Spatial Proteomics with Fiona Ginty Ph.D. – Translating Proteomics

Chapters

00:00 – Introduction
01:54 – Fiona’s journey to biology
05:26 – Fiona’s transition to tool development
07:20 – Working at GE Research
11:26 – Identifying the importance of spatial biology
14:43 – How Cell DIVE^TM works
18:25 – The importance of single cell
23:01 – When Fiona realized the technology worked
28:04 – Spatial biology projects Fiona is excited about
30:08 – Fiona’s role in HuBMAP
36:50 – Learnings from HuBMAP so far
38:35 – The future of spatial proteomics in the clinic
46:56 – Current limits on spatial proteomics
49:56 – Current and future uses of AI in spatial proteomics
53:30 – The most exciting thing Fiona learned in her spatial proteomics journey
56:08 – Outro

Resources:

• Method of the Year 2024: Spatial Proteomics
• Paper covering the spatial proteomics technology Fiona worked on at GE Healthcare
  • Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue
• HubMAP – Human BioMolecular Atlas Program
• Human Tumor Atlas Network
• Cell DIVE Multiplex Imaging Solution
• Papers discussing what makes colorectal cancer cells undergo apoptosis in response to chemotherapy
  • An atlas of inter- and intra-tumor heterogeneity of apoptosis competency in colorectal cancer tissue at single-cell resolution
  • Integrated multiplex analysis of cell death regulators in stage II colorectal cancer suggests patients with ‘persister’ cell profiles fail to benefit from adjuvant chemotherapy
• Paper discussing how the distance between tumor cells and cytotoxic t-cells correlates to caspase level
  • Spatial effects of infiltrating T cells on neighbouring cancer cells and prognosis in stage III CRC patients – Azimi – 2024 – The Journal of Pathology – Wiley Online Library
• Paper showing it takes 3 hits from cytotoxic t-cells to kill cancer cells
  • Cytotoxic T cells are able to efficiently eliminate cancer cells by additive cytotoxicity | Nature Communications
• Paper focused on generating new pathology image patches using AI
  • Predicting Breast Cancer Events in Ductal Carcinoma In Situ (DCIS) Using Generative Adversarial Network Augmented Deep Learning Model – PubMed

Acknowledgements

Dr. Ginty wanted to acknowledge the many people she’s worked with on Cell DIVE^TM and as part of HuBMAP. She stresses that these are highly collaborative projects, and just some of the many great team members she’s worked with are listed below.

Cell DIVE:

Anup Sood, Sean Dinn, Yunxia Sui, Sanghee Cho, John Graf , Kathleen Bove, Musodiq Bello, Sudeshna Adak, Michael Lazare, Anirban Bhaduri, Thomas Treynor, Dileep Vangasseri, Alberto Santamaria-Pang, Maureen Bresnahan, Micheal Gerdes, Megan Rothman, Colin McCullough, Chris Sevinsky, Liz McDonough, Christine Surrette, Max Seel, Alex Corwin, Bob Filkins, Kevin Kenny, Brion Sarachan, Mike Montalto, Christoph Hergersberg, John Burczak, Jens Rittscher, Steve Zingelewicz, Dr. Sunil Badve (Emory U), Dr. Yesim Gokmen Polar (Emory U), Eli Lilly collaborators

HuBMAP:

Lou Falo (U. Pitt), Arivarasan Karunamurthy (U. Pitt), John Hickey (Duke), Chenchen Zhu (Stanford), Ioannis Vlachos (BIDMC), Liz McDonough (GE HealthCare Technology and Innovation Center [HTIC]), Sammi Abate (GE HealthCare Technology and Innovation Center [HTIC]), Soumya Ghose (GE HealthCare Technology and Innovation Center [HTIC]), Christine Surrette (GE HealthCare Technology and Innovation Center [HTIC]), Dr. Katy Borner (Indiana U)