Category Archives: IPF

Holiday Reading

CRISPR, fibrosis, immunology, inflammation, autoimmunity, fibrosis, immunotherapy, IPF, lupus, Lymphomas, Leukemias, Myelomas, MS, oncology, TALEN, TILs, tumor microenvironment, Zinc Finger Nuclease

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some of the stuff we’re reviewing over the holiday break. N.b. paywalls ahead!  And at the very end, some current non-science favorites.

Tumor Mutational Landscape

Age related variants of variants occurred in three genes (DNMT3A, TET2, and ASXL1) are associated with hematological malignancy risk  http://www.nejm.org/doi/full/10.1056/NEJMoa1408617 and  http://www.nejm.org/doi/full/10.1056/NEJMoa1409405

News and Views on the NEJM papers  http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3889.html

using siRNA to identify driver genes in breast cancer  http://www.nature.com/nrg/journal/v16/n1/full/nrg3875.html

Immunotherapy

a primer on the role of PD-1 pathway inhibitors in Hodgkin’s Lymphoma, from Nat Rev Clin Oncol  http://www.nature.com/nrclinonc/journal/vaop/ncurrent/full/nrclinonc.2014.227.html

the role of TILs and TIL-associated TNF in the survival of CRC patients  http://www.jci.org/articles/view/74894

nivolumab in metastatic RCC, published data  http://jco.ascopubs.org/content/early/2014/12/22/JCO.2014.59.0703.abstract

resistance to T cells in melanoma (hint: they lose MHC expression)  http://clincancerres.aacrjournals.org/content/20/24/6593.abstract

interesting look at PD-L1 expression of the response of RCC to targeted therapies  http://clincancerres.aacrjournals.org/content/early/2014/12/23/1078-0432.CCR-14-1993.abstract

it’s hard to control ipilimumab-induced tox  http://clincancerres.aacrjournals.org/content/early/2014/12/23/1078-0432.CCR-14 2353.abstract

IO combination review  http://clincancerres.aacrjournals.org/content/20/24/6258.abstract

tumor/microenvironment cross-talk mediated by microRNAs  http://clincancerres.aacrjournals.org/content/20/24/6247.abstract

functional blockade of miR-23a releases TILs in an ex vivo NSCLC assay  http://www.jci.org/articles/view/69094

neutrophils, T cells and lung cancer  http://www.jci.org/articles/view/77053

Given the new immunotherapy data in bladder cancer, a review of the molecular drivers of this tumor type is most welcome  http://www.nature.com/nrc/journal/v15/n1/abs/nrc3817.html

MDSC requirements for survival  http://www.cell.com/immunity/abstract/S1074-7613(14)00436-1

Gene Therapy and CAR T

Novel gene therapy methods puts a safety brake on a retrovirus-based vector  http://www.nature.com/nrd/journal/v13/n12/full/nrd4495.html

a new review of the CRISPR, Talen, and ZFN technologies for gene editing  http://www.jci.org/articles/view/72992

NY-ESO-1 CAR T P1 results in solid tumors: long term follow-up and correlates of response  http://clincancerres.aacrjournals.org/content/early/2014/12/23/1078-0432.CCR-14-2708.abstract

Targeted Therapies

A very timely primer of the role of different PI3K isoforms in diverse cancers  http://www.nature.com/nrc/journal/v15/n1/abs/nrc3860.html

a Notch in the cancer treatment belt? Nope, a bit of a toxic mess made with anti-DLL4 antibody Demcizumab from OncoMed  http://clincancerres.aacrjournals.org/content/20/24/6295.abstract

IL-17 and colon cancer?  http://www.cell.com/immunity/abstract/S1074-7613(14)00446-4

Hematological Malignancies

von Adrian and Sharpe tease apart Follicular Lymphoma  http://www.jci.org/articles/view/76861

the role of one of gp130 in multiple myeloma  http://www.jci.org/articles/view/69094

Fibrosis, Inflammation, Metabolism, MS

a brand new fibrosis review  http://www.jci.org/articles/view/74368

the TRPV4 pathway, TGFbeta and IPF  http://www.jci.org/articles/view/75331

The role of novel branched fatty acid esters of hydroxy fatty acids in Type 2 diabetes  http://www.nature.com/nrd/journal/v13/n12/full/nrd4501.html

will STING finally yield a useful target in lupus?  http://www.jci.org/articles/view/79100

an animal model of JCV infection and PML  http://www.jci.org/articles/view/79186

Investment and Deals

Pharma funding to pull programs out of the academic space  http://www.nature.com/nrd/journal/vaop/ncurrent/full/nrd3078-c2.html

some color from NRDD on the Genentech + NewLink IDO-1 inhibitor deal  http://www.nature.com/nrd/journal/v13/n12/full/nrd4502.html

Also notable

300,000,000. A violent graphic lurid hypnotic novel of the dissolution of consciousness and the consequence of multiple realities converging within our unprepared empty minds and upon our decadent culture. Horrific and wonderful, but not for the squeamish.

Thug Kitchen – eat like you give a #$%@^. Fun, but you get the idea.

Death & Co: Modern Classic Cocktails. Drink like an adult.

Creating a New Therapeutic Focus

Case Studies, fibrosis, IPF, Pathological Cells and Processes, Pathways for Drug Development, TGFbeta

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In 2012 we were engaged by a large local biotech company to evaluate a new therapeutic area. This effort was driven by the desire of the client to move aggressively into a new suite of diseases. We began by doing a deep dive into the client’s existing portfolio in order to identify assets already in development that could be directed to novel diseases. Concurrently we began a comprehensive review of preclinical and clinical stage assets available for partnering or in-licensing. Finally we engaged in pathological pathway analysis to identify novel targets for discovery programs. This effort, initiated and completed within two quarters, led to the eventual acquisition of a private company and its Phase 2 clinical stage assets, for nearly 100MM $USD. Based on our analyses the client also started several new discovery and preclinical development programs to complement the clinical stage acquisition.

Cool Science: Pathways Driving Fibrosis and Related Drug Development

autotaxin, fibrosis, integrins, IPF, LPA and LPA receptors, TGFbeta

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December 10, 2013, by P.D. Rennert
Some recent interesting papers reveal new mechanisms for the regulation of fibrotic pathways, and suggest drug discovery opportunities.
Fibrosis is a huge medical problem and encompasses many different diseases across most organs and tissues: lung, kidney, liver, gut, vasculature, skin, ocular, cardiac, etc. Lets just assume upfront that we recognize that TGFbeta (TGFb) signaling is a critical pathologic pathway in the induction and persistence of the fibrotic state. I want to take that as a given. TGFb is also showing up more and more often in the context of tumor genetics, as befits a critical growth factor. From the drug development perspective, TGFb antagonism not yet been successful due to the toxicities encountered: TGFb is very pleiotropic and controls many normal functions as well. As a result several alternative means to target the TGFb pathway are under development for the treatment of fibrosis.
A very clever strategy for targeting TGFb was developed by researchers at Biogen, along with a top notch group of outside collaborators (see for example Horan et al. 2008). It was determined that activation of TGFb at sites of inflammation and injury, which are sites for the initiation or promotion of fibrosis, depended on an integrin, namely alphavbeta6 (avb6). Biogen developed a monoclonal antibody (mAb) to avb6 and subsequently outlicensed this mAb to Stromedix. I helped bring that mAb back into Biogen 5 years later (early 2012). By then the mAb, now called STX-100, was Phase 2 ready, a testament to the strength of the Stromedix team. Stromedix was acquired for 75MM upfront, plus milestones: a good deal for both companies. 
On the science side, how avb6 activated TGFb was not well understood, but this was thought to involve a conformational change in the beta6 strand of the integrin.
So lets jump ahead, or sideways anyway.
A parallel basic research and drug discovery effort had uncovered an interesting role for the bioactive lipid lysophosphatidic acid (LPA), and for the LPA receptors, in fibrosis. LPA receptor gene-deficient mice (LPAR knock-out or KO) were resistant to the development of fibrosis in a variety of models, and across diseases in different organ systems. This was interesting since it suggested that somehow LPA and the LPARs were regulating the TGFb pathway (see here, and here). How this occurred was not known, and the available data were correlative: when LPARs were blocked, disease was lessened and there was less TGFb, but was this specific to the LPA pathway or was it due to reduced disease activity? It turned out that the LPA/LPAR pathway interacted with integrin biology, in a couple of interesting ways. The first concerned signaling through one of the LPARs, LPAR2. LPARs are G-protein-coupled receptors, that is, they signal using G proteins. We won’t go into these, but its enough to say that signaling from LPAR2 through a specific G-protein induced a conformational change in the beta chain of avb6, and that this conformational change was associated with the ability of avb6 to activate TGFb. The second way has to do with the manner in which LPA is produced by the enzyme autotaxin, and we’ll come back to that later. This is not the only manner in which LPA impacts fibrosis, as was demonstrated by the Amira drugs that are selective antagonists for LPAR1 and perhaps also LPAR3 (see for example, here). This drug also blocked the development of fibrosis in multiple models, and showed activity in early clinical development for idiopathic pulmonary fibrosis (IPF). The data were suggestive enough that Bristol-Myers Squibb bought the company for $325MM upfront in 2011.
Now lets jump ahead.
In 2011 Tim Springer’s lab published a remarkable paper (Shi et al). What this paper explored, using structural biochemical and biophysical techniques, was how TGFb was kept in an inactive state by its own protein structure (called the “straightjacket”). Breaking this inactive state required distinct and critical interactions, one in which TGFb was embedded into the cell membrane in complex with latent TGFb binding proteins (LTBP), which in turn bound to the extracellular matrix, and the other by which TGFb interacted with the avb6 integrin. Productive binding of the integrin required interaction with cell’s the actin filaments, the protein fibers that hold the cell together and also rearrange themselves in order to allow the cell to move. We should note here that integrin:actin interaction is most often mediated by talins, the proteins that sort of cross link the actin filaments (think of rungs on a ladder as a simple picture). This complex interaction of TGFb, avb6, the cell membrane and the actin fibers imposed enough force on TGFb to break its lock, and free it for activation and release from the cell surface. Its as if you had to rearrange the walls of your house in order to open a window. This is a highly regulated system. So, how did avb6 accomplish this trick? Spinger’s lab didn’t give an answer – they were intently focused on the TGFb structure. But a recent paper on a different integrin provides a clue, and maybe brings us back to the LPAR pathway.
A few weeks ago Shen et al (in Nature) elucidated differential signaling by the integrin alphaIIb-beta3 (aIIb-b3), focusing on the interaction of the b3 subunit with talin and with a G-protein, Galpha13 (Ga13). They found a specific amino acid motif – EXE – mediated binding to the G-protein. This motif is found in many beta subunits, including b6. The protein domain in which this motif is found is within a region known to mediate binding to talin, and Shen et al. go on to show that the two binding phenomena are mutually exclusive. Importantly, interaction with the G-protein required binding to fibrinogen, a ligand for the aIIb-b3 integrin. Integrins transmit signals bidirectionally. Inside-out signalling, the process by which an integrin undergoes conformational change in response to ligand binding, is a talin-dependent mechanism. aIIb-b3 integrin ligation mediates platelet aggregation and triggers outside-in signalling, which requires Ga13 and greatly expands thrombus formation. Switching back to interaction with the G-protein corresponds to clot retraction. So this model proposes waves of signaling controlled in part by which component of the cellular machinery – talin or G-protein – is engaged.
It has been demonstrated in lung and kidney fibrosis models that avb6-mediated activation of TGFb can be triggered by the LPAR2 signaling through Galphaq (Gaq) to the Rho/Rac kinase pathway (see here, and here). The connecting dots from Rho/Rac kinase to avb6 activation are not yet described, by may work by regulating the interaction of avb6 with a G-protein (eg. Ga13) v talin or actin. In KO mouse experiments, Ga12/13 were shown to be required for basal TGFb activation in embryonic fibroblasts (MEFs), but not in LPAR2 transfected MEFs. The relevance of this data to the fibrotic condition however is unclear, and I think it remains worth exploring this link further.
There is an independent link between the LPA/LPAR2/avb6/TGFb pathway and integrin biology. The production of LPA is controlled by the enzyme autotaxin. In settings of tissue injury and inflammation, autotaxin and the LPARs are upregulated by various cells. In this way the LPA production machinery (autotaxin) and the responding receptors are operating in tandem. More remarkably, autotaxin is carried into the inflamed or injured tissue by activated cells – platelets, T cells, and likely other cells types. The manner in which autotaxin is transported is by binding to integrins with b1 or b3 subunits, carried on the cell surface and maneuvered into place by the coordinated action of the activated cell (see a review here). This has likely evolved to maximize the production of LPA at sites where it is required – the half life of LPA in circulation is very short, minutes only. Indeed the half-life of TGFb is even shorter, less than one minute.

So, this is a highly coordinated and highly regulated system, as might be expected when dealing with a potent growth factor like TGFb. The implications of the model for drug development are several. First it seems clear that LPA receptor antagonists that can target LPAR2 would be therapeutic and differentiated from the Amira assets now owned by BMS. The benefit of targeting avb6 was discussed earlier in the context of the Stromedix/Biogen deal. Another target that appears here is autotaxin, and several companies are pursuing autotaxin antagonists – I developed a beautiful compound series at X-Rx Discovery, as one example. Finally, there is the very exciting prospect of using the new structural information about TGFb and related proteins (its a big family) to design drugs that selectively block TGFb activation in the context of an activated cell response. This may be one of the things that Scholar Rock Therapeutics, a venture-company founded by Tim Springer and colleagues, is up to now. We’ll have to wait and see.
Bottom line: we are learning a lot about fibrosis pathophysiology, only a little of which is touched on here. With that knowledge will come a new wave of drug development, and ultimately we hope to provide relief for patients suffering from these chronic and very serious diseases.
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