A sex-specific protein panel detects early-stage cancers

Ashkan Afshin founded the company Novelna with the mission of making early cancer detection accessible, accurate, and affordable. Working alongside chemist Bogdan Budnik, the pair led the development of a cost-effective, early cancer detection test that could identify sex-specific protein signatures to locate the cancer’s origin. In a proof-of-concept study published in BMJ Oncology, they revealed a sex-specific panel of 10 proteins that detected 93 percent of stage one cancers in men and 84 percent in women with 99 percent specificity (1). 

“Our aim is to identify cancer at the earliest stage,” said Afshin. “This requires targeting patients identified in primary care settings such as routine check-ups, ideally before they show pronounced symptoms that indicate advanced disease.” This protein-based plasma test can serve as a population-wide screening tool for early cancer detection, potentially becoming part of routine checkups. 

How did you become interested in designing an early cancer detection test?

Afshin: There are recommended screenings for lung, cervical, breast, and prostate cancers, but many of them are not cost effective. The early 21^st century was marked by a focus on genomics, followed by a decade dedicated to transcriptomics. Currently, the shift towards proteomics offers promising potential for developing more accurate and cost-effective diagnostic tests. 

Budnik: I have been doing mass spectrometry, the leading analytical technology for proteomics, for more than 20 years. I have a good understanding of what the limitations of mass spectrometry are, and why we do not yet have biomarkers for any diseases. That’s why I started talking to Ashkan about the challenges in the field and what we could do to solve them. I proposed a collaboration with Olink Proteomics, a company that specializes in plasma analysis through proteomics. Their technology allowed us to find low abundance proteins that are key for early cancer detection. We aimed to create tests that are analytically advanced and also affordable and accessible, addressing the dual challenges of specificity and cost. 

How does this test compare to existing cancer diagnostics? 

Afshin: The most well-known cancer test is GRAIL’s Galleri test, which has a specificity of 99 percent and a sensitivity of 18 percent for stage one solid cancers. Our test has 99 percent specificity and a sensitivity almost five times greater than that of the currently available tests. 

Our aim is to identify cancer at the earliest stage. This requires targeting patients identified in primary care settings such as routine check-ups, ideally before they show pronounced symptoms that indicate advanced disease. 
– Ashkan Afshin, Novelna

GRAIL’s Galleri test offers a single package to detect cancer via a methylation assessment plus a subsequent determination of the cancer’s location, which costs around 1000 USD. In contrast, our test is structured into two distinct components. The first component is an initial screening to detect cancer presence, which would cost less than 100 USD. This eliminates the need for all individuals to undergo the second phase of testing for cancer localization, which is only necessary if the initial result is positive. For those proceeding to the second component, the cost is anticipated to be less than 20 percent of GRAIL’s Galleri test.

Budnik: We identified a saturation point in the number of proteins needed to achieve optimal sensitivity and specificity for different cancers. Depending on the type of cancer, we found that the inclusion of up to 20 proteins was sufficient to reach a plateau beyond which additional proteins did not enhance the test’s performance. This demonstrates that a carefully selected subset of proteins can provide comprehensive diagnostic information without the need for exhaustive testing. 

Why is there a need for sex-specific diagnostic approaches in cancer detection?

Afshin: It is common to encounter different reference ranges for blood proteins between male and female patients. This difference is not limited to highly abundant proteins but extends to those of lower concentration, indicating inherent biological differences that call for a tailored approach to diagnostics. The difficulty of detecting the same type of cancer varied significantly between male and female patients, even when using sex-specific panels. For instance, certain cancers like osteosarcoma, which are relatively rare, had noticeable differences in the ease of detection between sexes. 

Budnik: There are sex-specific differences in biological processes that must be acknowledged and addressed in any comprehensive diagnostic tool. Our decision to focus on sex-specific proteins comes from the observation that certain proteins perform significantly better in one sex over the other, and that unisex tests often fall short in accuracy due to inherent biological differences. Given that a patient’s sex is a known factor, it’s logical to use this information to maximize the test’s effectiveness right from the early stages of cancer detection. 

What are the main challenges in integrating your new cancer detection test into clinical practice?

Afshin: To make a test work, we need to address three different groups: patients, providers, and payers. Having an accurate and sensitive test is part of the story. The next step is working out the financial aspects, including the cost of the test and the reimbursement model. 

We also need to figure out whether to offer this test to everyone or only to those at high risk for any type of cancer. We need to clearly define what to do once we identify a cancer’s organ of origin, including what further diagnostic procedures to perform and any treatment plans. 

Addressing what to do in case of false positives is another critical component, given that even a test with 99 percent specificity and over 90 percent sensitivity will generate false positives. Lastly, we need to replicate this study in a larger sample size in various populations.

Budnik: The journey ahead involves not only proving the efficacy of our findings on a larger scale but also addressing the logistical challenges of accessibility. You can have a beautiful test, but if 90 percent of the population cannot afford it, it will be useless. The test also needs to be scalable, which includes integrating our tests into hospital settings and reaching out to those unable to visit medical facilities, ensuring that our technology is adaptable from discovery to confirmation modes and ultimately capable of handling hundreds of thousands, if not millions, of tests annually. 

This interview has been condensed and edited for clarity.

Reference

1. Budnik, B., Amirkhani, H., Forouzanfar, M. H. & Afshin, A. Novel proteomics-based plasma test for early detection of multiple cancers in the general population. BMJ Oncol  3, (2024).

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Ashkan Afshin founded the company Novelna with the mission of making early cancer detection accessible, accurate, and affordable. Working alongside chemist Bogdan Budnik, the pair led the development of a cost-effective, early cancer detection test that could identify sex-specific protein signatures to locate the cancer’s origin. In a proof-of-concept study published in BMJ Oncology, they revealed a sex-specific panel of 10 proteins that detected 93 percent of stage one cancers in men and 84 percent in women with 99 percent specificity (1). 

“Our aim is to identify cancer at the earliest stage,” said Afshin. “This requires targeting patients identified in primary care settings such as routine check-ups, ideally before they show pronounced symptoms that indicate advanced disease.” This protein-based plasma test can serve as a population-wide screening tool for early cancer detection, potentially becoming part of routine checkups. 

How did you become interested in designing an early cancer detection test?

Afshin: There are recommended screenings for lung, cervical, breast, and prostate cancers, but many of them are not cost effective. The early 21^st century was marked by a focus on genomics, followed by a decade dedicated to transcriptomics. Currently, the shift towards proteomics offers promising potential for developing more accurate and cost-effective diagnostic tests. 

Budnik: I have been doing mass spectrometry, the leading analytical technology for proteomics, for more than 20 years. I have a good understanding of what the limitations of mass spectrometry are, and why we do not yet have biomarkers for any diseases. That’s why I started talking to Ashkan about the challenges in the field and what we could do to solve them. I proposed a collaboration with Olink Proteomics, a company that specializes in plasma analysis through proteomics. Their technology allowed us to find low abundance proteins that are key for early cancer detection. We aimed to create tests that are analytically advanced and also affordable and accessible, addressing the dual challenges of specificity and cost. 

How does this test compare to existing cancer diagnostics? 

Afshin: The most well-known cancer test is GRAIL’s Galleri test, which has a specificity of 99 percent and a sensitivity of 18 percent for stage one solid cancers. Our test has 99 percent specificity and a sensitivity almost five times greater than that of the currently available tests. 

Our aim is to identify cancer at the earliest stage. This requires targeting patients identified in primary care settings such as routine check-ups, ideally before they show pronounced symptoms that indicate advanced disease. 
– Ashkan Afshin, Novelna

GRAIL’s Galleri test offers a single package to detect cancer via a methylation assessment plus a subsequent determination of the cancer’s location, which costs around 1000 USD. In contrast, our test is structured into two distinct components. The first component is an initial screening to detect cancer presence, which would cost less than 100 USD. This eliminates the need for all individuals to undergo the second phase of testing for cancer localization, which is only necessary if the initial result is positive. For those proceeding to the second component, the cost is anticipated to be less than 20 percent of GRAIL’s Galleri test.

Budnik: We identified a saturation point in the number of proteins needed to achieve optimal sensitivity and specificity for different cancers. Depending on the type of cancer, we found that the inclusion of up to 20 proteins was sufficient to reach a plateau beyond which additional proteins did not enhance the test’s performance. This demonstrates that a carefully selected subset of proteins can provide comprehensive diagnostic information without the need for exhaustive testing. 

Why is there a need for sex-specific diagnostic approaches in cancer detection?

Afshin: It is common to encounter different reference ranges for blood proteins between male and female patients. This difference is not limited to highly abundant proteins but extends to those of lower concentration, indicating inherent biological differences that call for a tailored approach to diagnostics. The difficulty of detecting the same type of cancer varied significantly between male and female patients, even when using sex-specific panels. For instance, certain cancers like osteosarcoma, which are relatively rare, had noticeable differences in the ease of detection between sexes. 

Budnik: There are sex-specific differences in biological processes that must be acknowledged and addressed in any comprehensive diagnostic tool. Our decision to focus on sex-specific proteins comes from the observation that certain proteins perform significantly better in one sex over the other, and that unisex tests often fall short in accuracy due to inherent biological differences. Given that a patient’s sex is a known factor, it’s logical to use this information to maximize the test’s effectiveness right from the early stages of cancer detection. 

What are the main challenges in integrating your new cancer detection test into clinical practice?

Afshin: To make a test work, we need to address three different groups: patients, providers, and payers. Having an accurate and sensitive test is part of the story. The next step is working out the financial aspects, including the cost of the test and the reimbursement model. 

We also need to figure out whether to offer this test to everyone or only to those at high risk for any type of cancer. We need to clearly define what to do once we identify a cancer’s organ of origin, including what further diagnostic procedures to perform and any treatment plans. 

Addressing what to do in case of false positives is another critical component, given that even a test with 99 percent specificity and over 90 percent sensitivity will generate false positives. Lastly, we need to replicate this study in a larger sample size in various populations.

Budnik: The journey ahead involves not only proving the efficacy of our findings on a larger scale but also addressing the logistical challenges of accessibility. You can have a beautiful test, but if 90 percent of the population cannot afford it, it will be useless. The test also needs to be scalable, which includes integrating our tests into hospital settings and reaching out to those unable to visit medical facilities, ensuring that our technology is adaptable from discovery to confirmation modes and ultimately capable of handling hundreds of thousands, if not millions, of tests annually. 

This interview has been condensed and edited for clarity.

Reference

1. Budnik, B., Amirkhani, H., Forouzanfar, M. H. & Afshin, A. Novel proteomics-based plasma test for early detection of multiple cancers in the general population. BMJ Oncol  3, (2024).

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