Open Science Forum: The DIPG Tumor Cell Hotel

This is the weekly blog update of a joint effort by Storm the Heavens and cc-TDI to find a treatment for Diffuse Intrinsic Pontine Glioma (DIPG).  Please bookmark this page, and visit weekly!  Please SCROLL DOWN a little bit to see the latest update!

about DIPG

Diffuse intrinsic pontine glioma (DIPG) is the greatest unmet need among childhood brain tumors, and this is in part because DIPG tumor cells weave themselves into the fabric of the pons nerve cell tracts. Our goal is to un-weave them!

about our Team

Dr. Alexandria Harrold (Ali) is a neuroscientist at cc-TDI began leading this project team.  Now Dr. Anju Karki leads the team in partnership with Dr. Jinah Kim. Their mentor is Dr. Charles Keller.

about our Inspiration

Storm the Heavens was established to honor the legacy of Philomena “Bean” Stendardo, who was diagnosed with Diffuse Intrinsic Pontine Glioma at the age of 7. After fighting DIPG for 10 months, she was called home to our Lord. She leaves behind a legacy of faith that touched the lives of everyone that met her. In her wake, Storm the Heavens aims to bring advancements in DIPG research to the forefront.

updated 06/29/2020:

Thank you, Tumor Cell Hotel/Storm the Heavens supporters!  So much is going on:

  • funding completed April 30, and experiments (just about all) are now done!
  • Anju has drafted a full scientific manuscript, which is now in the hands of our expert statistician, Dr. Joel Michalek (we’ve published 25+ papers with Joel because, as the head of the Air Force agent orange study for more than a decade, he takes statistics very seriously!)
  • We’ve begun a collaboration with Dr. Rebecca Packer, Colorado State University, a neurologist for dog brain tumor patients (yes, pet dogs get brain tumors … and get treated like kids and adults do!)
  • Once the paper is published, we’ll seek additional foundation or NIH funding for the Tumor Cell Hotel’s second phase of building a prototype treatment to test in dog cancer patients before moving to humans (eg, kids with brain tumors)

Thank you again for your support of this project!

updated 03/03/2020:

Since our last update on the first week of February, the TCH project was presented to Dr. Doug Hawkins as a part of the speed science presentation at cc-TDI. Also, on the 13th of February 2020, the TCH project was presented at Shriners Hospitals for Children, Portland and Oregon Health & Science University in the department of Cell, Development and Cancer Biology. Lastly, Dr. Charles Keller attended the Annual Beans Ball in Philadelphia and presented our project update to the STH funders and supporters.

One of the key progresses made this month was updating the manuscript figures. In last update, our experimental data alluded that use of a combination of baits to trap DIPG cells might be an attractive approach instead of an individual bait. Hence, we conducted invasion assays using the baits ‘A’, ‘B’ and ‘C’ on four total cell lines. As expected, not all DIPG cells responded to the baits in a similar manner. Furthermore, we also conducted experiments using a second set of combined baits i.e. ‘c’ and ‘d’. Indeed, this combination might serve as a promising bait for the project. Additionally, based on a published research whereby the scientists have identified a set of four chemoattractant that play a critical role in tumor invasion in DIPG. Hence to determine whether the same chemoattractants would serve as baits for the TCH, we performed similar experiments. The results show that in one of the DIPG cell lines the bait complex does serve as a good attractant. However, the other two cell lines did not show similar response.

Finally, Samuel Rasmussen, our bioengineer designed a few hydrogel models for the ‘trap’ and performed some preliminary experiments. He is meticulously working to optimize the conditions!

Thank you, Storm the Heavens, for the support!

updated 02/03/2020:

During the month of January 2020, the Anju continued to perform experiments using various ligands, i.e. baits to attract the tumor cells. This time we wanted to determine if a combination of baits would serve as a better model to capture the DIPG cells. Interestingly, after multiple rounds of trials, we found a combination of baits that worked well in one set of cell lines.  The combination may vary from patient-to-patient, but that is good to know.  Hence, we have focused on conducting similar experiment in other cell lines of interest in the next few weeks.

As mentioned in our earlier report update, the bioengineers and neuroscientists are working on optimizing the hydrogel experiments to use as a sticky bait for the tumor cells. Hopefully by the end of this month we will have some optimized conditions on the sticky bait.

updated 01/06/2020:

The tumor cell hotel (TCH) project funded by Storm the Heavens (STH) has been an intriguing and challenging scientific venture at cc-TDI. Our scientific group has been constantly dedicated to bring about a novel contribution in defeating the horrendous childhood brain cancer i.e. the DIPG.

With the advent of 2020, we are determined to complete and wrap up the project in a timely manner.  Our quest to find the best bait/s for DIPG cells is ongoing. Accordingly, in the later part of the year, we have focused to expand the bioengineering aspect of the project.

Since our last project update on 12-4-2019, we continued to conduct experiments to investigate the invasive nature of the DIPG tumor cells using a few more baits ‘S1’, ‘S2’ and ‘D’ on various DIPG cell lines maintained in the laboratory. As elucidated earlier, we also repeated some of the experiments to confirm the absolute invasive properties of tumor cells on the bait ‘A’.  Furthermore, we have found yet another growth factor receptor protein that needs an expression analysis experiment and subsequent assays to precisely characterize its capacity to serve as another bait for the tumor cells.

Lastly, in regard to our bioengineering part of the project, we are vigorously performing experiments to try out the sticky bio-material with some of the baits such as ‘A’, ‘S1’, etc. Ideally, we want to utilize some red and green tagged DIPG cells for the data analyses. Hence, we are excited to explore this approach in the upcoming month.


Anju and cc-TDI Neuroscience TEAM

ps.  next update we’ll try to have some neat pictures!

updated 12/7/2019:

Since our  STH update on 11-06-2019, we have performed preliminary experiments using a hydrogel biomaterial on the selected baits ‘A’ and ‘P’ on one of the DIPG cell lines. The data seems promising; however, we will repeat and optimize the experiments before we draw any scientific conclusions.  We might need to make the hydrogel less dense to encourage DIPG cells to enter.

After our optimizations, we will be repeating this experiment across multiple DIPG cell lines along with our shortlisted cytokines.

As mentioned in our previous update, we are also validating the new cytokines using molecular studies such as protein expression analyses, cell growth and cell attracting abilities in the DIPG cell lines.

Anju & Team

updated 11/06/2019:

Since our last update we have performed new experiments to determine whether the selected new baits play a role in DIPG tumor cell invasion. The new findings hint that the two baits, “S” and “A” might be playing important roles for DIPG disease invasion.

Also, we have been deeply invested in creating a library of the bait proteins based on the current literature and the laboratory experiments performed thus far.  Thus far, we have 20+ baits on the list and based on the genetic expression, we have ordered a total of 8 cytokines for further study. Because some of the bait proteins are new to our list, we of course have to perform the same experiments to assess their ability in attracting tumor cells and their potential to bind to respond to the prey and participate in tumor cell growth.

We are as eager to identify the best “super-bait” as soon as possible and we will keep you posted on our new findings.   Anju & Team

update 10/09/2019:

hi, Everyone.  A year ago we moved to facebook posts, and now we’re moving back to monthly updates via this blog.  This entry is a recap of everything in the project so far!

here it goes …

Storm The Heavens supports our project, The Tumor Cell Hotel.  The overall idea was that curing DIPG will require removing DIPG tumor cells from the pons part of the brain.  It’s complicated to do this, because tumor cells interleave with normal cells.  Most other labs (and our lab) have tried finding an Achille’s heel that causes DIPG cells to die in place.  Immunotherapy would be another option (and there are hints this is a good approach from groups in Pittsburg, City of Hope and elsewhere).  The Tumor Cell Hotel supposes that we can get tumor cells to move out of the pons.  Like fly paper, we want tumor cells to ‘smell’ something good, move over to the bait, and then get trapped on sticky paper that has the good-smelling bait.

Here’s what we’ve done and know so far:

  • most of the ‘smell’ receptors that the scientific field has studied are expressed for some children’s tumors, but not all children’s tumor.  These receptors sense a bait that is floating free outside the cell.  We like receptor “E”, “C”, “P” and perhaps “A” because 70% of children’s DIPG tumors have at least one of these smell receptors.
  • the bait for receptors “E’, “C”, “P” and “A” are relatively safe to use, because DIPG tumor cells don’t grow when you add these baits.
  • we can get tumor cells to move to “E”, “A” and somewhat to ”C” baits. But tumor cell movement/attraction is slow (maybe 20% of cells move). Movement/attraction to “P” is better, but given our & other lab’s work on “P”, it might only get 2/3 of cells to move.  We want all cells moving  – and at 10 – 100 times the speed!

Here’s what’s important to know about DIPG research:

  • like every other lab studying DIPG, we spend a lot of time growing DIPG tumor cells in between experiments.  DIPG tumors take a long time to form and grow in children (that’s why it seems like a slow-motion tragedy happening).  In the same way and for the same reasons, it takes a relatively long time to grow DIPG tumor cells in petri dishes.  We have a dozen or more cell lines from different children growing at any given time … all that TLC with petri dishes takes time.

Here’s where science gets interesting:

  • the basic principles of a bait and sticky trap are still fine, but we need to up our game to find a super-bait. No one knows of a super-bait.  We’re going to discover one!
  • it’s relatively easy to order up dozens or hundreds of baits to test.  But we have to be a little smart about our experiments, because DIPG cells grow *so* slowly that it takes weeks to be ready for one experiment.  If we had a test system for movement/attraction that took fewer cells, our experiments could test more baits and results would happen more quickly.  The solution? we’re building a special microfluidics system for testing cell movement/attraction that uses tiny levels of fluid and tumor cells to test dozens if not hundreds of baits at a time.  This is a different microfluidics system that you saw in our videos this summer, but it works on the same principles.
  • we are also branching out on what we call a “bait”.  We’ve decided that the bait doesn’t need to mimic only free-floating substances … we’re using ways to take “anchored-down” baits found in connective tissue and make free-floating versions that we can add to our sticky paper.  This approach  really opened new doors for us:  we found a “smell receptor” that seems to be on all DIPG cell lines we’ve tested.  More about this alternative approach in the weeks and months to come.

How would we rate our progress?

  • we’re doing well.  Not all experiments turn out how you expect, and it’s worth stepping back every once in a while to ensure you’re taking the right road.  We could have pushed ahead with bait “E” or “P” two months ago, but then the Tumor Cell Hotel’s overall performance might have been less than we wanted.  This small step to the side to discover a super-bait will be worth it.  All that we have on the to-do list afterward finding a super-bait is selection of the sticky paper biomaterial.  Fortunately, we already know which hyaluran biomaterial we want to use, so the super-bait discover side project is worthwhile and the project can stay on track.

There’s a saying among scientists that research is searching, thinking critically, then re-searching.  We’re in the thinking critically and re-searching stages, which is where you want to be for every worthwhile project.

update 6/06/2018:

By popular demand, we are switching to less-frequent, more content-rich monthly posts.  These will appear as new blog posts on our website.  For exclusive! week to week updates of late-breaking results, email to be subscribed.  Thank you for supporting this DIPG research!

update 04/20/218:

The project has launched! and the press release has been published.  Tune back in every week at this webpage for updates added below!

update 05/03/2018:

The funding kickoff for this project was May 1st – in anticipation of the start, additional DIPG cell lines and reagents for growing the cells and doing experiments have been ordered.  Cells are coming out of liquid nitrogen storage and into the incubator this week to start experiments.  DIPG cells can require TLC … so don’t be surprised if this takes a few weeks to get them ‘just right’ for experiments.  more soon!

update 05/10/2018:

We should have cell images by the end of the week (we just received the media for the cells on Monday).  I’ve also been working out some kinks with our migration assays (aka Boyden chamber assays) with some less precious cell lines with another lab member in preparation for a similar assay with DIPG cells to see if we can attract DIPG tumor cells to migrate to “the tumor cell hotel.”  Additionally, I’m testing out a new means of introducing fluorescent proteins into primary and neuronal cells, like DIPG cells, which will be helpful to track DIPG cells in all our future experiments.

update 5/31/2018:

We have several DIPG cell lines in culture right now, a couple of which are pictured below.  Many of these are extremely slow growing but once we have enough cells of a given cell line we’ll begin experiments with them to see if the cells will migrate to particular chemotractants (many of which we have in-house ready and waiting).  For good measure, too, we’re confirming the identity of each of these cell lines prior to starting an experiment (this is a best practices measure we always do).

update 6/06/2018:

By popular demand, we are switching to less-frequent, more content-rich monthly posts.  These will appear as new blog posts on our website.  For exclusive! week to week updates of late-breaking results, email to be subscribed.  Thank you for supporting this DIPG research!

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