Democratising proteomics for cancer and beyond


DDW Editor Reece Armstrong speaks to Nautilus Co-Founder and Chief Scientist Parag Mallick, about the company’s recent collaboration which aims to uncover the proteins that could be behind a rare and fatal childhood cancer.

At the beginning of 2023, proteomics company Nautilus Biotechnology announced a partnership with the Translational Genomics Research Institute (TGen), to study the specific proteins at work in the rare and often fatal childhood cancer, diffuse intrinsic pontine glioma (DIPG).

Nautilus and TGen will work together to interrogate the different forms of proteins at a single-molecule level seen throughout the disease in order to gain a better understanding of the epigenetic mechanisms at work in DIPG.

To do this, Nautilus will use its protein analysis platform to provide TGen with data on the proteins involved in DPIG. The hope is that a better understanding of the entire set of proteins (proteome) behind DIPG could help researchers develop better therapies and diagnostics for the disease.

DIPG is known as a high-grade malignant brain tumour due to both its location and how rapidly it can progress. Whilst the cause of DIPG isn’t known, the disease is characterised by specific mutations in genes coding for histone proteins – a family of basic proteins which can associate with DNA due to their positive charges. These mutated proteins then reprogramme the epigenome, from which the cancer develops.

Nautilus was founded six years ago with the aim of “introducing a novel complementary proteomics technology that would be a complement to the mass spectrometry based and affinity- based techniques that really have dominated the field for the last 20-30 years,” Nautilus Co-Founder and Chief Scientist, Parag Mallick, tells DDW.

Mass spectrometry is one of the most common high- throughput tools used to study proteins. In proteomics, mass spectrometers are used to identify a protein’s characteristics such as its chemical modifications and its structure. It does this by digesting proteins into peptides, following which the peptides are separated, fragmented and ionised by the system. Proteins can then be identified using computational methods, such as running peptide sequences through a protein database to confirm which proteins are present in the sample. However, the accuracy of this process varies and existing methods might only identify 50% of fewer of the proteins in a complex sample1. As such, new protein identification methods that are more accurate and reliable are needed in the study of proteomics and respective disease areas such as oncology.

Through its platform Nautilus is moving away from the peptide-based methods such as mass spectrometry currently used for protein analysis, into single-molecule analysis which the company says could potentially quantify over 95% of the proteome. Another key differentiator of the company’s platform is that it does not digest proteins into peptides, meaning it allows Nautilus “to look at a series of modifications on each individual molecule,” Mallick says.

All of this translates into Nautilus’ goal of developing a better understanding of DIPG and what drives the disease. In particular the company is exploring the relationship between histone proteins and pontine gliomas. For instance, Mallick says he believes “80% of pontine gliomas have mutations in histone H3,” which in turn has a consequence on the “downstream chromatin landscape,” – a structure of DNA, RNA, histones and proteins which house the eukaryotic genome and in which mutations can lead to the development of cancers.

“We also know that these modifications may change the methylation profile of the histone itself, which again impacts the chromatin landscape,” Mallick goes onto explain. The methylation profile can provide insight into why genes are expressing at a certain level and it’s these epigenetic processes that have been linked to diseases such as cancer2.

“To date, it’s very hard to know, do I have a triple modification here and alongside a methylation there, and so being able to say that you’ve got three, four different modifications on a per molecule basis and measure that molecular heterogeneity, that’s really the goal of the collaboration. To look at the mutations alongside the modifications, which can play a role in both enhancing activity or silencing activity, or targeting different promoters and potentially even impacting mitosis itself,” Mallick says.

Dr Patrick Pirrotte, Associate Professor at TGen and Director of Integrated Mass Spectrometry Shared Resource at City of Hope Comprehensive Cancer Center explains the goal of the Nautilus and TGen’s collaboration more concisely.

In a press release about the collaboration, Dr Pirrotte said: “Nautilus’ ability to measure mutations and post-translational modifications on individual histone molecules will provide critical new insights into how proteoform variation drives the biology of this terrible disease.”

How does it work?

Nautilus’ proteome analysis platform works in multiple stages. First, intact protein molecules are immobilised via conjugation to proprietary scaffolds for deposition onto an array with billions of landing pads. “If you picture, essentially a giant chessboard, where every single cell of that chessboard holds one protein molecule, that’s really the heart of our platform,” Mallick says.

Once the proteins are immobilised, researchers can probe them again and again and ask questions that determine their structure. This is done through multi-cycle imaging that allows repeat experiments to be done on proteins without them degrading. Lastly, results are digitised and analysed through machine learning, offering insights into the proteome.

One of the main considerations Nautilus had when developing its platform was really to do with the ease of use compared to mass spectrometers for studying proteins.

“Mass spectrometers are amazingly powerful instruments but require a very specialised skill set to use them,” Mallick says. “The goals of our platform are really to make it more analogous to genome sequencing technologies, which are accessible to just about any biologist.” Mallick tells me that the design of the platform is more akin to a DNA sequencing instrument and includes pattern flow cells and operates the readout by microscopy, a much more accessible tool for researchers to use.

And whilst proteomics isn’t a new field of study, it has largely been left in the hands of proteomics scientists. “If you hand a pharmaceutical company a protein target, they know what to do with it. They have decades and decades of knowledge of how to take that target and turn it into a therapeutic,” Mallick says. “But can we do that faster? Can we do that more effectively? Can we bring those tools to not just the proteomics researcher, but to everybody in that entire ecosystem?”

The goal then is the democratisation of a research tool that can offer amazing discoveries on a much wider scale.

“I think that’s where a substantial gap has been for the field ­– just making it fully accessible to every biologist who wants to study proteins,” Mallick says. The applications for this technology are varied. As the partnership between Nautilus and TGen shows that the companies want to understand the drivers of disease and gaining a deeper understanding of the proteome behind cancers such as DIPG could be key to this. Target discovery then is a key application for Nautilus. Being able to pinpoint specific proteins on diseased tissue, which are not present in the rest of the body or healthy tissue, can help show what the drivers of toxicity are in disease.

“Having the sensitivity to find not only rare protein targets, but also to differentiate that something is exceedingly low in other tissues, that other pieces is actually incredibly important,” Mallick explains.

In the later stages of drug discovery and development, proteomics could be essential to mechanism of action and toxicology studies. If a company has a lead compound, they’d like to understand how it is impacting the cell. Mallick explains that knowing what cells certain forms of proteins have, could help researchers understand whether their lead compounds will be more or less effective.

Mallick stresses that the platform Nautilus has developed isn’t the be all and end all for proteomics studies and that depending on the research questions, some will be best suited to mass spectrometry over the Nautilus platform. “I really do believe that there are going to be a range of proteomic tools, and they’ll just help us elevate the whole ecosystem of proteomics.”

Mallick draws reference to the field of genomics and how research since became more accessible as technology and processes have become cheaper and easier to run.

“Part of my thesis from day one in starting the company was saying we want to bring proteomics technologies into parity with genomics platforms. Anyone who wants to study the proteome should be able to and so I think we’re now seeing that message resonating in the community and seeing other companies beginning to adopt it.”

DDW Volume 24 – Issue 2, Spring 2023


  1. Wang P, Wilson SR. Mass spectrometry-based protein identification by integrating de novo sequencing with database searching. BMC Bioinformatics. 2013;14 Suppl 2(Suppl 2):S24. doi: 10.1186/1471-2105-14-S2-S24. Epub 2013 Jan 21. PMID: 23369017; PMCID: PMC3549845.
  2. genetics-glossary/Gene- Expression#:~:text=Gene%20 expression%20is%20the%20 process,molecules%20that%20 serve%20other%20functions

Parag MallickBiography:

Dr Parag Mallick is Co-founder and Chief Scientist of Nautilus Biotechnology and an Associate Professor at Stanford University who has developed multi-scale approaches to accelerate protein biomarker discovery. He holds a BS in Computer Science from Washington University in St Louis and a PhD in Chemistry & Biochemistry from UCLA.

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