Kasey altman's hackathon updates

Weekly Update Meetings

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Table of Contents

June 3, 2021: Launch & Introductions

Meeting notes

Thanks for your interest in the Kasey Altman hackathon to find the best next treatment for this rare cancer patient.

On Thursday, June 3, we launched the Kasey Altman Hackathon with a presentation of her medical history by her oncologist, Dr. Lenny Wexler of Memorial Sloan Kettering Cancer Center.

Here are some highlights from Dr. Wexler’s presentation and the following discussion:

  • Kasey is a 24 year old woman, diagnosed in October 2020 with stage 4 Fusion-positive (PAX3-FOX01) Alveolar Rhabdomyosarcoma with lymph node and bone involvement

  • Her tumor cells are positive for B7-H3; negative for NY-ESO-1, Her2, PD-L1, EGFR.
    On November 7th she received her first cycle of a standard chemotherapy – “VAC” (Vincristine, Actinomycin-D,and Cyclophosphamide).

  • After three cycles (9 weeks) she had an expected prompt and dramatic improvement. Normally this cancer is highly responsive to chemotherapy, but it often recurs.

  • In early January, she began the first of three cycles of Vinorelbine and Irinotecan.
    Subtle evidence of slight interval progression at primary site between first and second staging scans prompted repeat biopsy in early March

  • March 2021 biopsy results: Microsatellite stable (MSS), tumor mutational burden 1.6 (low Tumor Mutational Burden)
    • MYCN amplification change: 59.1 (increased x20 since Oct. 2020 bx)
    • TP53 deletion, mutation

  • In March, she resumed “VAC” and “VC” chemotherapy while having 33 rounds of radiation – proton therapy – to her primary site, hip bones and sites of initial nodal involvement.

  • On May 17, she began her first of three final planned cycles of another chemo combination (VAI with Ifosfamide replacing Cyclophosphamide), which is gentler on the immune system in anticipation of her eventual consolidation with a personalized vaccine.

  • Whole exome sequencing and RNA sequencing has been performed by Tempus. Three attempts to do RNA sequencing at Memorial Sloan Kettering failed.
    • Concern was shared over results of the RNA sequencing report, prompting need to follow-up with Tempus (method?) and MSK (residual tissue available?)
    • Questions pending include biopsy changes due to genetic evolution or subclonal expansion, why PDX attempts have failed, Dr. Ezra Cohen’s ASCO presentation on UCSD precision immunotherapy trial requested
    • Expectation – MYCN increase x20 would yield other findings on RNA report

  • The Target Cancer Foundation’s Jim Palma will be helping with their TRACK program.
    Conner O’Brien of Ciitizen described their services to host and share Kasey’s medical data.

 

Please see the lightly edited transcription of the meeting and the recording below for more details. Action and pending items will be revisited next Thursday.

If you have any questions, please feel free to contact Kasey or Delsee Altman at kaseyhackathon@gmail.com or Brad Power at bradfordpower@gmail.com.

Best,
Kasey Altman, Delsee Altman, Lupe Montes, and Brad Power

Intro + Dr. Wexler summary (15 min video)
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Discussion + Q&A (45 min video)
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June 10, 2021: Meeting #2 - Getting Organized

Meeting notes

Thanks again for your interest in the Kasey Altman hackathon to find the best next treatment for this rare cancer patient. This is our weekly update, especially for those who were unable to join us in person on Thursday (June 10).

The focus of the conversation was getting our efforts organized moving forward, including three critical paths: (1) what data (diagnostics) we should be gathering, (2) what treatment options exist, and (3) who to participate, especially who best to help prioritize, assess, and decide on Kasey’s best treatment. As people shared questions and ideas, they briefly introduced themselves, and we learned about the wide and deep expertise in the group.  

Here is the latest news from Kasey and Delsee:

• Kasey joined the meeting “live from MSKCC” and reported that she is undergoing 2.5 days of hyperhydration along with 24 hour chemo infusions, and had a false alarm. Her next scan (PET/MRI and CT) is scheduled for Monday, June 21, and we are keeping our fingers crossed for a diagnosis of “No Evidence of Disease”.


• Picking up on an issue raised in the conversation with Kasey’s oncologist (Dr. Lenny Wexler) last week, Tempus is re-running the RNA sequencing (originally ordered for Kasey’s plan to enter this clinical trial).


• We are going to be drafting three foundational documents and updating them as we go: (1) tests that Kasey should get, (2) treatment option candidates, and (3) review board candidates.


Here are some highlights of recommendation from the group as we get the hackathon underway:

• From Bill Passman, an expert in hackathons, having run one for himself in 2018 for his rare kidney cancer: You may want to wait to run tests on the tissue until you have all the people on board who will be reviewing the data. Tissue is precious and may need to be saved. Note whether tests are clinical (can be  used for patient recommendations) vs. research grade.


• From Grace Cordovano, a leader in cancer patient navigation: You should save >30% of the biopsy tissue for Kasey. You should have a system to scan the literature and conferences for new developments that may be relevant.


• From Rebecca Owens, an expert in diagnostics developing patient navigation services: You should strongly consider getting whole genome sequencing over various oncopanels or whole exome sequencing. It is like “defensive driving” — you are covered if things change.


• From Rick Stanton, a pharmaceutical veteran, prostate cancer patient, and developer of a cancer navigation app: You should get a comprehensive immunohistochemistry panel of Kasey’s tissue, RNA sequencing, and spatial analysis that describes the tumor microenvironment.


Several people offered the services of their organizations to help Kasey:

• Stefano Pacifico of Epistemic AI offered their AI platform to the group for uncovering treatment options and personalized matching with patients.


• Berkley Gryder of Case Western, with a rhabdomyosarcoma specialty, will contribute his advice. If RNA seq data is available, he will compare Kasey to his hundreds of other rhabdomyosarcoma RNA seq samples from a gene expression profile.


• Nahuel Villegas of Vivian offered to develop a fruit fly model for Kasey to test treatment options under consideration.


• Simon Davies and Hilary Gan of Teen Cancer America offered to help with publicity and engagement.


Our Requests

1. Tests: If you know of any tests Kasey should get to add data to the treatment decision process, please let us know.


2. People: If there is anyone who you think would enjoy the hackathon or would be a useful contributor, please invite them to participate at cancerhackerlab.com.


3. Treatments: If you have any ideas on treatment options, please submit them.


4. Online discussion: Please use our online discussion forum (Slack) if you have questions, suggestions, or comments.


Please see the lightly edited transcription of the meeting below, and the recording below for more details.

Best,
Kasey Altman, Delsee Altman, Lupe Montes, and Brad Power

Meeting #2 Update (9 min video)
Kasey Altman Meeting Update Title Slide
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Discussion + Q&A (49 min video)
Kasey Altman Q&A Update #2
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June 17, 2021: Meeting #3 - A Personalized Neoantigen Vaccine

Meeting notes

Thanks again for your interest in the Kasey Altman hackathon to find the best next treatment for this rare cancer patient. This is our weekly update (#3), especially for those who were unable to join us in person on Thursday (June 17). Each call has its own flavor, and this one turned into a tutorial/education session with the crowd experts helping us (the lay people/patients/caregivers) understand the science and the choices Kasey faces, especially for her plan to get a personalized cancer vaccine.

Kasey’s Update: In the Hospital Due to Chemo Side Effects

Kasey joined our call from Memorial Sloan Kettering. She was hospitalized at midnight on Wednesday with a fever (over 102) and neutropenia (low neutrophil count) before her Neulasta shot could augment her numbers. (Unfortunately, she missed Tuesday night’s Nets playoff game. She had surprised her dad with tickets for Father’s Day.) It is typical to reach a low ebb 8-10 days after heavy chemotherapy. She got labs, cultures, and IV antibiotics. 

Kasey is scheduled to get scans (PET/MRI and CT) on Monday (June 21). We should have results by our next update on Thursday. Hopefully “No Evidence of Disease”!

Delsee’s Update: Worried about Bridging Kasey to Her Immunotherapy Trial

Delsee reported that Dr. Ezra Cohen’s projections for the availability of a personalized cancer vaccine for Kasey is estimated to be 16 weeks out (which works out to be in early October). This timing creates a possible coverage gap between the end of Kasey’s 9-month frontline treatment (which is coming up in a week) and the beginning of the cancer vaccine. While Kasey’s cancer is responsive to front line treatment, it is known to be aggressive. The challenge is keeping a possible recurrence at bay.

Delsee also updated us on Kasey’s tests: Tempus is performing whole exome sequencing (WES) on the March biopsy tissue, per Dr. Cohen’s request, to provide a complement to the RNA sequencing done on the same tissue sample.

Roundtable Discussion: The Science of Targeted Immunotherapies

The majority of our roundtable discussion revolved around questions, explanations, and suggestions relating to immunotherapy: from differentiating typical vaccines from cancer vaccines and CAR-T cell therapy from precision immunotherapy treatment. Elena Brin (CSO of Athae Bio) helped shed light on these concepts fundamental to Kasey’s current plan and options. For example, among options for patients who express the B7-H3 antigen (which Kasey’s cells highly express), there is a CAR-T clinical trial, eligible to those who experience recurrence or who are refractory (not responding to treatment.)

Data Gathering Update: Recommendations for Potential Tests and Treatment Options

The conversation last meeting and at this meeting reinforced the importance of having working documents that capture the discussion around things like best tests and best treatments. We now have shared docs drafted on tests and treatments for Kasey. Besides a simple spreadsheet, we are also capturing the rationale or explanation that underlies some of the diagnostics and the treatments. At your convenience, please review and comment on these working documents:


In Closing: Our Requests

  • Please review the working documents on Kasey’s possible tests and treatments and edit and comment.
  • Please check out the online conversation (on Slack) and add your comments, questions, and suggestions.
  • For more details, please reference the lightly edited transcription of the meeting (Google docs link below) and the recording (also below).

Best,
Kasey Altman, Delsee Altman, Lupe Montes, and Brad Power

Status update - In the hospital with fever and low immune system (3 min video)
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Discussion - transitioning to a personalized cancer vaccine clinical trial (53 min video)
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