H. Bühler
- Ruhr University Bochum, Bochum - Germany
| | | | - P. Schmid
- Charing Cross and Hammersmith Hospital, Imperial College, London - United Kingdom
| | - R. Kreienberg
- Department of Obstetrics and Gynecology, University Ulm, Ulm
| | - G. Emons
- Department of Obstetrics and Gynecology, Georg-august University Göttingen, Göttingen
| | - M. Kriner
- Department of Medical Statistics and Epidemiology, Technical University Munich, Munich
| | - D. Elling
- Department of Obstetrics and Gynecology, Berlin-Lichtenberg Hospital, Berlin
| | - J.-U. Blohmer
- Department of Obstetrics and Gynecology, University of Duisburg-Essen, Essen
| | - A. Thomas
- Department of Obstetrics and Gynecology, University of Duisburg-Essen, Essen
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Schneider A, Wilhelm D, Schneider M, Schuster T, Kriner M, Leuxner C, Can S, Fiolka A, Spanfellner B, Sitou W, Feussner H. Laparoscopic Cholecystectomy - a Standardized Routine Laparoscopic Procedure: Is it Possible to Predict the Duration of an Operation? Journal of Healthcare Engineering 2011. [DOI: 10.1260/2040-2295.2.2.259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Wagner KJ, Valet M, Kochs EF, Kriner M, Tölle TR, Sprenger T. The mu-opioid receptor agonist remifentanil induces acute dysphoria irrespective of its analgesic properties. J Psychopharmacol 2010; 24:355-61. [PMID: 18801832 DOI: 10.1177/0269881108095811] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mu-opioidergic agonists are believed to induce euphoria, whereas kappa-agonists are thought to lead to dysphoria. Our study investigated mood effects of remifentanil, a mu-receptor opioid agonist, in healthy male volunteers. Moreover, we examined interactions between mood and pain. Three conditions were investigated in 21 volunteers: saline, 0.05 and 0.15 microg kg(-1) min(- 1) remifentanil. Each condition was investigated during non-painful heat and during painful heat stimulation. Mood was measured with the von Zerssen's mood scale (Bf-S score) and pain intensity using a Visual Analogue Scale (VAS). High Bf-S scores are reflecting discontent and dysphoria. Changes were tested for significance using a linear mixed model approach. Remifentanil significantly increased Bf-S scores during painful heat (+91.4%), indicating a negative mood effect, although it reduced VAS scores of painful heat intensity (-49.0%). The type of sensory stimulation (non-painful versus painful) had no effect on mood. There was no interaction between remifentanil dose and type of stimulation. Our results provide evidence for negative mood effects of remifentanil. These effects occur with and without pain. Taken into account that remifentanil reduces pain, one could have expected analgesia-related amelioration of mood instead. In clinical practice, these remifentanil effects should be considered and a comedication might be advisable.
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Affiliation(s)
- K J Wagner
- Klinik für Anaesthesiologie, Technische Universität München, Klinikum rechts der Isar, München, Germany.
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14
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Paul J, Sagstetter A, Kriner M, Imhoff AB, Spang J, Hinterwimmer S. Donor-site morbidity after osteochondral autologous transplantation for lesions of the talus. J Bone Joint Surg Am 2009; 91:1683-8. [PMID: 19571091 DOI: 10.2106/jbjs.h.00429] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Autologous osteochondral transplantation is accepted as one of the major treatment options for cartilage defects of the talus. One disadvantage of this technique is the need to harvest a donor graft from a normal knee. The potentially detrimental effect of graft harvest on knee function remains unclear. METHODS Two hundred patients who had transplantation of an autologous osteochondral graft obtained from an asymptomatic knee for the treatment of an osteochondral defect of the talus were evaluated. Of the 200 patients, 112 were followed for a minimum of two years (mean duration of follow-up, fifty-five months). The WOMAC (Western Ontario and McMaster Universities Osteoarthritis Index) and the Lysholm score were used to assess functional outcome. Variables that were examined included the number of grafts, total size of the harvested cylinders, patient age, body mass index, and overall satisfaction of the patient with the result of the procedure at the knee. A multiple linear regression analysis was utilized to determine the influence of each parameter on the WOMAC and Lysholm scores. In addition, the Lysholm scores for the entire patient group were reviewed to determine how long after the index surgery clinical improvement ceased. RESULTS The mean postoperative WOMAC score (and standard deviation) for the 112 patients who had been followed for a minimum of two years was 5.5% +/- 0.1%, and the mean postoperative Lysholm score was 89 +/- 17 points. The number of grafts, the size of the transplanted cylinders, and patient age did not influence either the Lysholm or the WOMAC score. A higher body mass index and lower general satisfaction ratings did negatively influence the Lysholm and WOMAC scores. Gradual clinical improvement, as measured with the Lysholm score for all 200 study subjects, continued throughout the postoperative period. CONCLUSIONS Donor-site morbidity of a knee from which a graft has been harvested can potentially lead to functional impairment. In our study, the functional outcome of the knee was not affected by the number of donor grafts, the size of the donor grafts, or the age of the patient. Surgeons performing osteochondral transplantations and harvesting autografts from the knee should be aware of the potentially negative effect of a higher body mass index on clinical outcomes after surgery.
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Affiliation(s)
- J Paul
- Abteilung für Sportorthopädie, Klinikum rechts der Isar, TU München, Connollystrasse 32, 80809 München, Germany.
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15
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Sprenger T, Valet M, Kochs E, Kriner M, Tölle T, Wagner K. Remifentanil induziert eine akute Dysphorie unabhängig von seiner analgetischen Wirksamkeit. Akt Neurol 2008. [DOI: 10.1055/s-0028-1086935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Matevossian E, Novotny A, Knebel C, Brill T, Werner M, Sinicina I, Kriner M, Stangl M, Thorban S, Hüser N. The Effect of Selective Inhibition of Inducible Nitric Oxide Synthase on Cytochrome P450 After Liver Transplantation in a Rat Model. Transplant Proc 2008; 40:983-5. [DOI: 10.1016/j.transproceed.2008.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Thorban S, Hüser N, Novotny A, Raggi MC, Matevossian E, Schwarznau A, Assfalg V, Kriner M, Stangl M. High-risk constellation in living renal transplantation. Transplant Proc 2007; 39:505-8. [PMID: 17362768 DOI: 10.1016/j.transproceed.2007.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is only limited information about recipient risk factors for graft survival in living- donor kidney transplantation. This study aimed to investigate prognostic factors and their impact on living-related and unrelated renal transplant recipients. From October 2000 until October 2004, 81 adult living-related renal transplantations were performed at our institution. Using multivariate analysis, the association of the following variables with kidney graft outcome was studied: ages of donors and recipients, gender and body mass index, cold and warm ischemia, HLA mismatches, identity and compatibility of blood group, duration of dialysis, cytomegalovirus (CMV) status, recipient original disease, surgical and general complications, and status of retransplantation. Multivariate analysis revealed significant reduction of graft function and graft survival in recipients with retransplantation, more than 4 mismatches, and a high body mass index. Thus, living-donor kidney transplantation can be regarded as a safe and standardized operation relating to surgical technique, but further consideration of the recipient body mass index and the number of mismatches are recommended during the preparation for transplantation.
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Affiliation(s)
- S Thorban
- Division of Transplantation, Technical University, Munich, Department of Surgery, Munich, Germany.
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Abstract
BACKGROUND Preoperative autologous blood donation is an effective method to reduce allogeneic transfusion requirement. However, this method is only rarely utilized in cardiac surgery. Besides economic concerns one essential argument against predonation is the lack of sufficient time due to the short waiting lists. The aim of the present study was to investigate the efficacy of autologous predonation to reduce allogeneic blood transfusion in routine cardiac surgery on a center without longer preoperative waiting lists. PATIENTS AND METHODS A total of 2,626 cardiac surgery patients were included. Primary endpoint of the study was the perioperative incidence of allogeneic packed cell transfusion. If time between diagnosis and admission to the hospital was >10 days, predonation was offered to the patients. Data were stratified for preoperative risk score. Logistic and linear regression analysis tested the influence of different variables on the incidence of allogeneic blood transfusion and the total amount of allogeneic blood. RESULTS Of all patients 267 (11.2%) underwent predonation. The incidence of allogeneic packed cell transfusion was reduced from 53% to 19% by autologous predonation (p<0.001). The total amount of allogeneic blood transfused was significantly different between the groups (2.2+/-4.2 vs. 0.84+/-6.3 units; p<0.001). DISCUSSION Autologous predonation in cardiac surgery was effective in reducing blood transfusions even in the absence of longer preoperative waiting times. It is a safe and effective method to minimize blood transfusion in cardiac surgery.
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Affiliation(s)
- W Dietrich
- Institut für Anästhesiologie, Deutsches Herzzentrum, Klinik an der Technischen Universität München, Lazarettstr. 36, 80636, München.
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19
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Hull ME, Kriner M, Schneider E, Maiman M. Ovarian cancer after successful ovulation induction: a case report. J Reprod Med 1996; 41:52-4. [PMID: 8855076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Questions have been raised regarding the potential association of ovulation-inducing drugs and ovarian cancer. Worldwide there have been 13 cases of ovarian carcinoma reported to occur in women previously treated with ovulation-inducing drugs (clomiphene citrate and/or gonadotropins). CASE A 40-year-old woman complained of secondary infertility. She conceived after five cycles of human menopausal gonadotropins with intrauterine insemination. Eight months after cesarean delivery, she presented with right lower quadrant pain and a right adnexal mass. At exploratory laparotomy the patient was found to have a poorly differentiated papillary serous carcinoma of the ovary. CONCLUSION Ovarian carcinoma developed within 18 months of exposure to ovulation-inducing agents, human menopausal gonadotropins. It would be prudent to gather a registry of cases to assess the risk associated with human menopausal gonadotropins with or without gonadotropin-releasing hormone analogs.
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Affiliation(s)
- M E Hull
- Division of Reproductive Endocrinology, State University of New York at Stony Brook, USA
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