An mRNA Vaccine that Works

By KLG, who has held research and academic positions in three US medical schools since 1995 and is currently Professor of Biochemistry and Associate Dean. He has performed and directed research on protein structure, function, and evolution; cell adhesion and motility; the mechanism of viral fusion proteins; and assembly of the vertebrate heart. He has served on national review panels of both public and private funding agencies, and his research and that of his students has been funded by the American Heart Association, American Cancer Society, and National Institutes of Health.

Although pancreatic ductal adenocarcinoma (PDAC) is relatively uncommon with about 60,000 cases per year in the United States, it is expected to be the second leading cause of cancer-related mortality by 2030 (current cancer statistics).  Of all the cancer diagnoses, PDAC may rival glioblastoma as one of the most dreaded.  Both appear “out of the blue” so to speak.  In contrast, 90% of lung cancer patients have a well-known risk factor that is a matter of personal choice, granted followed by addiction.  While glioblastoma is essentially a terminal diagnosis, PDAC does not lag far behind.  In 2020 the 5-year survival rate [1] for PDAC was 5%.  By 2020 this had risen to nearly 10%.  Although 5-year survival can be a useful metric, in the case of PDAC most of this increase has been due to improved clinical management of the disease using multiagent cytotoxic therapies, primarily in the form of FOLFIRINOX.  This cocktail includes flurouracil, irinotecan, leucovorin, and oxaliplatin and is frankly scary.  The side effects will be severe for many patients, with the ultimate outcome predetermined.

Surgery is the only “cure” for PDAC but is possible in relatively few cases, largely because this cancer is not often diagnosed until it is advanced and frequently metastatic.  Earlier this year I was tutoring a group of medical students when the subject of pancreatic cancer surgery came up.  We went to the online three-dimensional anatomy resources, and one look illustrates why a good surgeon cannot simply “cut PDAC out.” (Figure 1) There is way too much going on around the head of the pancreas, involving the superior mesenteric artery and superior mesenteric vein, for a surgeon to be able to intervene without killing the patient. Any successful treatment of PDAC will require a different approach.

And this brings us to the topic for today: Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer, which was published online in Nature on 10 May 2023.  The conclusion from this report is that this mRNA vaccine works in a proof-of-principle study.  Highlights of this current paper will be covered below, but a deeper understanding of how a novel mRNA cancer vaccine was developed is required for a full appreciation of why this research has such great potential.

Although PDAC usually kills relatively quickly, long-term survivors exist, and this has been attributed to T cell-mediated immunity in these patients.  This research team previously published Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer (November 2017), which supports this observation.  A cascade of mutations is the hallmark of cancer development and progression, and neoantigens are novel protein products of mutant genes in transformed/cancer cells.  They appear both early and late during cancer progression, which is usually a long, multistep process.  If they are recognized as non-self, they can become targets of the immune system.

In this very detailed paper, Vinod P. Balachandran of Memorial Sloan Kettering Cancer Center (MSKCC) in New York and a large international team [2] took a multidisciplinary approach to identify T-cell antigens in long-term PDAC survivors.  They found that “tumors with both the highest neoantigen number and the most abundant CD8+ T-cell infiltrates (indicative of an immune response to the tumor), but neither alone, stratified patients with the longest survival.”  Moreover, neoantigens were found in MUC16, which is also known as CA125.  Cancer Antigen 125 was identified more than 40 years ago as characteristic of ovarian and many other cancers and is used frequently as a clinical marker of cancer.  It is a cell surface glycoprotein (a membrane protein exposed on the outer surface of the cell with sugars attached to it) and therefore readily “visible” to the immune system.

A primary result of this study is that long-term survivors of PDAC [median survival of 6 years (n = 82) versus 0.8 years (n = 68)] mounted the best immune response to the neoantigens.  The survival curves in Figure 1 and Figure 2 of this paper are convincing.  And notably, this research “observed selective loss of high-quality and MUC16 neoantigenic clones on metastatic progression, suggesting neoantigen immunoediting (more on this below).”   Thus, this research published in 2017 identified high-potential markers that can be targets for immune therapy specific for PDAC and showed that the loss of these neoantigens correlates with PDAC progression/metastasis.

The theory proposed by Macfarlane Burnet [3] that immunosurveillance “eliminates transformed cells (i.e., cancer cells) as an evolutionary necessity to maintain tissue homeostasis” goes back to the 1950s.  Otherwise, spontaneous mutations that lead inexorably to tumors would win.  As noted subsequently in Neoantigen quality predicts immunoediting in survivors of pancreatic cancer (May 2022):

“This theory of ‘cancer immunosurveillance was later redefined more broadly as ‘cancer immunoediting’ – as a consequence of the immune system protecting the host from cancer, the immune system must also sculpt developing cancers.  When cancers develop, they accumulate mutations, some of which generate new protein sequences (neoantigens). As neoantigens are mostly absent from the human proteome, they can escape T cell central tolerance in the thymus to become antigens in cancers. However, neoantigens typically arise in passenger mutations, and therefore distribute heterogeneously in cancer cell clones with variable immunogenicity. Thus, T cells selectively ‘edit’ clones with more immunogenic neoantigens, inducing less immunogenic clones to outgrow in cancers.”

This is complicated for the non-immunologist (me) and the layperson, but the theory is that immunoediting allows the immune system to kill the more immunogenic cancer cells and this can lead to less immunogenic clones, i.e., cancer cells that are less susceptible to attack by the immune system, to predominate in the population of cancer cells of a tumor.  This has been proven in mice but has remained unclear in humans.  To address this question, the evolution of 70 human PDAC tumors over 10 years was studied.  The result is that “despite having more time to accumulate mutations, rare long-term survivors of pancreatic cancer who have stronger T cell activity in primary tumors develop genetically less heterogeneous recurrent tumors with fewer immunogenic mutations (neoantigens).”  The conclusion reached after extensive experimental and theoretical analysis is that the human “immune system fundamentally surveils host genetic changes to suppress cancer.” Macfarlane Burnet was correct as expected, and as he had to be.

Which leads us back to the current paper from this research group: Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer (May 2023).  Their previous research showed that cells in PDAC express cancer-specific neoantigens that are suitable for the development of cancer vaccines.  An mRNA vaccine was developed to test this hypothesis.  The techniques used are sophisticated, but they are not experimental, in that any well-supported molecular biology laboratory could do this work.  This is also why the COVID-19 mRNA vaccines were feasible in principle and were developed so rapidly before and during Operation Warp Speed.

The novel part of the research described here is that the mRNA neoantigen vaccines were “synthesized in real time from surgically resected PDAC tumors” from individual patients.  Sixteen (16) patients were treated with this autogene cevumeran mRNA vaccine and the immune checkpoint inhibitor atezolizumab [4] and then 15 of these 16 patients were treated with conventional FOLFIRINOX adjuvant chemotherapy.  Figure 1 is a composite describing the trial design.  This figure is complicated, but the results show that the protocol is both feasible and safe.  Well-chosen clinical endpoints included vaccine-induced neoantigen-specific T cells and 18-month recurrence-free survival (RFS).  Half (8 of 16) of the patients receiving the vaccine induced high levels of neoantigen T cells, which indicates that the immune response to the tumor neoantigens was robust in half of the trial participants.

The key finding in this study is that subjects who mounted an immune response to the neoantigens showed a longer period of recurrence-free survival (Figure 3).  Figure 3a shows the responses (OS, overall survival) and RFS in the safety-evaluable cohort.  Figure 3b illustrates the primary result.  Median RFS was not reached in either time from surgery or time from landmark (date of the last vaccine priming dose) as shown by the red survival curves.  Median RFS for the non-responders was 13.4 months from surgery and 11.0 months from landmark (blue survival curve).  These results demonstrate that the mRNA vaccines to PDAC are effective when the neoantigens induce an immune response, which they did in 50% of the patients in the first test of this experimental and clinical approach to PDAC.

Perhaps just as importantly, the vaccine may be effective against metastatic PDAC, which is incurable by surgery and eventually fatal.  Directly from the paper (Figure 4; the links in this excerpt are functional in manuscript; I have followed each of them and they support the reported results based on my understanding of the experimental rationale and techniques used):

“Patient 29 responded to autogene cevumeran with the second-highest maximal percentage of expanded blood T cells (Fig. 2b) that included vaccine neoantigen-specific polyfunctional CD8⁺ T cells…Patient 29 developed increased serum CA19-9 (a marker of pancreatic cancer somewhat analogous to MUC16/CA125) levels with a new 7-mm liver lesion suggestive of a metastasis after vaccine priming (Fig. 4a).  A biopsy sample did not reveal malignant cells but a dense lymphoid infiltrate (Fig. 4b, left) that included all 15 autogene-cevumeran-expanded (Fig. 4b, middle) CD8⁺ T cell clones with phenotypic evidence of lytic and effector potential (Fig. 4d) (i.e., immune cells that can kill cancer cells).  Digital droplet PCR revealed that this lymphoid infiltrate contained rare cells harboring the TP53R175H mutation, identical to the R175H (the amino acid arginine replaced by the amino acid histidine at position 175 in the protein TP53, previously called p53) driver mutation in the primary tumor of this patient (TP53 mutants that affect DNA repair are common in cancer cells)…This liver lesion disappeared on subsequent imaging (Fig. 4a), which suggests that autogene-cevumeran-expanded T cells may possess the capacity to eradicate micrometastases.”

Yes, this is only one patient, but this could be the one patient that allows the research to be extended to the treatment of metastatic PDAC, and perhaps other cancers for which this mRNA vaccine strategy may be useful.

The title of this post is “An mRNA Vaccine that Works.”  Do the results reported here support that conclusion? Yes, in my view they do.  The number of patients enrolled it the trial was necessarily small, but the outcomes are clear.  Those patients who mounted an immune response to the vaccines had longer recurrence-free survival times than those whose immune response was minimal.  Moreover, in one patient who developed a pancreatic cancer metastasis after the beginning of the trial eliminated the metastasis.

Is this approach feasible at scale?  That depends on the scale.  60,000 PDAC patients per year is a large number.  But the foundation for continued success is strong, especially given the resources available at MSKCC and at other similar cancer research institutions/hospitals.  Expensive?  Yes, but that will also depend on the future of our healthcare system (few reasons for hope on that horizon).  Generalizable to other cancers?  Probably.  The “holy grail” of cancer therapy has always been to find an intervention that kills the cancer while sparing the host, who would be you and me.  So far, the best we can do much of the time is kill cancer cells faster than we kill healthy cells.  Surgery, when possible, plus chemotherapy and radiation oncology often work very well, and these interventions have been a triumph of clinical oncology.

Regarding a “magic bullet” for cancer, one of my tasks in the laboratory a long time ago was to purify ricin from castor beans, which would then be conjugated to antibodies that recognize specific cancer cells.  This antibody-ricin conjugate would be taken up by these cells and the passenger ricin would then kill them [5].  I have not looked lately, but this particular approach did not seem likely to work.  Prostate brachytherapy (insertion of radioactive pellets) has been useful in the treatment of prostate cancer and is a nearly literal magic bullet of another sort that kills cancer cells in the tumor while not affecting surrounding areas.

A current directed approach to cancer is CAR T-cell therapy (CAR: chimeric antibody receptor) for various leukemias and lymphomas.  This is very promising but difficult and extremely labor intensive and expensive as described at the link:

“Currently available CAR T-cell therapies are customized for each individual patient. They are made by collecting T cells from the patient and re-engineering them in the laboratory to produce proteins on their surface called chimeric antigen receptors, or CARs. The CARs recognize and bind to specific proteins, or antigens, on the surface of cancer cells… After the revamped T cells are “expanded” into the millions in the laboratory, they’re then infused back into the patient. If all goes as planned, the CAR T cells will continue to multiply in the patient’s body and, with guidance from their engineered receptor, recognize and kill any cancer cells that harbor the target antigen on their surfaces.”

The cellular and molecular mechanisms of CAR T-cell therapy are similar to those of the PDAC vaccines described here.  The mRNA vaccine approach seems more direct and more likely to work for solid tumors.  And mRNAs tunable to an individual cancer in real time.  It is important to remember that cancer is a thousand different diseases, and each individual cancer consists of a genetically heterogenous population of cells that are most likely derived from one progenitor mutant cell.  As shown in the research described here, the PDAC vaccine can be prepared from an individual tumor in real time and used in a matter of days as personalized therapy.  In this first study, only 50 percent of the patients mounted the necessary immune response.  Further research should identify the reasons for this.  But if even if the exact mechanisms are never known, which has been true for sometimes successful immune approaches to cancer that have preceded CAR T-cell therapy, a 50% success rate based on well understood underlying biology is a strong result.

Nevertheless, mRNA vaccines have had a checkered past and present, even though an mRNA vaccine has been more or less obvious since Francis Crick proposed the Central Dogma of Molecular Biology in the late-1950s: DNA makes RNA makes Protein.  With an mRNA vaccine the protein produced in host cells is the antigenic component of the vaccine.  However, mRNA vaccines against Zika virus are still a work in progress, to my knowledge.  The mRNA vaccines against SARS-CoV-2/COVID-19 have not met expectations, which were probably unreasonable for a respiratory virus.  Plus, it has long been known that lasting immunity to coronaviruses has been difficult to induce by vaccines or to sustain after infection.  That may eventually change.  In the meantime, COVID-19 is still here.

Which brings us to a final point about immune surveillance and the maintenance of tissue homeostasis in animals, meaning us, that helps keep us mostly cancer-free.  The work described here has shown that our immune system can identify pancreatic cancer cells and kill them.  A well-known cancer antigen (MUC16/CA125) is a prominent target neoantigen in PDAC.  After showing that immune surveillance is involved in the development of PDAC, the mRNA vaccine followed.  Half of the patients who received the vaccine mounted an effective response to PDAC, including perhaps to a liver metastasis.  This is remarkable in every good way, an example of good science done well, and while the effort was large this science is not the “Big Science” that Karl Popper rightly feared would eclipse good science.  Nor is it typical of what has become evidence-based medicine.

One of the worries about COVID-19 is that immune system dysregulation that seems to follow SARS-CoV-2 infection in many pandemic survivors will lead to impaired immune surveillance in these individuals.  Will a cancer epidemic follow the COVID-19 pandemic as immune surveillance in COVID-19 survivors is attenuated?  This is a good question, one that has been asked here from time to time.  The answer is currently unknown.  In the meantime, go long on masks and encourage good behavior when and where necessary.  Other non-pharmaceutical interventions (NPI) such as air filtration and improved ventilation are engineering solutions that work.  Also trust that scientists out there are following David Ho and others, who introduced the triple therapy that rendered AIDS a manageable chronic condition that is symptom-free among many of those infected with HIV.  Since coronaviruses may be persistent but do not insert themselves into the host genome, antiviral compounds for COVID-19 seem to be a likely solution to the pandemic, along with broadly active intranasal vaccines that interfere with initial infection.

But regarding pancreatic cancer, an mRNA vaccine has shown great promise.  The RNA World has been a thing for the past 30 years.  Now RNA therapeutics are beginning to show their utility along with proteins (e.g., atezolizumab and trastuzumab).  We need only vision and resolve to make them work in the wider clinical world.

NOTES

[1]  Many years ago, a measurable increase in 5-year survival rate for lung cancer was trumpeted as a success story by the Cancer Establishment.  I was initially very hopeful, given that my father had been a smoker since the US Navy taught him the habit as a 19-year-old in 1949, and he had been a chemical worker since leaving the Navy in 1953.  Thus, his risk factors were considerable.  It turns out that when the data were analyzed further, most of the 5-year survivors eventually died of lung cancer anyway, and the increase in survival rate was an artifact if improved clinical management.  My father died of a brainstem tumor secondary to lung cancer five weeks after his 55^th birthday.

[2]  This research was supervised jointly by Taha Merghoub and Steven D. Leach, with MSKCC and other relevant affiliations.  Following the current necessary convention, “competing financial interests” are available in the online version of the paper at the link.  For what it’s worth, the list seems shorter than usual.  In my view the data presented are very strong, without the necessity of statistical reasoning to make their argument.  Statistical significance here seems very correlated with clinical relevance, which is not a given in modern “evidence-based medicine.  This is true of all the primary research covered here.

[3]  And others.  Throughout the middle of the 20^th century the discipline of immunology was developed by a large group if biologists and physicians.  It is still very much a work in progress.

[4]  From the National Cancer Institute link: Atezolizumab is a type of targeted therapy drug called an immune checkpoint inhibitor. It is a monoclonal antibody that works by binding to the protein PD-L1 on the surface of some cancer cells, which keeps cancer cells from suppressing the immune system. This allows the immune system to attack the cancer cells.

[5]  Ricin is justifiably infamous.  One molecule is probably enough to kill one cell, and the poison was the agent used to assassinate the Bulgarian dissident Georgi Markov in London in 1978.  But ricin is poisonous only when injected, although consumption of castor beans is not recommended.  Ricin, which is also a lectin (carbohydrate binding protein) is not soluble in oil, so castor oil is not dangerous, for this particular reason.