Abstract 5626: Multiomic spatial profiling of the tumor immune microenvironment at single cell resolution

Background: It has been well established that the tumor microenvironment (TME), which comprises cancer cells, stromal cells, and surrounding extracellular matrix, plays a critical role in cancer development, progression, and control. The immunological components within tumors, known as the tumor immune microenvironment (TiME), have also been implicated in tumor development, recurrence, and metastasis. Effective strategies for cancer immunotherapies will require a deep understanding of the factors that shape both the TME and TiME. Here, we describe a spatial multiomics approach that utilizes RNAscope™ ISH technology paired with high-plex whole-slide spatial phenotyping with the PhenoCycler™-Fusion platform. This two-step approach is compatible with human FFPE tissues and enables researchers to characterize the spatial biology of the TiME more accurately by detecting RNA and protein markers on serial sections. The resulting multiomic data more accurately reveal the interplay between TME and TiME by giving insight into cell lineages, surrounding structures, as well as secreted chemokines and cytokines that exist within the TME ecosystem.

Methods: We performed ultrahigh-plex spatial phenotyping on the PhenoCycler-Fusion on FFPE tumor tissue sections, using an antibody panel that is designed for immune cell phenotyping, evaluation of immune contexture and proliferation across the TME. Using serial sections from the same tissue blocks, we then ran the RNAscope HiPlex v2 assay automated on the PhenoCycler-Fusion system. This assay consisted of a 12-plex immuno-oncology panel of RNA target probes, which were selected to detect macrophages, chemokines, and cytokines within tumors. We used Phenoplex software to analyze the protein and RNA datasets and to compute cell phenotypes and spatial associations.

Results and Conclusions: In this proof-of-concept study, we demonstrate the utility of multiomic spatial profiling on the PhenoCycler-Fusion platform. Analysis of the resulting multiplex imaging data not only revealed the structural organization of cells within the TME, but also activation states of immune cells. Together, this information provides a more complete functional map of immune cells within the TME and TiME and thereby enriches our understanding of tumor biology that may be deterministic of immunotherapy responsiveness. This work paves the way for future research that will rely on deep spatial phenotyping with protein biomarkers coupled with accurate quantification of the expression of regulatory cytokines, chemokines, growth factors, or non-coding RNAs that only RNA probes can detect.

Citation Format: Niyati Jhaveri, HaYeun Ji, Anushka Dikshit, Jessica Yuan, Emerald Doolittle, Steve Zhou, Maithreyan Srinivasan, Bassem B. Cheikh, Fabian Schneider, James Mansfield, Julia Kennedy-Darling, Oliver Braubach. Multiomic spatial profiling of the tumor immune microenvironment at single cell resolution. [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 5626.

49 Highly multiplexed detection of critical immune checkpoints and immune cell subtypes in cancerous FFPE tissues using CODEX

Background

There is growing consensus that spatial biology is the key to unlocking the underlying mechanisms of cancer immunotherapy and to predicting patient outcomes. Indeed, a recent example using the Akoya Phenoptics technology revealed a unique phenotypic signature of CD8/Foxp3 positive cells embedded within the tumor microenvironment of patients that responded favorably to PD-1 checkpoint inhibition.1 In this case, the combination of both multiparameter and spatial readouts was required to correlate significantly with outcome. As the number of treatment options expands and knowledge regarding cell types that contribute to treatment mechanisms improves, so too do the number of markers required to analyze responses that enable discovery of new signatures.

Methods

Here, we present data from the analysis of human FFPE cancer tissues using an expanded CODEX antibody catalog targeting a variety of immune, immune checkpoint and transcription factors. CODEX enables the highly multiplexed detection of more than 40 targets within the same tissue sample, with single cell resolution and without degradation of the sample.

Results

Our expanded target list enables detection of key macrophage populations, T and B cell subtypes, granulocytes, dendritic cells, natural killer cells, stromal, tumor and epithelial cells. Additionally, the activation state of these immune and tumor cell types can be measured through detection of key immune checkpoints, including PD-1 and PD-L1. Through the addition of these critical markers, both cells known to contribute to treatment outcome and new biomarker signatures can be identified.

Conclusions

Continued expansion of spatial biology discovery capabilities will be critical to continuing to improve patient outcomes and to develop new treatment options of solid tumors using cancer immunotherapies.

Reference

Berry S, Taube J, et al. Analysis of multispectral imaging with the AstroPath platform informs efficacy of PD-1 blockade. Science. 2021; 372: 6547.

CODEX multiplexed tissue imaging with DNA-conjugated antibodies

Advances in multiplexed imaging technologies have drastically improved our ability to characterize healthy and diseased tissues at the single-cell level. Co-detection by indexing (CODEX) relies on DNA-conjugated antibodies and the cyclic addition and removal of complementary fluorescently labeled DNA probes and has been used so far to simultaneously visualize up to 60 markers in situ. CODEX enables a deep view into the single-cell spatial relationships in tissues and is intended to spur discovery in developmental biology, disease and therapeutic design. Herein, we provide optimized protocols for conjugating purified antibodies to DNA oligonucleotides, validating the conjugation by CODEX staining and executing the CODEX multicycle imaging procedure for both formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissues. In addition, we describe basic image processing and data analysis procedures. We apply this approach to an FFPE human tonsil multicycle experiment. The hands-on experimental time for antibody conjugation is ~4.5 h, validation of DNA-conjugated antibodies with CODEX staining takes ~6.5 h and preparation for a CODEX multicycle experiment takes ~8 h. The multicycle imaging and data analysis time depends on the tissue size, number of markers in the panel and computational complexity.

Abstract 387: Analysis of FFPE human tumor tissues using CODEX with signal amplification

Analysis of FFPE human tumor tissues using CODEX with signal amplification

Characterizing the complexities of the tumor microenvironment is fundamental to understanding disease mechanisms. The spatial relationships between infiltrating immune cells and the remodeling of the cellular matrix is widely recognized as a key component to defining tumor heterogeneity. Current methodologies for studying cells within the context of tissue architecture, like traditional immunofluorescence (IF) and immunohistochemistry (IHC), are limiting–allowing the assessment of only a few parameters at a time. The CODEX technology has overcome this limitation through a DNA-based labeling strategy, involving adding and removing dye-labeled oligonucleotides (reporters) across multiple cycles to oligonucleotide-labeled antibodies. In this manner, tens of markers can be analyzed on the same tissue. Additionally, CODEX interfaces with existing inverted microscopes and provides a cost-effective, fully automated platform for highly multiplexed imaging. Recently, we expanded our workflow to amplify the fluorescent signal intensities of low expressing biomarkers by combining Tyramide Signal Amplification (TSA) with CODEX. This approach is associated with key markers used to analyze the tumor microenvironment, including PD-L1 and PD-1. We demonstrated signal amplification of more than 50X compared with non-amplified signal. Here, we present the analysis of CODEX data for a panel of over 20 biomarkers on human FFPE tissue including signal amplification of PD-L1, PD-1 and foxp3. Through amplification of key markers as the final cycle of a CODEX experiment, low expression can be measured and used to identify key cell types, including Treg cells and PD-L1 positive tumor and stromal regions.

Citation Format: Sejal Mistry, Gajalakshmi Dakshinamoorthy, Jessica Yuan, Pieter Noordam, Joseph Kim, Won-Mean Lee, Julia Kennedy-Darling. Analysis of FFPE human tumor tissues using CODEX with signal amplification [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 387.

Abstract 1654: Highly multiplexed analysis of FFPE breast tissues using the codex technology

Highly multiplexed imaging has emerged as a critical tool in understanding the complexities of the tumor microenvironment. This technology enables detection of tens of markers within the same tissue specimen, thereby allowing for key cell identification, quantification and spatial localization. These measurements can in turn provide insights into disease mechanisms and effective treatment modalities. In particular, with the high incidence of breast cancer and the need for early diagnosis and precise treatment regimens, highly multiplexed imaging could improve our understanding of this disease and provide the necessary data for improvements to patient health. Here, we demonstrate the development of a breast cancer specific CODEX panel for the measurement of more than 30 specific markers. The CODEX (Co-Detection by indEXing) platform enables detection of tens of markers within the same tissue specimen through a DNA-based tagging approach, whereby antibodies are labeled with specific oligonucleotide tags (barcodes) and dye-oligonucleotides (reporters) are iteratively hybridized and dehybridized across multiple cycles. This process is completely automated through the CODEX instrument in combination with existing fluorescent microscopes.

Using FFPE Human breast cancer tissues at different stages as well as normal FFPE Human breast tissue utilizing the CODEX platform, data was generated for 30+ different biomarkers. This antibody panel was designed to detect cancer cells as well as non-malignant cells as part of tumor microenvironment to enable a better understanding of communication between the cells. The CODEX generated data was analyzed using the CODEX software suite to identify key cell types and analyze the spatial association between them. Upon analysis of data obtained, it was found that the biomarkers expression between the three samples were distinctly different. Using the CODEX technology, we were able to identify and classify key cell types and map the spatial localization of more than 20 key cell types.

Citation Format: Nadezhda Nikulina, Oliver Braubach, Sayantani Basak, Maria Elena Gallina, Won-Mean Lee, Joseph Kim, Cassandra Hempel, Edek Williams, Olive Shang, Ben Cheung, Julia Kennedy-Darling. Highly multiplexed analysis of FFPE breast tissues using the codex technology [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 1654.

Abstract 490: Highly multiplexed single-cell spatial analysis of tissue specimens using CODEX

Characterizing the complexities of the tumor microenvironment is elemental to understanding disease mechanisms. The spatial relationships between infiltrating immune cells and the remodeling of the cellular matrix is widely recognized as a key component to defining tumor heterogeneity. Current methodologies for analyzing the spatial dimension in tissues, like traditional immunofluorescence (IF) and immunohistochemistry (IHC), are limited to a few parameters at a time, restricting the scope of identifiable cells. Conversely, single-cell technologies like mass cytometry and NGS-based tools provide multiplexing capabilities, but at the expense of the associated spatial information. Here, we present a novel multiplexed imaging technology, termed CODEX, (CO-Detection by indEXing) that combines the high parameter capabilities of single-cell methodologies with the associated spatial dimension. The CODEX technology involves labeling antibodies with oligonucleotide-based Barcodes followed by a single staining step. Over 50 parameters are measured within a single tissue through fully-automated, iterative cycles of adding and removing corresponding dye-conjugated Reporters. Unlike other cyclic IF approaches involving multiple antibody staining and stripping steps, the CODEX platform involves a single initial staining step and subsequent gentle and relatively fast manipulation of the tissue thereafter. This provides a faster workflow and prevents tissue degradation. Other multiplexed imaging technologies, including imaging cytometry and MIBI, require expensive equipment precluding their routine use across various labs. The CODEX technology, developed by Akoya, is comprised of a fluidics instrument that interfaces with existing microscope hardware, as suite of reagents and associated control and analysis software. Over 100 antibody clones have been validated for this platform with more than ten tissue types analyzed, including both FFPE and fresh-frozen from human and mouse samples. The CODEX technology can be used to ascertain complex cellular niches and spatial associations between multiple cell types based on the staining pattern of more than 50 parameters. The CODEX viewer software package enables users to interact with both raw data and cell annotated tissue maps to determine the underlying spatial relationships within each dataset. CODEX data from various normal and cancer tissue types is shown here with corresponding single-cell analysis of key tissue features. Overall, the CODEX platform is an accessible and versatile technology for high parameter, spatial profiling of tissue specimens.

Citation Format: Gajalakshmi Dakshinamoorthy, Jaskirat Singh, Joseph Kim, Nadya Nikulina, Roya Bashier, Sejal Mistry, Maria E. Gallina, Atri Choksi, Meenu Perera, Ashley Wilson, Julia Kennedy-Darling. Highly multiplexed single-cell spatial analysis of tissue specimens using CODEX [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 490.

Highly multiplexed single-cell spatial analysis of tissue specimens using CODEX

Characterizing the complexities of the tumor microenvironment is elemental to understanding disease mechanisms. The spatial relationships between infiltrating immune cells and the remodeling of the cellular matrix is widely recognized as a key component to defining tumor heterogeneity. Here, we present a novel multiplexed imaging technology, termed CODEX, (CO-Detection by indEXing) that combines the high parameter capabilities of single-cell methodologies with the associated spatial dimension. Over 50 parameters are measured within a single tissue through fully-automated, iterative cycles of adding and removing dye-conjugated Reporters to corresponding nucleic acid based Barcodes. The CODEX technology, developed by Akoya, is comprised of a fluidics instrument that interfaces with existing microscope hardware, a suite of reagents and associated control and analysis software. Over 100 antibody clones have been validated for this platform with more than ten tissue types analyzed, including both FFPE and fresh-frozen from human and mouse samples. The CODEX technology can be used to ascertain complex cellular niches and spatial associations between multiple cell types based on their staining pattern. CODEX data from various normal and cancer tissue types are shown here with corresponding single-cell analysis of key tissue features. Overall, the CODEX platform is an accessible and versatile technology for high parameter, spatial profiling of tissue specimens.

Abstract A074: Spatially resolved deep antigen profiling of single cells in FFPE tissue samples through CODEXTM

Spatially resolved, deep antigen profiling of tissue specimens is crucial for investigating the architecture and cell diversity in complex matrices, such as the tumor microenvironment (TME). The correlation of these two parameters with the progression of a variety of pathologies, ranging from cancer to autoimmune diseases, is still vastly unknown due to the lack of technologies that enable the detection of both high content and spatial resolution. Formalin-fixed, paraffin-embedded (FFPE) tissues constitute the ideal sample for these investigations as they retain tissue morphology at room temperature for long periods of time, which is convenient and cost-effective, and are available in vast specimen archives. Akoya Biosciences, Inc., is commercializing CODEXTM (CO-Detection by indEXing), a multiparameteric imaging platform that performs the concurrent detection and quantification of dozens of antigens with single cell resolution within a tissue specimen. The CODEX platform uses a DNA-based barcode library to label antibodies and iterative cycles of adding and removing cognate dye-labeled oligonucleotides to reveal the staining pattern for a subset of the target markers per cycle. The entire data acquisition process is fully automated using the CODEX instrument, which integrates with existing microscopes. To support high-multiplexing capabilities, more than 45 different antibody clones have been screened and validated for the detection of target epitopes in human FFPE secondary lymphoid tissues for both healthy and cancerous specimens using the CODEX platform. Proof-of-concept data have also been obtained for different cancer types, including melanoma and head and neck cancer in both normal and TMA formats. Analysis software has been developed to extract meaning from CODEX datasets and is included as part of the CODEX platform. The analysis pipeline includes image drift compensation, deconvolution and segmentation to measure integrated fluorescence intensity for each cell across tens of parameters. In this manner, infiltrating lymphocytes and other immune cells have been identified within the TME. With the high multiplexing capabilities, a variety of T-cells can be identified to detect the ratios of both immunosuppressive and immune-activating subtypes. Analysis of FFPE tissues using the CODEX platform demonstrates the unparalleled opportunities for simultaneously detecting tens of antigens with single-cell resolution within a tissue specimen.

Citation Format: Maria Elena Gallina, Atri Choksi, Nadya Nikulina, Jaskirat Singh, Gajalakshmi Dakshinamoorthy, Joseph Kim, Sejal Mistry, Julia Kennedy-Darling. Spatially resolved deep antigen profiling of single cells in FFPE tissue samples through CODEXTM [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A074.

Abstract A073: CODEXTM: A novel platform for spatially resolved deep antigen profiling of single cells in tissue samples

The tumor microenvironment (TME) comprises a multitude of cell types that collectively create an immunosuppressive environment, enabling tumor growth. Understanding the spatial organization of these tissues requires a technology that can identify the presence of multiple markers and correlate it to their specific spatial location within the same tissue. Characteristics of the TME including infiltrating immune cells, angiogenesis and the presence of other nonmalignant cells influence important phenomena like drug delivery, treatment effectiveness and, ultimately, clinical outcomes. Current methodologies for analyzing the spatial dimension of tissues, e.g., traditional immunofluorescence (IF) and immunohistochemistry (IHC), are limited to measuring a few parameters simultaneously, thereby restricting the number of phenotypes that can be identified. Conversely, single-cell technologies like mass cytometry and next-generation sequencing-based tools provide multiplexing capabilities, but at the expense of the associated spatial information. Akoya Biosciences, Inc., is commercializing CODEXTM (CO-Detection by indEXing), a multiparameteric imaging platform that allows the simultaneous detection and quantification of dozens of target epitopes in single cells within a single tissue section. This innovative platform is an end-to-end solution that comprises three components: 1) the CODEX fluidics instrument, 2) a suite of specialized CODEX reagents, and 3) an analysis pipeline. The CODEX workflow involves a barcoding system such that each antibody moiety is conjugated to a proprietary tag. Panels of CODEX antibodies are used to stain tissue specimens en masse in a single step. Staining data for sets of antibodies are revealed across iterative cycles using corresponding dye-labeled barcodes. The CODEX fluidics instrument integrates with existing microscope units for a fully automated data collection process. CODEX data are processed to achieve noise reduction and analyzed at the single-cell level through a segmentation algorithm based on nuclear staining.More than 80 antibodies have been validated on the CODEX platform for analysis of human and mouse fresh-frozen and FFPE tissues. Preliminary studies on fresh-frozen tissues with developed antibodies demonstrate an unprecedented capability for revealing the spatial correlation between a variety of target epitopes. These results demonstrate the enormous potential of the CODEX technology to identify spatial correlations in the TME through highly multiplexed detection with single-cell resolution.

Citation Format: Maria Elena Gallina, Atri Choksi, Nadya Nikulina, Jaskirat Singh, Gajalakshmi Dakshinamoorthy, Joseph Kim, Sejal Mistry, Julia Kennedy-Darling. CODEXTM: A novel platform for spatially resolved deep antigen profiling of single cells in tissue samples [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A073.

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

A highly multiplexed cytometric imaging approach, termed co-detection by indexing (CODEX), is used here to create multiplexed datasets of normal and lupus (MRL/lpr) murine spleens. CODEX iteratively visualizes antibody binding events using DNA barcodes, fluorescent dNTP analogs, and an in situ polymerization-based indexing procedure. An algorithmic pipeline for single-cell antigen quantification in tightly packed tissues was developed and used to overlay well-known morphological features with de novo characterization of lymphoid tissue architecture at a single-cell and cellular neighborhood levels. We observed an unexpected, profound impact of the cellular neighborhood on the expression of protein receptors on immune cells. By comparing normal murine spleen to spleens from animals with systemic autoimmune disease (MRL/lpr), extensive and previously uncharacterized splenic cell-interaction dynamics in the healthy versus diseased state was observed. The fidelity of multiplexed spatial cytometry demonstrated here allows for quantitative systemic characterization of tissue architecture in normal and clinically aberrant samples.

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Autoimmunity analyzed by multiplexed DNA-tagged antibody staining (CODEX)

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CODEX data reveal pairwise interactions and niches changing with disease

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First tier of neighbors significantly impacts marker expression in the index cells

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Changes in splenic morphology correlate with shifts in cell frequencies

Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry

The centromere is the chromosomal locus where the kinetochore forms and is critical for ensuring proper segregation of sister chromatids during cell division. A substantial amount of effort has been devoted to understanding the characteristic features and roles of the centromere, yet some fundamental aspects of the centromere, such as the complete list of elements that define it, remain obscure. It is well-known that human centromeres include a highly repetitive class of DNA known as alpha satellite, or alphoid, DNA. We present here the first DNA-centric examination of human protein-alpha satellite interactions, employing an approach known as HyCCAPP (hybridization capture of chromatin-associated proteins for proteomics) to identify the protein components of alphoid chromatin in a human cell line. Using HyCCAPP, cross-linked alpha satellite chromatin was isolated from cell lysate, and captured proteins were analyzed via mass spectrometry. After being compared to proteins identified in control pulldown experiments, 90 proteins were identified as enriched at alphoid DNA. This list included many known centromere-binding proteins in addition to multiple novel alpha satellite-binding proteins, such as LRIF1, a heterochromatin-associated protein. The ability of HyCCAPP to reveal both known as well as novel alphoid DNA-interacting proteins highlights the validity and utility of this approach.

Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins

Comprehensive understanding of a gene's expression and regulation at the molecular level requires identification of all proteins interacting with the gene. HyCCAPP (Hybridization Capture of Chromatin Associated Proteins for Proteomics) is an approach that uses single-stranded DNA oligonucleotides to capture specific genomic sequences in cross-linked chromatin fragments and identify associated proteins by mass spectrometry. Previous studies have shown HyCCAPP to provide useful information on protein-DNA interactions, revealing the proteins associated with the GAL1-10 region in yeast. We present here a multiplexed version of HyCCAPP. Utilizing a toehold-mediated capture/release strategy, HyCCAPP is targeted to multiple genomic loci in parallel, and the protein binders at each locus are eluted in a programmable and selective fashion. Multiplexed HyCCAPP was applied to four genes (25S rDNA, ARX1, CTT1, and RPL30) in S. cerevisiae under normal and stressed conditions. Capture and release efficiencies and specificities were comparable to those obtained without multiplexing. Using mass spectrometry-based bottom-up proteomics, hundreds of proteins were discovered at each locus in each condition. Statistical analysis revealed 34-88 enriched proteins in each gene capture. Many of these proteins had expected functions, including DNA-related and ribosome biogenesis-associated activities. Multiplexed HyCCAPP provides a useful strategy for the identification of proteins interacting with specific chromatin regions.

Abstract A089: Multiparametric immunofluorescence analysis of the tumor microenvironment using CODEX

The tumor microenvironment plays a critical role in cancer progression and has implications for the efficacy of various cancer immunotherapy treatment options. Immune infiltrates within the tumor microenvironment can correlate with both positive and negative outcomes, depending upon the both the type of cancer as well as infiltrating immune cell(s). These analyses are typically performed using standard immunofluorescence and immunohistochemistry assays where no more than four simultaneous parameters can be visualized on the same tissue. Unfortunately, these tools cannot fully characterize the complexity of the tumor microenvironment due to the inherent limitations of fluorophore spectral overlap. In order to identify each type of immune and tumor cell within a single tissue, at least 40 parameters need to be measured simultaneously. We have developed a multiparametric immunofluorescence technology, entitled CODEX (Co-Detection by IndEXing), which utilizes unique DNA tags as a means of iteratively measuring more than 40 parameters within the same tissue. More than 40 human antibodies have been validated using this approach, including numerous immune markers, checkpoint ligands, tumor markers and cellular activity markers. We are currently analyzing tissue sample from patients with lung cancer. By measuring nearly 50 simultaneous markers within the same tissue, CODEX has the potential to greatly enhance our knowledge of the tumor microenvironment and more accurately define immune infiltrates at the single-cell level.

Citation Format: Julia Kennedy-Darling, Garry P. Nolan, Yury Goltsev, Nikolay Samusik. Multiparametric immunofluorescence analysis of the tumor microenvironment using CODEX [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A089.

HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae

Currently available methods for interrogating DNA-protein interactions at individual genomic loci have significant limitations, and make it difficult to work with unmodified cells or examine single-copy regions without specific antibodies. In this study, we describe a physiological application of the Hybridization Capture of Chromatin-Associated Proteins for Proteomics (HyCCAPP) methodology we have developed. Both novel and known locus-specific DNA-protein interactions were identified at the ENO2 and GAL1 promoter regions of Saccharomyces cerevisiae, and revealed subgroups of proteins present in significantly different levels at the loci in cells grown on glucose versus galactose as the carbon source. Results were validated using chromatin immunoprecipitation. Overall, our analysis demonstrates that HyCCAPP is an effective and flexible technology that does not require specific antibodies nor prior knowledge of locally occurring DNA-protein interactions and can now be used to identify changes in protein interactions at target regions in the genome in response to physiological challenges.

Multiplexed programmable release of captured DNA

Nucleic-acid hybridization is widely used for the specific capture of complementary sequences from complex samples. It is useful for both analytical methodologies, such as array hybridization (e.g. transcriptome analysis, genetic-variation analysis), and preparative strategies such as exome sequencing and sequence-specific proteome capture and analysis (PICh, HyCCAPP). It has not generally been possible to selectively elute particular captured subsequences, however, as the conditions employed for disruption of a duplex can lack the specificity needed to discriminate between different sequences. We show here that it is possible to bind and selectively release multiple sets of sequences by using toehold-mediated DNA branch migration. The strategy is illustrated for simple mixtures of oligonucleotides, for the sequence-specific capture and specific release of crosslinked yeast chromatin, and for the specific release of oligonucleotides hybridized to DNA microarrays.

Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae

DNA–protein interactions play critical roles in the control of genome expression and other fundamental processes. An essential element in understanding how these systems function is to identify their molecular components. We present here a novel strategy, Hybridization Capture of Chromatin Associated Proteins for Proteomics (HyCCAPP), to identify proteins that are interacting with any given region of the genome. This technology identifies and quantifies the proteins that are specifically interacting with a genomic region of interest by sequence-specific hybridization capture of the target region from in vivo cross-linked chromatin, followed by mass spectrometric identification and quantification of associated proteins. We demonstrate the utility of HyCCAPP by identifying proteins associated with three multicopy and one single-copy loci in yeast. In each case, a locus-specific pattern of target-associated proteins was revealed. The binding of previously unknown proteins was confirmed by ChIP in 11 of 17 cases. The identification of many previously known proteins at each locus provides strong support for the ability of HyCCAPP to correctly identify DNA-associated proteins in a sequence-specific manner, while the discovery of previously unknown proteins provides new biological insights into transcriptional and regulatory processes at the target locus.

Measuring the formaldehyde Protein-DNA cross-link reversal rate

Protein-DNA binding interactions play critical roles in important cellular processes such as gene expression, cell division, and chromosomal organization. Techniques to identify and characterize these interactions often utilize formaldehyde cross-linking for stabilization of the complexes. Advantages of formaldehyde as a cross-linking reagent include cell permeability, relatively fast cross-linking kinetics, and short cross-linker length. In addition, formaldehyde cross-links are reversible, which has the advantage of allowing complexes to be dissociated if desired but may also present a problem if undesired dissociation occurs in the course of an experiment. While the kinetics of formaldehyde cross-link formation have been well-established in numerous studies, there have been no reports of the rate of cross-link dissociation, even though it is clearly a critical variable when developing a biochemical protocol involving formaldehyde cross-linking. We present here a method for measurement of the rate of formaldehyde cross-link reversal based upon the Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) procedure and use it to determine the rate of cross-link reversal for cross-linked protein-DNA complexes from yeast cell lysate. The half-life of the protein-DNA cross-links varies from 179 h at 4 °C to 11.3 h at 47 °C, with a rate that increases exponentially with temperature and is independent of salt concentration.

Plug-based microfluidics with defined surface chemistry to miniaturize and control aggregation of amyloidogenic peptides

Small with control: For miniaturization of protein aggregation experiments the interfacial chemistry must be controlled to avoid protein aggregation caused by interfacial adsorption. Plug-based microfluidics with defined surface chemistry (see schematic picture) can then be used to perform hundreds of aggregation experiments with volume-limited samples, such as cerebrospinal fluid from mice.