Advancing cancer vaccine research with new tools and technologies

By Papia Chakraborty, Assoc. Dir. and Head of Immuno-Oncology, Amit Chaudhuri, VP, R&D


Cancer vaccines are an upcoming therapeutic modality mobilizing body’s own immune system to eradicate advanced tumors and holds tremendous promise for cancer patients unresponsive to checkpoint inhibitors.

Theoretically, targeting cancer with cancer vaccines has a clear advantage over other targeted therapies in that every cancer patient can be treated with a unique set of cancer vaccine cocktail derived from a set of tumor-specific mutations present in the patient. Although conceptually attractive, the field of cancer vaccines has not delivered on the promise as results from several Phase I/II clinical trials have shown. Surprisingly, in all clinical trials, patients treated with the vaccine cocktail mount an antigen-specific immune response, which in a large subset of patients fail to control tumor growth. There are many reasons for this disconnect between immune response and benefit; quality and magnitude of response, the lack of generation of T-cells that will eliminate tumor cells, the inability of primed and activated T-cells to enter the tumor compartment, the hostile immune-suppressive tumor microenvironment that blunts the T-cell response and finally the absence of T-cell targets on tumor cells.

Antigen Selection – one side of the story

A formidable challenge in the field of vaccines, in particular cancer vaccines, is identifying epitopes that will engage T-cells and induce a robust T-cell response. Thirty years of vaccine development in infectious diseases has taught us that it is relatively easier to produce a prophylactic than a therapeutic vaccine. One of the early approved prophylactic vaccine that significantly reduces the risk of developing human papilloma virus (HPV)-induced cervical cancer in young women combines two proteins expressed by the virus at an early stage of infection. Other successful vaccines that protect us from influenza, yellow fever, polio for example, use attenuated or killed viruses exposing our immune system to a gamut of viral antigens thereby ensuring that most individuals mount their own virus-specific immune response. Through these studies, many immunodominant epitopes restricted to specific HLAs were discovered. In contrast, a large body of work on cancer vaccines has yet to identify similar immunodominant cancer neoepitopes. It is an open question whether tumor cells can harbor immunodominant epitopes without getting eliminated by the immune system?

The exposure of the immune system to cancer cells for a prolonged period of time before disease manifestation may act against the origination of immunodominant epitopes in cancer in contrast to infections, which occur at a much shorter time scale. It is likely that tumor antigens mounting a strong immune response at the time of cancer initiation eliminates tumor cells – thereby erasing the existence of an immunodominant epitope at the very outset. By contrast, tumors that have broken the immune barrier and manifested as a full-blown disease may have eliminated, anergized or suppressed the relevant population of T-cells that were tumor reactive. The field of cancer vaccines requires two different sets of cancer neoepitopes – one that the immune system have encountered, but failed to mount a sustained response due to tumor-mediated immune suppression, and a second set of neoepitopes that T-cells may not have encountered to create an army of activated tumor-directed T-cells. The efficacy of checkpoint blockade antibodies can be enhanced by combining the reinvigoration of antigen-experienced suppressed T-cells and by mobilizing antigen-inexperienced T-cells to become antigen-specific. Finding cancer epitopes that mount both recall (epitopes already encountered by T-cells in the patient) and de-novo (epitopes not seen by T-cells earlier) responses may favor the generation of a broad tumor-directed host immune response. Therefore, assays to identify robust T-cell epitopes is a priority area and a variety of technologies to identify antigen-specific T-cells is pursued both in academia and industry.

Antigen-specific T-cells (other side of the story)

For cancer neoepitopes to mount an effective anti-tumor response, they must engage T-cells, expand them and equip them with ammunition to kill the tumor cells. Antigen-specific T-cell activation starts by the engagement of a neoepitope, a mutated peptide-MHC (peptide-major histocompatibility complex, pMHC) complex with the T-cell receptor (TCR). The pMHC complex is presented on antigen-presenting cells (APCs) and on tumor cells. Engagement with neoepitope-presenting APC activates T-cells making them functionally competent to kill tumors (cytolytic T-cells) or inducing them to become helper T-cells that lack cytolytic activity, but performs other functions related to long-term disease control. Neoepitope cocktails that generate both cytolytic T-cells and helper T-cells may provide long-term survival benefit. Discovering TCRs that engage a pMHC complex to produce CTLs is difficult because one pMHC complex will engage and expand many unique T-cell clones. One has to characterize the function and phenotype of individual T-cells by interrogating a variety of intracellular and cell-surface markers and finally test the T-cells for their tumor killing potential. One approach is to isolate all T-cells that bind a specific pMHC complex (multimers) and analyze them for function, such as their cell killing activity. A second approach popularized by 10X Genomics’s single-cell sequencing platform is to label individual T-cells using a peptide-MHC multimer and characterize them transcriptionally for functional phenotype. A third approach is to combine multimer staining with cell surface marker staining (CITE-Seq) to identify antigen-specific polyfunctional T-cells. Identifying T-cell receptors that engage pMHC complex to deliver protective T-cell response is an active area and can bring novel T-cell directed therapies to treat cancer.

Besides, therapeutic use of T-cells, antigen-specific modulation of the host T-cell repertoire is turning out to be a useful biomarker in the field of cancer immunotherapy. Combining ex vivo and in vivo analysis of T-cell dynamics can be a powerful method to assess the effect of vaccines on patients. The expansion and contraction of specific T-cell clones over the course of therapy can give valuable insights on interactions between T-cells and tumor cells and impact on long-term disease control. Bulk TCR sequencing is a relatively cheaper technology that can provide information on T-cell dynamics through a TCR-centric lens is of considerable clinical value.

Where is the field heading?

Discovery of targets that engage the immune system will continue to remain a focus area in the field of cancer immunotherapy. Novel immunogenic T-cell epitopes will be identified by a variety of new technologies leveraging genomics and proteomics. For example, scientists are probing the dark matter of the genome, short open reading frames scattered within the non-coding regions of the genome to identify epitopes recognized by the immune system using Ribo-Seq. A variety of delivery platform for delivering neoepitopes is being considered for evoking a robust immune response. In addition, as single-cell-sequencing and spatial transcriptomics mature and become inexpensive, they will find greater usage in selecting optimal antigen-specific T-cells with properties to enter the tumor, thereby increasing their effectiveness as a therapy.

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