Leila.png

Leila

 

PATIENT CASE

Epithelioid Sarcoma

Epithelioid Sarcoma research for Leila, January 10th - 12th at Stanford Center for Genetics and Personalized Medicine.
Dates and Time

Friday January 10th: 6.00 PM - 10.00 PM

Saturday January 11th: 9.00 AM - 10.00 PM

Sunday January 12th: 9.00 AM - 5.00 PM 

Location

Stanford Center for Genetics and Personalized Medicine
3165 Porter Dr
Palo Alto, CA 94304

Google Map

Data

Data access is available for invited participants. Please apply here

  1. Timeline and Summary

  2. Nutritional Supplement Protocol

  3. CT Scans / PET Scans

  4. Genetic / Molecular Oncology Reports

  5. Lab Reports and Doctors Notes

  6. Visit Summaries @ Memorial Sloan Kettering

  7. Pathology Reports

  8. Neoepitope Prediction and Peptide Selection

  9. MSK-IMPACT Report

  10. MSK BAM files

  11. Whole Exome Sequencing from CeGat

  12. Raw CeGat sequence data in FastQ

  13. Aligned CeGat reads in BAM format 

  14. Variant lists in VCF format 

  15. Annotated variant lists

 

DNA and RNA Notes:

1) "A depth coverage of >120 sequence reads per base was attained for 65.09% of the targeted regions. The records denote that the detection of low frequency variation may be impaired and recommends sequencing a new sample." 2) "The quality and quantity of the tumor RNA from the sample 05-2019 was not sufficient for RNA sequencing." We are pursuing additional sequencing however no new data will be available for this event.

Computable Medical Records

Thank you Jason Chin from DNAnexus for putting Leila's medical records in machine readable format using Amazon Comprehend Medical

 
 
 

People

Leila

Patient

 

Leila is the Founder and CEO of SamasourceSamaschool, and LXMI, enterprises that #givework to low-income people around the world using cutting-edge social enterprise models in AI/machine learning, digital freelancing, and clean skincare, respectively. 

In March 2019 Leila was diagnosed with vulvar epithelioid sarcoma, an extremely rare and aggressive cancer. Leila and her medical team are urgently looking for: Potential Clinical Trials, Experimental Immuno-oncology (IO) Therapies,Vaccines, and Other Options for Epithelioid Sarcoma. Please see complete summary below.

Dr. Michael Castro

Leila's Oncologist

Keynote Speaker

Dr. Michael Castro is Leila's medical oncologist. He will deliver the Keynote address on Saturday morning January 11th covering Leila's case summary, and an introduction to Epithelioid Sarcoma. Dr. Castro is a board-certified neuro & medical-oncologist with more than 25-year experience in direct patient care, clinical research, and program development. His key interests include immunotherapy of cancer and precision medicine, i.e. the use of genomic testing and biomarkers to develop more effective and less toxic treatments for cancer patients.

Dr. Michael Snyder

Stanford W. Ascherman Professor and Chair, Department of Genetics
Director, Center for Genomics and Personalized Medicine

Dr. Michael Snyder received his Ph.D. training at the California Institute of Technology and carried out postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics, and one of the major participants of the ENCODE project.

His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has developed many technologies in genomics and proteomics. These including the development of proteome chips, high resolution tiling arrays for the entire human genome, methods for global mapping of transcription factor binding sites (ChIP-chip now replaced by ChIP-seq), paired end sequencing for mapping of structural variation in eukaryotes, de novo genome sequencing of genomes using high throughput technologies and RNA-Seq. These technologies have been used for characterizing genomes, proteomes and regulatory networks.

Seminal findings from the Snyder laboratory include the discovery that much more of the human genome is transcribed and contains regulatory information than was previously appreciated, and a high diversity of transcription factor binding occurs both between and within species.

Diana Saville

CCO, BrainMind

MC

Diana Saville is a close friend of Leila and has been involved in all aspects of her care. Diana is the founding CCO of BrainMind, an impact accelerator for brain science. Diana is an expert in creative communication of complex scientific concepts. She develops multimedia educational programs for doctors, investors, researchers, and patients, and organizes international expert summits on scientific and medical topics.

Aaron Marks Horning

Postdoctoral Research Scholar - Genetics, Stanford

Aaron Horning is a Postdoctoral Research Scholar in Genetics at the Snyder Lab. He is working on generating additional mets data from Leila's sample and will give a presentation on what he did and data that was able to be produced. Aaron studied Biochemistry an Cell Biology at UCSD and received his PhD at UT Health San Antonio in Biomedical Sciences, where he studied cell-free DNA methylation and single-cell RNA sequencing to predict biochemical recurrence in prostate cancer.

Benjamin Rolnik

Director - Stanford Healthcare Innovation Lab

Co-MC and Co-Organizer

Benjamin Rolnik is Director of Stanford's Healthcare Innovation Lab. Ben led Stanford's involvement in this case and facilitated the SCGPM venue. He will give a welcoming talk at the event. Ben has worked with some of the biggest YouTube Stars & personal development leaders in the world, launched 2 technology companies, and founded Integral Fitness, a bicoastal millennial personal development organization. Combining his experience in business with his research at Stanford & UCLA investigating Health, Happiness, Wellbeing, Stress & Resilience, he is engineering universal techniques that can assist anyone in living a life they love.

Ariel Ganz

Postdoctoral Fellow, Stanford

Co-Organizer

Ariel Ganz is a Postdoctoral Fellow in Genetics working with the Chair of Genetics and Personalized Medicine at Stanford, Dr. Michael Snyder. My work applies Precision Health techniques for understanding and improving human wellness.

I have a PhD in Molecular Nutrition with a focus on Chemistry, Biochemistry, and Nutrigenetics from Cornell University. I'm excited about psychoneuroimmunology and personalized approaches to health, nutrition, wellness, and personal growth.

David Gennert

PhD Candidate, Genetics, Stanford

Research Summary Lead Author

Dave Gennert received his B.S. in Biology from Tufts University and is currently pursuing his Ph.D. in Genetics at Stanford University.  His research explores transcriptional and epigenetic changes associated with immune cell function and dysfunction.  He is excited about communicating with the public about science and, as a producer and host for the science news podcast Goggles Optional, making sure everyone gets as excited about new scientific breakthroughs as he does.

Alivia Blount

Research Summary Co-Author

Alivia Blount is a writer with a background in computer science and machine learning. She has extensive medical volunteer experience and is a past participant in Research to the People's patient cases. 

Drew Merit

Graphic Illustrator

Drew Merit is a graphic facilitator, advisor, and performing artist. He leverages visual thinking to augment creative collaboration in academic settings. Drew has taught Visual Thinking and Communication at the Stanford Hasso Plattner Institute of Design (d.school). He has also spoken at the California College of the Arts in San Francisco and facilitated sessions at Google, Citrix, and Mozilla.

Celestine Schnugg

Investor

Friend of Leila 

Celestine Schnugg is an investor and advisor to deeply technical, under networked founders building companies of consequence at Boom Capital. Five years at Eric Schmidt & Dror Berman's VC, Innovation Endeavors. Operating experience at Apple. Innovation advisor to British Airways. Top 100 Most Innovative People award in 2015. Celestine's efforts to advance research for Leila led to Research to the People organizing this case.

 
 
 

Agenda

January 10th: 18.00 - 22.00

18.00 - Dinner

18.30 - Welcome, Introductions, Weekend Objectives

19.30 - Setup, Preliminary Group Formation and Case Discussion

January 11th: 9.00 - 22.00

9.00 - Breakfast

9.15 - Dr. Michael Castro Case Presentation and Keynote Address

10.00 - Aaron Horning PhD will give an update on the sample Stanford Received.

12.00 - Lunch

18.00 - Dinner

January 12th: 9.00 - 17.00

9.00 - Breakfast

12.00 - Lunch

15.30 - Results Presentations

 

Case Summary

Leila is a 37-year-old NYC-based entrepreneur who was diagnosed with vulvar epithelioid sarcoma in March 2019. She underwent two attempted resections and then a radical hemivulvectomy (left) and pelvic lymph node removal, but the tumor kept growing back aggressively. After 6 weeks on the experimental gene therapy drug Tazemetostat, she presented with lung mets in July and was switched to aggressive chemotherapy. The tumors are high-grade and despite shrinking 90% with two rounds of AIM chemo (doxorubicin/ifosfamide), by late summer it spread to a lymph node on her right clavicle and her lungs appeared to have more tumors forming. After switching to two rounds of gemcitabine/docetaxel in September, she developed pneumonitis and bone mets in her ribs and spine, so she did a round of steroids and started a new chemotherapy (liposomal doxorubicin). In November she had targeted radiation on her clavicle lymph node which was pressing painfully on the nerves of her jugular vein, as well as full lung radiation in December to the right lung (the left lung is clear). Also in December, she began immunotherapy (Opdivo) and was given another round of AIM when her lung symptoms became uncontrolled: this appears to have brought the disease back under control. We don’t have much time based on how quickly this is moving and how chemo-resistant it seems to be. We are looking for the best IO/vaccine/experimental options to pursue which can be developed within the next 6 months, the sooner the better. We are exploring vaccinesCRISPR-edited T-cell therapyHDAC targeting/valproic acid, a GSK-3β inhibitor, other chemo combos, and other IO combos. Leila’s Cancer was sequenced by Memorial Sloan Kettering (MSK) and a German company called Cegat and her primary oncologist is Dr. Mrinal Gounder at MSK and her consulting oncologist is Dr. Michael Castro.

 

UPDATE: Leila might have a good chance of responding to checkpoint inhibitor immunotherapy because of a specific mutation in her cancer: new research indicates that her SMARCB1 mutation causes endogenous retroviruses to become expressed as antigens. The challenge at the moment is that Leila’s T-cells will be depleted. We are looking for ideas on how to boost her immune system and target this cancer based on its unique genetic profile.

 

 

TIMELINE

• March: biopsy after cosmetic resection results in diagnosis of aggressive vulvar proximal-type Epithelioid Sarcoma

• April-May: two attempted resections, including a radical hemivulvectomy (left) and lymph node resection with lymph node transplant. Surgeries do not result in clear margins.

• May-Jun: Treatment with Tazemetostat (Epizyme) initiated (continued for 6 weeks)

• July: lung biopsy confirms metastasis; Leila is taken off Tazemetostat and switched to chemo (AIM = doxorubicin/Ifosfamide)

• August: CT scans show total tumor volume decreases significantly (90%) with two rounds of AIM

• Sep: Leila experiences extreme shoulder pain due to new swollen nodule near jugular vein; lung scans also show a region of opacity that might be malignant pleural effusion. Leila is taken off AIM and initiatives new chemo regime: Gemcitabine/Docetaxel combination

• Oct: minimal to no responsiveness to new chemo, pain and lung symptoms increase, mouse models initiated from lung tumor biopsy

• Early Nov: recurring low-grade fevers results in diagnosis of pneumonitis; fluid builds up in lungs, requiring intrusion of PleurX catheter; bone mets confirmed in vertebrae and ribs. Leila is taken off Gemcitabine/Docetaxel and put on steroids + Liposomal Doxorubicin, multiple rounds of targeted radiation administered on clavicle nodule, max dose of oxygen and fentanyl patch used for pain in the shoulder and lower back/spine

• Dec: Lung symptoms and pain worsen. Leila is taken off Liposomal Doxorubicin and put on Votrient. She then starts her first round of Opdivo and immediately undergoes five rounds of radiation to her right lung where the tumors are growing rapidly. After radiation, her platelet count decreases materially and pain and breathing difficulty is at an all-time high, so she was taken off Votrient and put on another round of AIM which, scans pending, seems to have been very effective. 

• Jan: Leila's primary oncologist recommends commencing a second round of AIM in 1-2 weeks (once she has fully recovered from the first round and her blood cell counts are up).  They also plan to do another dose of Opdivo as soon as it is safe to do so.  Her pain has decreased significantly, her white blood cell counts are starting to increase naturally, and her lung symptoms are much better after the AIM treatment.

 

**In Progress: mouse modeling has commenced via Champions Oncology (5 mouse lines implanted with cancer cells to test chemo drug combinations - should be ready in 2-3-months)

 

Communications
All weekend communications will happen on slack. Invited participants have been added to our slack channel.​ 

Transportation

Please note: SCGPM is located a little further from Stanford main campus:

From Palo Alto Cal Train: 3.5 miles - Directions

From Stanford Oval: 3.1 miles - Directions

Parking should be available.

 
 

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