Our approach

Our approach

Newsletter-summer-2020-bioinfo2

Frames are superior targets for immunotherapy

Frames are superior targets for immunotherapy

 
Our body is largely made up of proteins. Proteins are encoded in the DNA and stored in each cell of the body. Cancer is a disease caused by changes (mutations) in the DNA. The alphabet of DNA knows only the four letters G, A, T and C. The DNA is read in triplets; in three letter words. These can be combined into 64 different triplet words. Each ‘word’ codes for a single amino acid, which is needed for making a protein. If one position is changed in the DNA this can lead to only one amino acid change in the encoded protein. In this context we would call that novel amino acid a 'neoantigen' that resulted from a single 'point mutation'. If, however, one or more letters are added or lost in the DNA, this can result in a shift in the combination of letters that form a triplet word. A so called 'Frame shift' causes a track of novel amino acids (neoantigens) to be expressed in a protein.

The left side of figure 1 below shows a point mutation (A changes into T) in the DNA, which may cause a single amino acid change in the protein. The right side shows that a deletion of a DNA letter (A) results in a 'Frame shift' and a completely novel stretch of amino acids that follow the deletion, providing a strong antigenic target. The novel stretch of amino acids is termed Frame.

 
Our body is largely made up of proteins. Proteins are encoded in the DNA and stored in each cell of the body. The alphabet of DNA knows only the four letters G, A, T and C. The DNA is read in triplets; in three letter words. These can be combined into 64 different triplet words. If one position is changed in the DNA this can lead to an amino acid change in the encoded protein. In this context we would call that novel amino acid a 'neoantigen' that resulted from a single 'point mutation'. If, however, one or more letters are added or lost in the DNA, this can result in a shift in the combination of letters that form a triplet word. A so called 'Frame shift' causes a track of novel amino acids (neoantigens) to be expressed in a protein.

The left side of figure 1 below shows a point mutation (A changes into T) in the DNA may cause a single amino acid change in the protein. The right side shows that a deletion of a DNA letter (A) results in a 'Frame shift' and a completely novel stretch of amino acids that follow the deletion, providing a strong antigenic target:

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Figure 1: Point mutation (left) resulting in a single new amino acid and Frame shift (right) resulting in a stretch of novel amino acids (termed Frame).

FramePro: unique combination of DNA and RNA sequencing

We sequence the whole genome of the tumor

Frame Therapeutics has developed and patented a pipeline (FramePro) that detects Frames in tumor samples. FramePro combines the precise sequence of millions of mRNAs from a small tumor biopsy with the complete DNA sequence of the tumor. Our proprietary bioinformatics software uses the sequencing data to identify all expressed Frames resulting from any type of genetic mutation in the DNA of the tumor.

Frame has developed (and filed) a pipeline that allows to obtain the full length and precise sequence of 50 million mRNAs from a small tumor biopsy, combine that with the Whole Genome Sequence of the tumor, and apply proprietary bioinformatics to derive the complete 'Framome' of the tumor.

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Figure 2: (Left) Neoantigen discovery is often based on sequencing of only genes (exome sequencing). (Right) Instead, sequencing of the complete DNA of the tumor is used by Frame Therapeutics and is the only method that accurately detects structural genomic variations (SV), along with smaller mutations. The outer circle shows all the chromosomes, the second circle shows all point mutations and indels, and the inner circle shows the Structural Variations (arcs).

Hidden Frames are the major source of neo-antigenicity

Using FramePro, we have discovered a novel source of neo-antigenicity of tumors, termed Hidden Frames. Hidden Frames are derived from a combination of a structural genomic variation (SV) and splicing of a transcript that covers the SV junction (Figure 3). For many cancer types, Hidden Frames represent a major part of the tumor neo-antigenicity.

Frame Therapeutics has developed the FramePro technology to identify all the Frame shifts present in a tumor sample and determine the resulting novel expressed protein sequences, which we have termed Frames. The entire collection of Frames expressed by a tumor is referred to as the Framome. A Whole Framome immunotherapy (e.g. a cancer vaccine) targets the bulk of the antigenicity of the tumor. As a first therapy, Frame Therapeutics is developing a Framome personalized cancer vaccine for patients with lung cancer.

Figure 3 shows an example of a Framome. This lung tumor expresses many Frames, which altogether represent almost 1000 novel amino acids. Each of these Frames can be represented in a cancer vaccine.

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Figure 3: Identification of Hidden Frames that are caused by SV’s in the tumor DNA. Using  FramePro we are able to discover that novel spliced transcripts result from genomic structural variations in the tumor genome. These transcripts bring a non-coding DNA sequence into frame, and thus encode for a neoantigen.

Whole Framome: fully personalized

Whole Framome: fully personalized

With our FramePro pipeline we identify all the Frames present in a tumor sample, including those that are a result of short indels and large genomic SVs. The entirely collection of Frames expressed by a tumor is termed the Whole Framome of the tumor. A Whole Framome immunotherapy (e.g., a cancer vaccine) targets the bulk of the antigenicity of the tumor. As a first therapy, Frame Therapeutics is currently developing a Framome personalized cancer vaccine for patients with lung cancer.

Figure 4 shows an example of a Framome. Every horizontal sequence represents a Frame. Each color represents an amino acid. This lung tumor expresses many Frames, that altogether represent almost 1000 novel amino acids. Each of these Frames can be represented in a cancer vaccine.

Frame Therapeutics has developed the FramePro technology to identify all the Frame shifts present in a tumor sample and determine the resulting novel expressed protein sequences, which we have termed Frames. The entire collection of Frames expressed by a tumor is referred to as the Framome. A Whole Framome immunotherapy (e.g. a cancer vaccine) targets the bulk of the antigenicity of the tumor. As a first therapy, Frame Therapeutics is developing a Framome personalized cancer vaccine for patients with lung cancer.

Figure 3 shows an example of a Framome. This lung tumor expresses many Frames, which altogether represent almost 1000 novel amino acids. Each of these Frames can be represented in a cancer vaccine.

Screenshot 2020-09-14 at 12.13.35

Figure 4: Example of the Framome of a lung tumor.

Personalized yet partly off-the-shelf

Personalized yet partly off-the-shelf

By analyzing large amounts of Frames in tumor genomes using FramePro technology, Frame Therapeutics has discovered that particularly in genes whose function is to control the growth of cells there is a high level of Frame shifts (this is because these Frame shift mutations have inactivated the gene, contributing to the development of the tumor).

Thus, there are large numbers of patients whose tumor have a Frame shift in such a gene, and therefore can express antigens that are shared when compared with those of other patients.

Figure 5 shows the shared Frames that result from Frame shift mutations in the TP53 gene. Every line is the novel protein sequence that occurs in the tumor of a patient whose DNA has been sequenced and where a Frame shift has been observed in the TP53 gene (the actual mutation, insertion or deletion is in black). Only one of two possible frames is shown here. Colours indicate amino acids.

By analyzing large amounts of Frames in tumor genomes using FramePro technology, Frame Therapeutics has discovered that particularly in genes whose function is to control the growth of cells there is a high level of Frame shifts (this is because these Frame shift mutations have inactivated the gene, contributing to the development of the tumor).

Thus there are large numbers of patients whose tumor have a Frame shift in such a gene, and therefore can express antigens that are shared when compared with those of other patients.

Figure 4 shows the shared Frames that result from Frame shift mutations in the TP53 gene. Every line is the novel protein sequence that occurs in the tumor of a patient whose DNA has been sequenced and where a frame shift has been observed in the TP53 gene (the actual mutation, insertion or deletion is in black). Only one of two possible frames is shown here. Colours indicate amino acids.

Figure-3-TP53

Figure 5: Shared Frames that result from Frame shift mutations in the TP53 gene.

The shared property makes it possible to manufacture the vaccines against the Frames in advance, store them and supply them when a new patient is recognized as having that Frame in the tumor.

Besides, Frame neoantigens are much more different from the original protein than 'traditional' neoantigens. There are many reasons in the literature to confirm that Frames are on average very antigenic, stand out like a foreign sequence, almost an invader such as a virus, and will thus most likely elicit a strong immune response.

Also see the article in Nature.


The shared property makes it possible to manufacture the vaccines against the Frames in advance, store them and supply them when a new patient is recognized as having that Frame in the tumor.

A second advantage of the Frame neoantigens is that they are much more different from the original protein than 'traditional' neoantigens. There are many reasons in the literature to confirm that Frames are on average very antigenic, stand out like a foreign sequence, almost an invader such as a virus, and will thus most likely elicit a strong immune response.

Also see the article in Nature. 

 

Figure-2

Figure 6: Blow-up of a part of Figure 3, showing partially overlapping TP53 Frame peptide sequences resulting from Frame shifts in different patients with cancer.