# Patent

## Title
Process and system for analyzing the expression of biomarkers in cells

## Abstract

The invention relates generally to a process of analyzing and visualizing the expression of biomarkers in individual cells wherein the cells are examined to develop patterns of expression by using a grouping algorithm, and a system to perform and display the analysis.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation-in-part of pending U.S. patent application Ser. No. 12/580,651, filed Oct. 16, 2009.


BACKGROUND
The examination of cellular samples that have been treated to reveal the expression of biomarkers has long been a valuable tool for biological research and clinical studies. A common treatment has involved the use of antibodies or antibody surrogates such as antibody fragments that are specific for the biomarkers, commonly proteins, of interest. It is typical to directly or indirectly label such antibodies or antibody surrogates with a moiety capable, under appropriate conditions, of generating a signal. One approach has been to attach a fluorescent moiety to the antibody and to interrogate the sample for fluorescence. The signal obtained is commonly indicative of not only the presence but also the amount of biomarker present.
The techniques of tissue treatment and examination have been refined so that the level of expression of a given biomarker in a particular cell or even a compartment of the given cell such as the nucleus, cytoplasm or membrane can be quantitatively determined. Typically the boundaries of these compartments or the cell as a whole are located using well-known histological stains. Commonly the treated cellular sample is examined with digital imaging and the level of different signals emanating from different biomarkers can consequently be readily quantitated.
More recently a technique has been developed which allows testing a given cellular sample for the expression of numerous biomarkers. Generally this technique involves staining the sample with a fluorophore labeled probe to generate signal for one or more probe bound biomarkers, chemically bleaching these signals and re-staining the specimen to generate signals for some further biomarkers. The chemical bleaching step is convenient because there are only a limited number of signals that can be readily differentiated from each other so only a limited number of biomarkers can be examined in a particular step. But with bleaching, the sample may be re-probed and re-evaluated for multiple steps. This cycling method may be used on formalin fixed paraffin embedded tissue (FFPE) samples and cells. Digital images of the specimen are collected after each staining step. The successive images of such a specimen can conveniently be kept in registry using morphological features such as DAPI stained cell nuclei, the signal of which is not modified by the chemical bleaching method.
Another approach has been to examine cells obtained from a frozen tissue specimen by staining them iteratively and bleaching the labels from the previous staining step before applying the next set of stains. The strength of the fluorescent signal associated with each biomarker evaluated is then extracted from the appropriate image.
There have been efforts to utilize this data to identify patterns of biomarker expression. One approach has been to look for such patterns in an entire sample and to binarize the fluorophore signals using a threshold values and generate various expression profiles that are then overlaid on an image of the tissue of interest. However, the data values resulting from the multiplexing and image analysis of cells represents vast biological complexity that may be difficult to analyze. Thus a need exists for a process to enhance the analysis and visualization of the biological data.
BRIEF DESCRIPTION
The invention relates generally to a process of analyzing and visualizing the expression of biomarkers in individual cells wherein the cells are examined to develop patterns of expression by numerical evaluation and a system to perform this analysis.
In one embodiment a process is provided comprising measurement of the level of expression of multiple biomarkers in individual cells of a cellular sample. The measurement of biomarker expression of each cell is stored as a data point in a database and the database is interrogated for data points having a similar pattern of biomarker expression using a computer algorithm where such similarity is determined by a numerical analysis that uses the level of expression of each biomarker as at least a semi-continuous variable. The data points with minimum variance is identified and grouped together. The group is assigned a new biomarker expression profile represented by a new data point, which is based on a central value for each attribute considered by the algorithm, thus forming a new data set. The steps are repeated with the new data set until a predetermined number of groups are generated.
In another embodiment, a method for using the grouping data for displaying a group of cells having similar patterns of expression of certain biomarkers is provided. The method comprises creating an image of one or more groups, in a cellular sample, by which each cell in a group is given a visible designation that they belong to the same group. The image are registered to the original image of the sample to allow the images of the groups to be sequentially overlaid and analyzed
In another embodiment, an image analysis system for displaying a group of cells having similar patterns of expression of certain biomarkers is provided. The system comprises an imaging device adapted to capture a digital image of a cellular sample using multiplex sequential staining to identify biomarkers within individual cells; and a processing device adapted to perform the steps of generating groups based on a cell's biomarker expression profile and to display the results.



DRAWINGS
These and other features, aspects, and advantages of the present invention will become better understood when the following detailed description is read with reference to the accompanying drawings in which like characters represent like parts throughout the drawings, wherein:
FIG. 1 is a process map illustrating the steps for analyzing the expression of biomarkers in individual cells using a computer algorithm to determine similar patterns of expression.
FIG. 2 is a micrograph image at 20× magnification of showing all the cells measured in one field of view and the subgroup of cells belonging to Group 1 of 3, as described by Table 2, identified by stars.
FIG. 3 is the same base micrograph as FIG. 2 but in this case with the cells belonging to Group 2 of 3 identified by squares.
FIG. 4 is the same base micrograph as FIG. 2 but in this case with the cells belonging to Group 3 of 3 identified by diamonds.
FIG. 5 is a micrograph showing all the cells measured in one field of view with symbols for each group superimposed over the original micrograph.



DETAILED DESCRIPTION
The present invention involves capturing data on the expression of biomarkers within the compartments of individual cells to allow comparison of the individual cells to each other. The individual cells are part of a larger cell sample. For example the cell sample may be a group of cells from a cell culture, a tissue sample, organ, tumor, or lesion. The cells may also be from multiple cell samples representing one or more disease models, or samples representative of different stages within a disease model.
FIG. 1 is a process map of one embodiment. The process includes creating a dataset (A) comprising a plurality of data points, each data point representing a biomarker expression profile for an individual cell of a cellular sample. The dataset is interrogated looking for data points having similar patterns of expression (B). More specifically, each data point is compared for similarity values, using a computer algorithm wherein similarity is determined by a numerical analysis, which identifies the two or more data points with minimum variance (C). The data points having the minimum variance are grouped together and assigned a new biomarker profile, which represents a numerical averaging of the biomarker expressions of the cells (D). The comparing and grouping steps are repeated on the new data set until a predetermined number of groups are generated (E).
The process describes a hierarchical approach, which allows grouping of cells that are most distinct from each other. The process may further provide for, visualizing the occurrence of these subsets on images of the cellular sample and analyzing the occurrence of certain biomarkers in the subsets of cells for association to the diagnoses or prognoses of a condition or disease or to the response to treatment.
Capturing data on the expression of biomarkers in the cells may be obtained through a variety of laboratory means such as through a multiplexing staining-destaining technique. Automated image registration and analysis may also be used to quantitate the biomarker concentration levels for individual cells, or even sub-cellular compartments, such as nuclei, cytoplasm, and membrane.
The data values resulting from the multiplexing and image analysis of cells may then be subjected to further analysis. One approach is to group cells mathematically based on the expression data of biomarkers (unsupervised grouping). This mathematical approach, which may also be defined as a hierarchical or agglomerative approach, consists of sampling the data and assigning cells to the group that is most similar to their biomarker expression profile.
In one embodiment, an agglomerative approach is applied to the sub-cellular biomarker data. A sample of cells may be used to develop a dendrogram, illustrative of hierarchical grouping. This analysis begins by assuming each cell is an individual group represented by a single data point. It computes the similarity values between the cells, which are an estimation of the degree of similarity between the biomarker data. In certain embodiments, the similarity value is based on the Euclidean distance in biomarker space between each pair of cells. The two cells that form a group with minimum variance is joined together into a cellular group and assigned a new biomarker value represented by a single data point. In certain embodiments, the new data point may be based on a central value for each attribute considered by the algorithm. The process is repeated until all cells are members of one large group or a predetermined number of groups. The end-user can select the number of cellular groups for downstream analysis.
Alternatively the number of cellular groups can be automatically determine for a given data set by computing the point of diminishing returns for increasing the number of identified cellular groups. An advantage of the hierarchical approach is that the solution minimizes global error, thus yielding the cellular groups that are most distinct from one another.
In certain embodiment, the average biomarker expression for cells in each group is computed along with the spatial distance between each cell or group center. This factor may be used to assign cells to a particular cellular group, such that cells are assigned to the closest group within a given range of similarity values. From these assignments it is possible to assign a biomarker profile of the population of cells that belong to each cellular group. Expression levels are expressed relative to the mean expression of each protein for all cells.
In certain embodiments, the data can be initially captured by the treatment and imaging of cellular samples. The treatment typically involves preparing slides of a cellular sample, such as tissue specimens and appropriately staining them to identify cell boundaries, cell compartment boundaries and levels of expression of selected biomarkers. The imaging typically involves digital imaging of selected fields of view from microscopic examination of the slides in a manner that the same field of view can be imaged after successive rounds of staining and the successive images can be placed in registry. The imaging also typically involves a segmentation routine that allows each pixel examined to be associated with a particular cell and a particular compartment of that cell. The data from this imaging is conveniently stored in a database such that each cell examined is associated with certain attributes reflective of the expression of the selected biomarkers within that cell. This database is then typically interrogated with numerical tools to group together those cells that have similar patterns of biomarker expression with the tools being able to create various size groups based on how similar the members of each group are to each other.
One or more of these groupings can be conveniently visualized by an overlay of one or more markers or indicators on images of the tissue of origin of a given set of cells. In one embodiment an image of a selected field of view of a given slide is generated on which are marked all the cells which belong to a given group created by the application of the numerical tools. In one embodiment the pattern of biomarker expression within any given group of cells is analyzed for associations to the source of the tissue. In this embodiment tissue specimens are taken from at least two distinct groups of the same organism for instance an animal model or human subjects that differ in a biological feature under examination.
The techniques of the present invention can be applied to any cellular sample that is likely to vary in some manner as a result of its biological condition or history. For instance, the technique can be applied to the diagnoses of a condition by obtaining appropriate tissue specimens from subjects with and without a particular condition or disease. Thus one could take breast tissue or prostate tissue if the object were to diagnose breast or prostate cancer. Alternatively it could be applied to the prognoses of a disease or condition using appropriate historical tissue from subjects whose later clinical outcomes were known. Thus the techniques of the present invention could be applied to try to improve the prediction of survival rates in colon cancer patients from that available from the ratio of cMET expression in cytoplasm to that in membrane in which the ratio is based upon all the cells in the examined tissue. Additionally the techniques of the present invention could be applied to assess the effects of various treatments on a disease or condition. Thus one could use it to compare tumor tissue from untreated model animals to tumor tissue from model animals treated with one or more cancer drugs.
The technique may also be applied to the analysis of cell cultures wherein the cell culture is prepared. For example cell cultures may be contained on a test well plate where by each test well holds multiple cells ranging in cell numbers from a few cells to more than 1000 cells.
The biomarkers used in practicing the present invention may be any which are accessible to a histological examination that will give some indication of their level of occurrence or expression and are likely to vary in response to the biological condition or history of a selected tissue. Examples of biomarkers may include, but are not limited to, DNA, RNA or proteins or a combination of them. Thus one could investigate whether there was a pattern of cells within a tissue with a given gene having a certain level of occurrence different from the average level of occurrence among all the cells in that tissue. One could similarly investigate for patterns of cells having a different level of RNA or protein expression.
The biomarkers may be conveniently selected in accordance with the biological phenomenon being examined. Thus for instance if a particular biological pathway were involved in the phenomenon under examination proteins involved in that pathway or the RNA encoding those proteins could be selected as the biomarkers. For instance, if the proliferation of neoplastic tissue were the focus the Ki67 protein marker of cell proliferation could be selected. On the other hand if the focus were on hypoxia the Glut 1 protein marker could be selected.
The level of expression of a biomarker of interest is conveniently assessed by staining the slides of a cellular sample with a probe specific to the biomarker associated with a label that can generate a signal under appropriate conditions. Two useful probes are DNA probes with sequences complimentary to the DNA or RNA of interest and antibodies or antibody surrogates such as antibody fragments with epitope specific regions that specifically bind to the biomarker of interest that may be DNA, RNA or protein.
A convenient probe from the point of view of availability and well established characterization is a monoclonal or polyclonal antibody specific for the biomarker of interest. There are commercially available antibodies specific to a wide variety of biomarkers. Mechanisms for associating many of these antibodies with labels are well established. In many cases the binding behavior of these antibodies is also well established.
A convenient label for the biomarker probes is a moiety that gives off an optical signal. A particularly convenient label is a moiety that gives off light of a defined wavelength when interrogated by light of an appropriate wavelength such as a fluorescent dye. Preferred fluorescent dyes are those that can be readily chemically conjugated to antibodies without substantially adversely affecting the ability of the antibodies to bind their targets.
A convenient approach for labeling if numerous biomarkers are to be examined is to directly label the antibodies. While there are sometimes certain advantages in using secondary or tertiary labeling like using an unlabeled primary antibody and a labeled secondary antibody against the species of the primary antibody such as signal amplification complications may arise in finding sufficient different systems for multiple rounds of staining and bleaching.
Slides, holding the cellular samples, may be conveniently stained with labeled biomarker probes using well-established cytology procedures. The initial staining of each slide may also involve the use of markers for one or more of the cell compartments of nucleus, cytoplasm and membrane. It is convenient to use markers such as DAPI that are not bleached when the labels attached to the biomarker probes are bleached. These procedures generally involve rendering the biomarkers in the slide cellular sample accessible to the labeled probes and incubating the labeled probes with the so prepared slides for an appropriate period of time. The slides can be simultaneously incubated with a number of labeled biomarker probes, each specific for a different biomarker. However, there is a practical limit to the number of labeled probes that can be simultaneously incubated with a slide because each labeled probe must generate a signal, which is fairly distinguishable from the signals from the other labeled probes.
A convenient approach to staining numerous biomarkers is to stain a limited number of biomarkers, take appropriate images of the stained slide and then optically or chemically bleach the labels to destroy their ability to generate signal. A further set of labeled probes specific to different biomarkers but with labeling moieties identical to those used in the prior staining step can then be used to stain the same slide. This approach can be used iteratively until images have been acquired of the same slide stained for all the biomarkers of interest. One-way of implementing such an approach is set forth in U.S. Published Patent Application 2008/0118934, incorporated herein by reference.
If more than one image is taken of a given field of view it is desirable that the successive images, commonly collectively referred to as a stack, be kept in registry. Thus if the approach of iteratively staining and bleaching a slide is used to obtain information on numerous biomarkers it is necessary to provide a mechanism for the images of each field of view from each round to be properly aligned with the images of the same field of view from previous rounds. A convenient approach is to ensure the presence of the same feature or features in each image of a field of view. One such feature that is particularly convenient is the pattern of cell nuclei as revealed by an appropriate stain such as DAPI. One of the images can then be taken as a reference, typically the first image taken, and appropriate transformations can be applied to the other images in that stack to bring them into registry. A technique for bringing images of the same field of view into registry with each other based on their cell nuclei pattern is disclosed in U.S. Published Patent Application 2008/0032328 incorporated herein by reference.
A representative number of fields of view are typically selected for each cellular sample depending upon the nature of the sample. For instance if a slide has been made of a cell culture or a single tissue specimen numerous fields of view may be available while if the target of examination is a tissue microarray (TMA) a more limited number of fields of view may be practical.
The images of each field of view are conveniently made with a digital camera coupled with an appropriate microscope and appropriate quality control routines. For instance the microscope may be designed to capture fluorescent images and be equipped with appropriate filters as well as being controlled by software that assures proper focus and correction for auto-fluorescence. One such routine for auto-fluorescence involves taking a reference image using the filter appropriate for a given fluorescent label but with no such label active in the image and then using this reference image to subtract the auto-fluorescence at that wavelength window from an image in which the fluorescent label is active.
Each image of each field of view may then be examined for segmentation of the cells into individual cells and compartments of nucleus, cytoplasm and membrane, and other cellular compartments. This segmentation is typically aided by the presence of stains from markers for these three compartments. As part of the segmentation procedure each pixel of each image is associated with a particular cell and a compartment of that cell. Then a value for the level of expression of each biomarker of interest is associated with each pixel from the level of signal from that pixel of the label for that biomarker. For instance if the label associated with the FOXO3a probe was Cy3, the pixels of the image of a given field of view that were stained with the labeled probe for FOXO3a would be evaluated for the fluorescent signals they exhibited in the wavelength window for Cy3. These values would then be associated with that biomarker for each of the pixels.
A database may be created in which each compartment of each cell examined is associated with a value for each biomarker evaluated which reflects the strength of the signal from the label associated with the probe for that biomarker for all the pixels associated with that compartment. Thus a mean or medium value is taken across all the pixels associated with a given compartment of a given cell for the signal strength associated with each biomarker evaluated.
The database may be subject to a quality control routine to eliminate cells of compromised analytic value. For instance all the cells that do not lie wholly within the field of view and any cells that do not have between 1 and 2 nuclei, a membrane and a certain area of cytoplasm may be eliminated. This typically results in the elimination of between about 25% and 30% of the data.
The remaining data in the database may now be transformed and interrogated. The data for a given biomarker across all the cells examined may not follow a distribution, which readily lends itself to standard statistical treatment. Therefore it may be useful to subject it to a transformation such as a Box Cox transformation that preserves the relative rankings of the values associated with a given biomarker but places such values into an approximate Normal distribution. Then it may be helpful to standardize the values associated with each biomarker so that the values for all the biomarkers have a common base. One approach is to determine the mean value and standard distribution of all the transformed values associated with a given biomarker and then to subtract this mean value from each value in the set for that biomarker and divide the difference by the standard deviation for that transformed dataset. The database may now be interrogated for groups of cells that have similar profiles of biomarker expression.
The data on biomarker expression levels in the database may be further transformed by creating three or more intervals of value and assigning a single value to each entry that falls within a given interval. This will make the biomarker expression level a semi-continuous variable. This may be useful for reducing the computational capacity needed for the computer algorithm, especially for particularly large datasets.
The database may be interrogated with numerical tools to group together cells with some similarity in their expression of the biomarkers being examined. In one embodiment an algorithm that can create groups at any level of similarity from treating each cell as its own group to including all the cells in a single group is used. This embodiment may use the transformed and standardized biomarker expression level data as an input and groups the cells by proximity in multi-dimensional value space. Additional cell attributes that serve as input values may include relationships between the data for different biomarkers for a given cell and relationships between the occurrence of the same biomarker in different compartments of the same cell. For instance an additional cell attribute that the algorithm considers could be the ratio between the expression level of two biomarkers in that cell or it could be the ratio of expression of a given biomarker in one compartment of that cell compared to the level of expression in another compartment of that cell. In this regard the level of similarity is just a shorthand way of referring to applying the grouping algorithm to yield a given number of groups.
The numerical tools used to implement the grouping algorithm may be any of those typically used to separate data into multiple groups. These range from the straightforward application of a set of rules or criteria to the more sophisticated routines of classical statistics including probability based analysis and learning algorithms such as neural networks.
The grouping algorithm may be applied in an unsupervised fashion meaning that no constraints beyond the level of similarity are applied with regard to how it creates groups or it may be applied in a partially supervised fashion, which means one or more constraints are applied. A typical constraint could be a requirement that all the cells possessing or lacking a particular attribute be included or excluded from one or more groups for that reason. For instance, the algorithm could be applied with the constraint that all cells expressing well above the mean amount of Glut1 be excluded from the groups it creates on the theory that these cells are suffering from hypoxia and therefore these cells do not provide representative information. The constraint may cause all the members of at least one group to share one or more attributes.
In an alternative approach the database may be interrogated with predefined profiles resulting in a fully supervised grouping. Thus one might extract a group of cells in which a biomarker for hypoxia, say Glut1 is expressed at levels well below the mean for all the examined tissue but that the marker for cell proliferation, say Ki67, is expressed at levels well above the mean for all the examined tissue.
Another approach is to combine unsupervised, partially supervised and fully supervised grouping in an iterative manner. For instance one could identify a group of cells that have a threshold level of expression of certain proteins and then create subgroups of that group using unsupervised grouping based on a panel of biomarkers that might or might not include the original criteria proteins. In another case one could create subgroups of a group created by unsupervised grouping using partially or fully supervised grouping. In another instance a group might be created by unsupervised grouping that is of particular interest and then a further application of the grouping routine could be used to identify other groups of cells that are similar to this group.
The cell attributes used to create the groups could include more than the patterns of biomarker expression. Additional attributes that could be considered include cell morphology and location in the tissue architecture such as proximity to a particular feature like a blood vessel.
The groupings created by the numerical tools or predefined profiles may be conveniently visualized by one or more overlays on images of the fields of view in which the analyzed cells appear. One approach is to take the images of one or more fields of view examined and overlay on such images symbols or colors representative of one or more of the groups such that the symbol or color representative of a given group is applied to all the cells in a given image that belong to that group. It is convenient to use an initial image or images in which cell boundaries are discernable but the signals from individual biomarkers are not displayed. In one embodiment the overlaid images are created by an electronic tool which allows the user to select the grouping iteration, i.e. the number of groups into which the cells have been classified and the number of those groups whose symbols are displayed. For instance, a user could select the grouping iteration that yielded seven groups and elect to display symbols for just two of those groups.
A numerical tool can be applied to the attribute data for all the cells belonging to a given group to determine whether there are any indications useful for diagnoses or prognoses of a disease or condition or for judging response to a treatment for a disease or condition. For instance, if samples are taken from tissue affected by a condition and tissues unaffected by the same condition all the cells belonging to a particular group can be examined to see if the cells in that group drawn from tissue which are affected by the condition display any attributes which distinguish them from the cells in that group drawn from tissue unaffected by that condition.
One application could be to sample tissue affected by a neoplasm and normal tissue of the same type from the same subject or to sample tissue of the same type from subjects whose sampled tissue is cancerous and from subjects whose sampled tissue is normal. Then each group of cells created by the grouping algorithm can be examined to determine if there is any attribute that distinguishes cells from cancerous tissue from cells from normal tissue. In another instance historical tissue from a number of subjects with a cancerous condition whose survival rates since diagnoses are known can be examined by grouping cells and examining the attributes of the members of a group for an association with survival rates. In yet another application tissue samples could be taken from both subjects treated with a given therapy such as a drug and subjects not treated or treated with a placebo and examining all the cells in one or more groups created by the grouping algorithm for any attributes that distinguish the treated subjects from the control subjects. This approach can conveniently be applied to model animals such as mice implanted with neoplastic xenograft tissue from a human cancer.
Another application may be in the analysis of cell cultures, such as samples affixed to a test well plate where by each test well may easily contain more than 1000 cells. Each cell could be automatically segmented into nuclear, cytoplasmic, and membrane region, in addition to considering the entire cell, for a total of 4 compartments. A typical study may test for 15 different biomarkers. This leads to 96×1000×4×15=5.7 million data points for this single plate. These data points typically relate to a highly complex and incompletely understood signaling pathway.
The process allows for a systematic procedure for enabling intuitive understanding of this vast data set. The process may also allow cross-referencing of the group data back to the original images. This is important for biologists and oncologists to provide cytological context to biomarker expression, as compared to gene array approaches where the tissue is disaggregated and the context is lost.
The attributes examined may include not only the expression level and compartment location of the biomarkers evaluated but also interrelationships between these biomarkers and interrelationships between the expression levels of a given biomarker in different cellular compartments. For instance one could examine the ratio of expression levels of two biomarkers in a group of cells created by a grouping algorithm to see if the ratio could be associated with the presence of a condition or disease, the prognoses of the condition or disease or the treatment of the condition or disease with a particular therapy. One could similarly make use of the ratio of the levels of expression of a given biomarker between compartments of the same cell. In this instance it might be found that the cells from treated tissue in a given group had a different ratio of biomarker expression in the nucleus as compared to the cytoplasm for a given biomarker than the ratio for the cells for untreated tissue.
Another approach is to determine whether there is any association between the distribution of the groups that may be applicable in identify a biological process, condition. An association may also aid in the diagnoses or prognoses of a condition or disease or the response of a condition or disease to a therapy. For instance it may be found that in a cellular sample from a tissue that has gone neoplastic there are more cells in one or more of the groups than there are in healthy versions of the same tissue.
A particularly convenient statistical tool for examining the attributes of the cells in a group for indications useful for diagnoses, prognoses or treatment is “p-value” for association or probability that an observed association is the result of chance or random distribution.
EXAMPLE
A study was conducted on fixed H1 and Hues16 human embryonic stem cells grown on mouse embryonic feeder cells in 96 well plates. Samples were fixed in paraformaldehyde, permeabilized with Triton-X100, blocked with serum, and then stained with antibodies against pluripotency specific proteins expressed on the cells.
The wells containing the cellular sample were examined with a digital imaging device comprising a Zeiss Axiovision Z1 microscope (Carl Zeiss MicroImaging, GmB, Germany), equipped with high efficiency fluorochrome specific filter sets (BrightLine® Filter set, Semrock Inc, Rochester N.Y.) for Nanog, Oct4, Sox2, and Lin28. Between 8 and 18 representative fields of interest were examined on each well and selected for staining. Stage coordinates for each field of interest are marked and controlled by a processor using the Axiovision software and these coordinates are saved so they may be re-imaged after each staining round. A Piezzo X-Y automated stage allows the slide imaging system to repeatedly return to the same fields of interest. Fluorescence excitation is provided by a 300 W Xenon lamp source (Sutter Instrument, Novato, Calif.). Images are captured with a ORCA-IR CCD camera (Hamamatsu Photonics K.K., Hamamatsu City, Japan) using Zeiss Axiovision software with initial exposure settings determined automatically within 75% saturation of pixel intensity.
Each well was stained in succession with four different fluorescently labeled antibodies, each one specific for one of the four protein biomarkers listed in Table 1. The staining methodology was similar to that disclosed in U.S. Pat. No. 7,629,125 incorporated herein by reference. The preselected regions of interest on each well were imaged on the system as described above. Then the multi-well plate was removed and chemically bleached to destroy the signal from this set of fluorescent labels so that a further set of antibodies labeled with one or more of these fluorescent labels could be used. The chemical composition of the bleaching agent is described in U.S. Published Patent Application 2008/0118934, incorporated herein by reference. Then a second set of antibodies was used to stain a further two protein targets on each well and so on until all the wells had been stained with antibodies specific to all four protein biomarkers. One or more images were taken of each region of interest on each well after each staining round. After bleaching, one or more images were taken of said regions of interest to confirm the destruction of the signal. Registration of the images using a common pattern within each image as a reference is used to apply a rigid spatial transformation to the subsequent images.
In the staining procedure each protein biomarker was associated with a particular fluorescent dye because the antibody used to detect that biomarker was coupled to a particular fluorescent dye. An image was then taken in the appropriate wavelength window for that fluorescent dye after the application of that antibody. Data was acquired for each compartment of each cell in each field of view representative of the level of expression of each protein biomarker for which a fluorescent stain had been applied. In particular, the intensity of the fluorescence at each pixel in each field of view was recorded for each protein biomarker.
Each pixel was associated with a particular subcellular compartment of a particular cell using software algorithms. The assignment of a given pixel to a given compartment of a given cell was based on an evaluation of the morphology of the cell observed in the field of view and the stains applied to develop the nuclei, cytoplasm and cell membranes of the cells in the field of view. Although proprietary software was used, comparable if somewhat less accurate assignments could be obtained from commercially available segmentation software.
The pixels associated with certain punitive cells were then removed from the data set as a quality control measure. In particular, pixels associated with cells that did not contain a cytoplasm and one to two nuclei were eliminated, as were those associated with cells in regions in which the image quality was poor, cells not wholly within a given field of view. In this process cell contained within the sample were counted to yield an initial count of 3455 and were reduced to a resulting cell sample size of 3112
A database was now created in which each cell remaining after the quality control procedure was associated with certain attributes including a value reflective of the auto-fluorescence corrected fluorescence intensity for each of the four protein biomarkers evaluated in total and in each of its subcellular compartments. In essence the fluorescence intensities of all the pixels associated with a given cell or a given compartment of a given cell associated with a given protein biomarker were summed. The distribution of fluorescence intensities associated with each protein biomarker over the entire dataset was subjected to a Box Cox transformation to obtain an approximately normal distribution. In most cases this led to the application of a power function of about 0.3. Then the transformed intensity values were standardized by determining the mean intensity value and the standard deviation of intensity values and subtracting the mean value from each actual value and dividing this difference by the standard deviation. Thus each cell and each compartment of each cell was provided with a post transformation standardized value for the fluorescent intensity of each of the four protein biomarkers. This value was taken as representative of the level of expression of that biomarker in that cell or cellular compartment.
The database was then interrogated to create groups of cells with similar patterns of protein biomarker expression. In particular, a computer algorithm was used to iteratively group cells beginning in the first iteration with placing every cell in its own group and ending in a final iteration with placing all the cells in a single group. In each intermediate iteration, cells that were more dissimilar in their patterns of protein biomarker expression were placed in the same group. The cell attributes used in this analysis were the standardized fluorescence level for each of the four protein biomarkers and four ratios.
Table 1 shows the cell attributes examined based on biomarker activity. Table 2 shows data expressed on a scale where mean expression for the entire population of cells is fixed at 0 and a standard deviation is fixed at 1. Data is the actual value for mean value for each parameter. The relative ranking, shown lower in the table, is a representation of relative expression. The indication “+/−” means that the value for that profile is essentially the same as the average value of that attribute for all the cells in the dataset. The indication “++” means a value of one standard deviation or more above the mean value and the indication “−−” means a value one standard deviation or more below the mean. The indications “+” and “−” mean a value between the mean and one standard deviation above or below the mean, respectively.
Table 3 applies the results of Table 2, and shows the percent of cells for each image that are assigned to each of the three group case. Cells are assigned to a group based on minimizing the Euclidean distance between cell and group level properties.
The biomarker profiles for the five cell group are shown in Table 4 and 5. The biomarker profiles for the seven cell group are shown in Table 6 and 7. In a similar fashion to Table 2, Tables 4 and 6 show the occurrence of each attribute for each profile as compared to the mean value of that attribute for all the cells in the dataset.
FIGS. 2, 3, and 4 are micrographs, which illustrate various ways of displaying the groups created in accordance with Table 2. The figures illustrate Group 1 indicated by a particular symbol on an image containing cells that were examined to create the groups. In a similar way FIG. 3 is Group 2 and FIG. 4 is Group 3.
FIG. 5 shows all the cells measured in one field of view as part of this experiment. Symbols for each group are superimposed over the original micrograph.
The groups may then be displayed individually or sequentially on a display device, where the cellular groups are represented visually either by different colors or symbols. This provides a method of distinguishing the groups if images are overlayed. Registering the images to the original digital image of sample further aids in the analysis.
In certain embodiments, the image analysis system may comprise an imaging device adapted to capture a digital image of a cellular sample using multiplex sequential staining and which may be used to identify biomarkers within individual cells and a processing device.
The processing device may be adapted to perform the steps of generating groups based on a cell's biomarker expression profile and to display the results as described above. The processing device may also be configured to analyzing the groups to identify a biological process, condition, state or combination thereof.







TABLE 1







Cell Attributes Examined










Attribute
Biomarker







Expression Level
Nanog



Expression Level
Oct4



Expression Level
Sox2



Expression Level
Lin28

















TABLE 2







Profiles for Three Group Analysis










Cell Attribute
Group 1
Group 2
Group 3













Nanog
0.069871
−1.13274
1.326458


Oct4
0.037467
0.972087
−1.41035


Sox2
0.009222
−1.02281
1.348123


Nanog
+/−
−−
++


Oct4
+/−
+
−−


Sox2
+/−
−−
++


Lin28
−
++
−−
















TABLE 3







Percent of cells for each image that are assigned 


to each data group for the 3 group case.














Image 1
Image 2
Image 2
Image 4

















Group 1
19.3
61.6
9.6
67.5



Group 2
4.1
35.5
90.4
12.6



Group 3
76.6
2.9
0
20.2

















TABLE 4







Profiles for Five Group Analysis












Cell Attribute
Group 1
Group 2
Group 3
Group 4
Group 5















Nanog
−0.20924
−1.24597
0.153077
1.012386
1.833265


Oct4
0.218364
1.08712
−0.0033
−0.9605
−2.15827


Sox2
−0.31769
−1.09822
0.13989
0.891569
2.111643


Lin28
0.392807
1.096397
−0.42806
−0.5298
−1.9434


Nanog
−
−−
+
++
++


Oct4
+
++
+/−
−
−−


Sox2
−
−−
+
+
++


Lin28
+
++
−
−
−−
















TABLE 5







Percentage of cells per image in each of the 5 groups














Image 1
Image 2
Image 2
Image 4

















Group 1
10.9
33.5
21.2
23.8



Group 2
2.7
29.1
78.5
10.7



Group 3
5.7
33.1
0.3
40.8



Group 4
29.4
4.3
0
23.8



Group 5
51.2
0.1
0
0.8

















TABLE 6







Profiles for Seven Group Analysis














Cell Attribute
Group 1
Group 2
Group 3
Group 4
Group 5
Group 6
Group 7

















Nanog
−0.14723
−1.2742
−0.16199
0.532814
1.042958
−1.10693
1.833265


Oct4
0.145463
1.074493
0.230977
−0.30679
−1.02818
1.047334
−2.15827


Sox2
−0.38348
−1.43573
0.097289
0.199159
0.968282
−0.48978
2.111643


Lin28
0.471085
1.547352
−0.53686
−0.17465
−0.63493
0.351808
−1.9434


Nanog
−
−−
−
+
++
−−
++


Oct4
+
++
+
−
−−
++
−−


Sox2
−
−−
+/−
+
+
−
++


Lin28
+
++
−
−
−
+
−−
















TABLE 7







Percent of Cells per image in each of the Seven Groups














Image 1
Image 2
Image 2
Image 4

















Group 1
9.0
22.1
22.2
20.7



Group 2
2.2
11.0
70.2
5.0



Group 3
1.9
26.9
0
18.1



Group 4
7.1
10.1
0.3
29.3



Group 5
27.5
3.5
0
19.6



Group 6
1.1
26.4
7.3
6.5



Group 7
51.2
0.1
0
0.8










While only certain features of the invention have been illustrated and described herein, many modifications and changes will occur to those skilled in the art. It is, therefore, to be understood that the appended claims are intended to cover all such modifications and changes as fall within the true spirit of the invention.

## Claims

1. A process comprising:
a. creating a dataset comprising a plurality of data points, each data point representing the biomarker expression profile for individual cells of a cellular sample;
b. interrogating said dataset for data points having a similar pattern of expression of said biomarkers using a computer algorithm wherein such similarity is determined by a numerical analysis that uses the level of expression of each biomarker as at least a semi-continuous variable;
c. identifying the two or more data points with minimum variance;
d. grouping the data points having the minimum variance together to create a group of cells whose members have a similar biomarker expression profile and assigning said group a new biomarker expression profile represented by a new data point in a new dataset, wherein said new data point is based on a central value for each attribute considered by said algorithm; and
e. repeating steps b, c, and d until a predetermined number of groups is generated.

2. The process of claim 1 wherein a step in creating a dataset is a quality control step in which the data point representing certain cells is eliminated from said data set.

3. The process of claim 1 wherein the numerical analysis comprises calculating Euclidean distance in biomarker space.

4. The process of claim 1 wherein the similarity values further comprises data related to cell morphology, cellular location within a tissue sample or cluster of cells, interrelationship between the levels of expression for two or more biomarkers within a cell, or a combination thereof.

5. The process of claim 1 wherein the group biomarker expression profile is the average value of biomarker expression for each cell in the group.

6. The process of claim 5 wherein the spatial distance between each cell and group is calculated and used as a factor in assign cells to a group, such that cells are assigned to the closest group within a given range of similarity values.

7. The process of claim 1 further comprising a supervised grouping of cells.

8. The process of claim 7 wherein the supervised grouping of cells comprises preselecting one or more biomarker expressions for grouping, statistical analysis, comparative analysis, or a combination thereof.

9. The process of claim 8 wherein statistical analysis is used to eliminate cells from the dataset to create a sub-population of cells for analysis.

10. The process of claim 9 wherein the analysis of the sub-population is used to determine single or multiple indices of biomarker expression.

11. The process of claim 1 wherein one or more groups are further analyzed to identify a biological process, condition, state or combination thereof.

12. A process for displaying cells within a cellular sample comprising:
a. acquiring a digital image of the cellular sample using multiplex sequential staining to identify biomarkers within individual cells;
b. creating a dataset comprising a plurality of data points, each data point representing the biomarker expression profile for individual cells of a cellular sample;
c. interrogating said dataset for data points having a similar pattern of expression of said biomarkers using a computer algorithm wherein such similarity is determined by a numerical analysis that uses the level of expression of each biomarker as at least a semi-continuous variable;
d. identifying the two or more data points with minimum variance;
e. grouping the data points having the minimum variance together to create a group of cells whose members have a similar biomarker expression profile and assigning said group a new biomarker expression profile represented by a new data point in a new dataset, wherein said new data point is based on a central value for each attribute considered by said algorithm;
f. repeating steps c, d, and e until a predetermined number of groups is generated; and
g. creating an image of one of one or more groups wherein the image is registered to the digital image of the cellular sample and by which each cell in a group is given a visible designation that they belong to the same group.

13. The process of claim 12 wherein the image displays the groups individually or sequentially overlaid on the digital image.

14. The process of claim 12 wherein the visible designation is a color, symbol, or combination thereof.

15. An image analysis system for displaying cells within a cellular sample comprising:
an imaging device adapted to capture the a digital image of the cellular sample using multiplex sequential staining to identify biomarkers within individual cells;
a processing device adapted to perform the steps of;
a. creating a dataset comprising a plurality of data points, each data point representing the biomarker expression profile for individual cells of a cellular sample;
b. interrogating said dataset for data points having a similar pattern of expression of said biomarkers using a computer algorithm wherein such similarity is determined by a numerical analysis that uses the level of expression of each biomarker as at least a semi-continuous variable;
c. identifying the two or more data points with minimum variance;
d. grouping the data points having the minimum variance together to create a group of cells whose members have a similar biomarker expression profile and assigning said group a new biomarker expression profile represented by a new data point in a new dataset, wherein said new data point is based on a central value for each attribute considered by said algorithm;
e. repeating steps b, c, and d until a predetermined number of groups is generated; and
f. displaying an image of one of one or more of said groups wherein the image is registered to the digital image of cell sample and by which each cell in a group is given a visible designation that they belong to the same group.

16. The system of claim 15 wherein the processing device is further configured to analyzing the groups to identify a biological process, condition, state or combination thereof.