Papers of the Week 4/13-4/19

Some interesting papers from last week (April 13th-19th):

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3841.html

This was a very cool paper from Novartis that was able to investigate the question of whether resistance mutations for kinase inhibitors are pre-existing, or spontaneously evolve during treatment. They were able to do this by "barcoding" the cells by inserting semi-random 30 nucleotide stretches of DNA into tumor cell lines that would essentially mark each cell within the population uniquely. They tested cell lines that can become resistant to an EGFR inhibitor (Erlotinib) in an EGFR-driven cell line or an ABL1 inhibitor (Imatinib) in a BCR-ABL driven cell line. In multiple replicates of experiments selecting for eventual resistance to each inhibitor, they found the same barcodes surviving in the repeats - which suggests that those cells had an innate resistance to the inhibitors, and did not evolve the resistance through mutation during treatment. One of the ways people hope to get much more durable responses with kinase inhibitors is to combine them, much like what has been done with anti-viral medications for diseases like HIV. If the resistance mutations are already present at low levels in the population, it would be much less likely for one cell to have simultaneous mutations that would confer resistance to both (or more) drugs. For this to work, there needs to be as few or no mutations that overlap in conferring resistance to both drugs. The barcoding system allowed the authors to test for overlapping resistance mechanisms, which they tested with new allosteric inhibitors of ABL1 in the same BCR-ABL cell line. They found the barcodes in resistant populations were largely distinct from those in imatinib-resistant cells. This suggests that the resistance mechanisms are largely non-overlapping, and that the combination of inhibitors could be more successful than either alone. Novartis is currently testing an allosteric ABL1 inhibitor in a phase I clinical trial. This approach of barcoding cells could be quite useful in determining resistance mechanisms, and in finding the best drugs for combination.

Further reading:
Paper from Martin Nowak using mathematical modeling to predict resistance to targeted inhibitors & why combinations of inhibitors with mutually exclusive resistance mechanisms are key to durable responses: http://www.ncbi.nlm.nih.gov/pubmed/23805382

Combination therapy being beneficial is also playing out in the clinic with BRAF + MEK inhibitors > BRAF alone in melanoma: http://www.nejm.org/doi/full/10.1056/NEJMoa1406037
The beneficial effect of this combination is probably not as strong due to multiple overlapping mechanisms of resistance: http://www.ncbi.nlm.nih.gov/pubmed/25673644

STING agonist formulated cancer vaccines can cure established tumors resistant to PD-1 blockade

http://stm.sciencemag.org/content/7/283/283ra52.full?utm_campaign=email-stm-toc&utm_src=email

Aduro timed the publication of this paper well, as it was released the same day as their IPO. They recently partnered this program with Novartis for the development of CDN STING agonists.
This paper details the use of synthetic Cyclic Dinucleotides (CDNs), previously shown to play an important role in the immune response to pathogens. This paper used a co-formulation of CDNs with the GM-CSF secreting vaccine Aduro had previously combined with their modified Listeria vaccine in clinical trials. They named this co-formulation STINGVAX, and administration of STINGVAX had activity by itself against a variety of mouse tumor models. They saw increased CD8+ T-cell infiltration of tumors & an increase in PD-L1 expression on the tumors themselves. Not surprisingly, they tested the combination of STINGVAX with PD-1 blockade and found significantly improved activity in models where either treatment alone had only modest effects. STING agonists look like an interesting and distinct method for stimulating an anti-tumor immune response, so interesting that Novartis was willing to pay over $200 million upfront to partner with them on preclinical data alone.

For further reading on the STING pathway, check out some of the work from Thomas Gajewski's lab, which has previously published on STING in cancer:
http://www.ncbi.nlm.nih.gov/pubmed/?term=sting+gajewski

More on STING agonists from Aduro:
http://www.aduro.com/pipeline/cdn/ 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991150/

The protein LEM promotes CD8⁺ T cell immunity through effects on mitochondrial respiration

http://www.sciencemag.org/content/early/2015/04/15/science.aaa7516.abstract

Impressively, this paper not only discovered and characterized a new protein, LEM, important in T-cell biology, but also suggested it may have uses in cancer therapy. They discovered LEM through a mouse forward genetics mutagenesis screen for mutations that increased the T-cell response to a viral infection model, LCMV. LEM upregulation not only improved the T-cell response to viral infection, but also to the immunogenic B16 melanoma mouse model. They went on to further characterize the role of LEM in T-cell biology to find it played a role in cellular metabolism in T-cells. Considering the mutation they found mediated its beneficial effects through increased protein production of T-cell protein LEM, the most direct application would be to overexpress it in adoptive T-cell transfer (TIL, TCR, CAR-T). This is, in fact, what the discoverers plan on doing, and have already formed a company called ImmunarT around this approach.

Robert writes more about it here:
http://www.biotechr.com/2015/04/lem-onade-for-car-ride.html

Further reading - Another screen that identified potential targets for adoptive transfer:
In vivo discovery of immunotherapy targets in the tumour microenvironment

Heparanase promotes tumor infiltration and antitumor activity of CAR-redirected T lymphocytes

http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3833.html

This paper looked at why longer-term cultured T-cells made into CAR-Ts were less potent, specifically looking at the expression of heparanse, and their invasive ability. They found the cultured CAR-T cells had lower heparanase expression & reduced invasiveness. Since heparanase degrades a key component of the extracellular matrix, they wondered if overexpression of herparanase in the cultured T-cells would restore their invasive ability and improve activity against "stroma-rich" solid tumors. They tested this with a GD2-CAR against a neuroblastoma xenograft model, and found improved activity of the T-cells if they overexpressed herapanase. This paper was interesting, as it focused on the quality of the T-cells, something not as frequently discussed, and perhaps overlooked. Additionally it suggests a way to additionally modify CAR-T cells to improve efficacy in certain tumor types.

Complement Is a Central Mediator of Radiotherapy-Induced Tumor-Specific Immunity and Clinical Response

http://www.cell.com/immunity/abstract/S1074-7613%2815%2900123-5

It has previously been shown that radiotherapy actually can improve the immune system's reaction against a tumor, however, the mechanisms of how this happens are not very clear. This paper surveyed what immune-related transcripts were upregulated post-irradiation and found that the complement pathway of the immune system appeared to be activated. This was surprising, as this pathway had previously been implicated as being immunosuppressive in the tumor microenvironment. In response to radiation, however, they found complement components C3a and C5a to be necessary for the immune response post-radiation therapy. Interestingly, they found dexamethasone, which blocks complement pathway activation and is commonly given to patients receiving radiotherapy, significantly reduced the immune effects & efficacy of radiotherapy. This paper suggests new pathways that may be important for inducing an immune response to tumors.

Further reading: Radiation and dual checkpoint blockade activate non-redundant immune mechanisms in cancer from Andy Minn's lab.
http://www.nature.com/nature/journal/v520/n7547/full/nature14292.html 

by Dan Marks