Presenter Bios

---

Salil Bhate, PhD – Broad Institute

---

Tullia Bruno, PhD - University of Pittsburgh Medical Center

Tullia C. Bruno, PhD, is an Assistant Professor in the Department of Immunology at the University of Pittsburgh and a faculty member in the Tumor Microenvironment Center and the Cancer Immunology and Immunotherapy Program at the UPMC Hillman Cancer Center. She obtained her Ph.D. in Immunology from Johns Hopkins in 2010 and completed her postdoctoral fellowship at the University of Colorado in 2015—both with a focus in tumor immunology.  While Dr. Bruno’s PhD training focused on inhibitory receptors on intratumoral T cells, she became interested in the role of B cells and tertiary lymphoid structures (TLS) in the tumor microenvironment (TME) during her postdoctoral fellowship and has built her independent research program around understanding intratumoral B cell and TLS function in multiple human cancers.  Dr. Bruno’s research lab has an overt focus on studying immunity within cancer patients, which makes her research highly translational with the potential for future clinical trials targeting B cells. Thus, Dr. Bruno’s overall research objective is to develop a B cell-specific immunotherapy in the next five to ten years.  Dr. Bruno is actively involved in the UPMC Hillman community, and is an advocate for women in science, as is evidenced by her current role as chair of the UPMC Hillman Women's Initiatives Taskforce and her contributions to the Society of Immunotherapy's Women in Immunotherapy group.

---

Jared K Burks, PhD - MD Anderson Cancer Center

I started my carrier at Texas A&M University learning about patterns in genes and proteins, allowing and facilitating subcellular protein trafficking.  As I have progressed to MD Anderson Cancer Center, I have scaled to cellular trafficking attempting to understand the spatial distribution of cells in organ systems during disease.  As in many parts of life, form equals functions.  How our cells organize speaks to how they function and respond to their local environment.  Bringing together multi-omics approaches allows for greater clarity in these imaging snapshots that are collected.

---

Jaime Rodriguez-Canales, M.D. – Daiichi-Sankyo

Jaime Rodriguez-Canales received his M.D. degree and Anatomic Pathology board certification at the Pontifical Catholic University of Chile (Santiago, Chile). Dr. Rodriguez is also certified by the European Board of Pathology (Utrecht, the Netherlands). From 2002 to 2005 he was fellow in oncologic surgical pathology under the direction of Dr. Juan Rosai, in Milan, Italy. From 2005 to 2012, Dr. Rodriguez was postdoc visiting fellow and research fellow at the Pathogenetics Unit and Laser Capture Microdissection (LCM) Core at the Laboratory of Pathology, National Cancer Institute, NIH. In 2012, Dr. Rodriguez joined Dr. Ignacio Wistuba’s lab at the University of Texas – MD Anderson Cancer Center (Houston, TX) being promoted in 2013 to Assistant Professor and Director of the Immunohistochemistry & Digital Pathology lab of the Department of Translational Molecular Pathology, where he and his team worked optimizing multiplex IHC and Vectra for cancer immunoprofiling. In August 2017, Dr. Rodriguez moved back to Maryland as Senior Pathologist at MedImmune, where he continues to work on multiplex IHC and Vectra - Polaris for immuno-oncology. Dr. Rodriguez has co-authored over 125 peer-reviewed papers, including a study on validation of multiplex IF and multispectral analysis for cancer immunoprofiling (Sci Rep. 2017). Dr. Rodriguez is member of the United States and Canadian Academy of Pathology (USCAP), American Association for Cancer Research (AACR) and the Society for Cancer Immunotherapy (SITC).

The Angelo lab uses custom built high dimensional imaging technologies and computational approaches to understand the interplay between single cell phenotype and tissue histology in health and disease.

They employ a method known as Multiplexed Ion Beam Imaging (MIBI) that uses secondary ion mass spectrometry to image antibodies tagged with isotopically pure elemental metal reporters. MIBI is capable of analyzing up to 100 targets simultaneously over a five-log dynamic range. Thus, MIBI enables highly multiplexed and sensitive immunohistochemistical analysis of complex tissues. The Angelo Lab applies MIBI to questions in the fields of cancer biology, infectious diseases, immune tolerance, allergy, and the maternal-fetal interface in addition to technology and methods development.

---

Chakra Chennubhotla, PhD - PredxBio

Chakra Chennubhotla earned his PhD from the Department of Computer Science at the University of Toronto specializing in computer vision, machine learning and AI. Before joining PredxBio (FKA SpIntellx), Chakra was a Tenured Associate Professor in the Department of Computational and Systems Biology at the University of Pittsburgh School of Medicine. The focus of his research group at Pitt was in building computational and systems pathology models to investigate the molecular origins of human epithelial malignancies from patient primary solid tumor pathology tissue sections. With an eye on translational medicine, his group pursued computer vision, machine learning and AI models that are explainable and spatially driven to capture the spatial hierarchy of intratumor heterogeneity, a key factor in predicting disease progression and therapeutic responses. Chakra co-founded PredxBio to actualize the translational potential of these Pitt IP-fueled platforms. Chakra’s experience encompasses years in both industry and academia. He was the lead PI on several National Institutes of Health and National Science Foundation grants covering broad areas of bioimaging, molecular biophysics, computational and systems biology, and spatial intratumor heterogeneity. He holds several patents and has published extensively, appearing in Science Translational Medicine and Nature Communications, among other prominent journals.

---

James Denegre, PhD - Lunaphore

James Denegre, PhD. received a degree in Developmental Genetics from Wesleyan University, and completed post-doctoral training in patterning of the embryo at Brown University. He eventually found his way to The Jackson Laboratory, where he built the Imaging Core and introduced imaging modalities such as intra vital imaging, optical projection tomography, and whole slide imaging-based image analysis. His proudest accomplishment at the Laboratory was participating in the Knockout Mouse Project (KOMP); an international collaborative effort to create a knockout mouse line for every gene in the genome, and ascribe gene function through extensive phenotyping.  Dr. Denegre led Laboratory efforts in the design and creation of the  Embryonic Lethal portion of KOMP, involving multiple imaging modalities and development of an Image Informatics database.  Dr. Denegre recently joined the commercial world as an Application Scientist, providing spatial biology support for Lunaphore customers.

---

Mark Landers – Akoya

---

Justin Lee, PhD - PathAI

Justin Lee, PhD, is the Senior Director of Machine Learning and Imaging at PathAI, where he is responsible for machine learning product research and development to enable PathAI’s mission of improving patient care using AI powered digital pathology. Justin received a PhD in Health Sciences and Technology from the Massachusetts Institute of Technology (MIT). He has an MS degree in Mechanical Engineering from MIT and B.S. degrees in Physics and Biology from MIT.

---

Kurt Schalper, MD, PhD – Yale University School of Medicine

Dr. Schalper trained as cell/molecular biologist and surgical pathologist. His professional experience includes clinical molecular diagnostics and development of cancer biomarkers. His laboratory focuses on understanding dominant immune evasion pathways in human solid tumors and deciphering the structural/functional determinants of the tumor immune microenvironment in lung cancer. Dr. Schalper is also the director of the Translational Immuno-oncology Laboratory at the Yale Cancer Center where he leads the standardized analysis of biomarkers in clinical trials using advanced cell/tissue analysis platforms.

---

Christian Schurch, PhD - Institute of Pathology, University Hospital Tübingen, Germany

Dr. Christian M. Schürch is a physician-scientist with over fifteen years of experience in basic and translational cancer immunology research, focusing on hematological malignancies and the tumor microenvironment. He obtained his MD and PhD degrees at the University of Bern, Switzerland, and is board certified in surgical pathology by the Swiss Medical Association. Dr. Schürch was a postdoctoral fellow in Dr. Garry Nolan’s lab at Stanford University, where he worked on high-dimensional tissue imaging of human and murine immune organs and cancer tissues using high-multiplex microscopy. He also worked on the application of computer vision and deep learning to big microscopy imaging datasets. Currently, Dr. Schürch is full professor of pathology, consultant pathologist, and principal investigator at the Institute of Pathology, University Hospital Tübingen, Germany. Dr. Schürch’s lab focuses on understanding the role of the tumor microenvironment in (immuno)therapy response in solid and hematological malignancies, including human tumors, in vitro tumor models, and mouse models.

---

Denis Schapiro, PhD - Heidelberg University Hospital, Germany

Dr. Denis Schapiro is a Research Group Leader at the Heidelberg University Hospital focusing on spatial omics technologies and analysis.
Before moving to Heidelberg, he was an Independent Fellow at the Laboratory of Systems Pharmacology at Harvard Medical School and the Klarman Cell Observatory at the Broad Institute where he was a Damon Runyon Quantitative Biology Fellow mentored by Prof. Peter Sorger and Prof. Aviv Regev. Previously, he was supported by the SNFS Mobility Fellowship.
Denis obtained his PhD from the University of Zurich and ETH Zurich in the laboratory of Prof. Bernd Bodenmiller where he worked on Imaging Mass Cytometry and corresponding analysis tools focusing on highly multiplexed image analysis. Denis is the lead developer of the histology topography cytometry analysis toolbox (histoCAT) and the multiple choice microscopy pipeline (MCMICRO).
Prior to this, he received his diploma (Dipl. Biol. (t.o)) at the University of Stuttgart and Harvard Medical School working with Prof. Peter Sorger and Prof. Alfred Goldberg. He was also an intern at the Complex Systems Modeling Group at Bayer AG in Leverkusen focusing on PBPK modeling.

---

Michael Surace, PhD, AstraZeneca

Michael Surace received a BS in Biology from JMU in 2004 before working as a laboratory technician in Pathology at UVA for two years. In 2006 he moved to Blacksburg, VA to pursue graduate studies in nuclear receptor/ TLR cell signaling crosstalk in the polarization of macrophage activation phenotypes. He received his PhD from Virginia Tech in 2010. He took two postdocs at MCV in Richmond, first in the Department of Anatomy and Neurobiology investigating the role of microglial activation in response to toxic insult in Parkinson’s Disease, then in Molecular Biology and Biochemistry, working on astrocytes as inflammatory immune cells in multiple sclerosis. In 2015 he joined STCube Pharmaceuticals as a research scientist where he started working with multiplex immunofluorescesce and image analysis to support mechanistic research, which led to his current position at Medimmune, as a scientist developing the company’s multiplex immunofluorescence program for research and clinical trials.

---

Dr. Janis Taube,  Johns Hopkins Medical Institute

Dr. Janis Taube is an associate professor of dermatology and pathology at the Johns Hopkins University School of Medicine and a member of the Johns Hopkins Kimmel Cancer Center. Her area of clinical expertise is dermatopathology. Dr. Taube serves as the Director of the Division of Dermatopathology and as the Assistant Director of the Dermatoimmunology Laboratory at the School of Medicine.
She is one of the lead scientific researchers in the Department of Dermatology at Johns Hopkins. Her research is related to the study of the B7-H1 molecule. Dr. Taube and her team are seeking to identify the signaling mechanisms behind B7-H1 expression.
She is a member of the College of American Pathologists, United States and Canadian Academy of Pathology, American Society of Dermatopathology and Dermatology Foundation.

---

Amaro Taylor-Weiner, PhD, PathAI

Amaro Taylor-Weiner, PhD, is the VP of Machine Learning at PathAI, where he is responsible for machine learning product research and development to enable PathAI’s mission of improving patient care using AI powered digital pathology. Amaro has worked at PathAI for over 3 years, in his previous role he was the founding member and Director of the Biomedical Data Science and Engineering teams. During his time as Director, Amaro led research efforts in machine learning and translational research programs resulting in patents and publications demonstrating the promise of machine learning for pathology. Prior to PathAI, Amaro was the head of Data Science at Nabla Bio, a computational antibody design company, where he led the development of novel machine learning methods for protein engineering. Amaro has spent his entire career in computational medicine and has led research efforts in cancer genetics, drug development, and precision medicine.

Amaro has his PhD from Harvard University, and his BS in Philosophy and Cognitive Science from Tufts University.

---

Angela Vasaturo, PhD, Associate Director Scientific Affairs, Ultivue

Dr. Angela Vasaturo is a Director of Scientific Affairs at Ultivue. Prior to Ultivue, Angela was a Senior Researcher in Dr. Jerome Galon’s Laboratory of Integrative Cancer Immunology at the Cordeliers Research Center. From 2010-2015 Angela was a postdoctoral researcher in the field of Tumor Immunology at the NCMLS in Nijmegen, NL, and was the recipient of an EMBO short-term fellowship, amongst others. In 2012, Angela was among the first postdocs in Europe to be involved in the development of multiplex IHC and multispectral imaging and analysis of up to six immunofluorescence markers, and today is considered a leading European expert in multiplex IHC techniques, digital pathology, spatial biology and tissue imaging.

Thursday, September 14, 2023

This lecture and hands-on in silico laboratory workshop will be utilizing the Enable Medicine platform to conduct the following exercises.  Instruction will be provided by Dr. Michael Surace (AstraZeneca) and Meredith Manuel (Enable Medicine) as well as others.  Attendees will receive electronic copies of all presentations; computers will be provided on site.

Session 1:

• Introduction to Spatial Biology
  • Core Concepts

• • Single Cell 2D Image Analysis Data Structures
  • Applications of Spatial Biology
    • Descriptive and Exploratory
    • Predictive and Prognostic
  • Types of Queries
    • Hypothesis-Driven
    • Hypothesis-Free
• Preparing Data for the Platform

Session 2:

• Data from multiple sources
• Structure - Stitching, image formats, conversions
• Tissue and Cell Segmentation
• Filtering, QC
  • Artifact removal
• Preprocessing/ Normalization
  • Scale by batch, image -> risks, utility
• Clustering - unsupervised/gating

Session 3:

• Data Analysis
• Review results
• Phenotyping
• Metadata: biomarkers, clinical metadata, survival, response
• Analysis Modules and Appropriate Questions
• Analysis Walkthrough
• Interpretation of Results

 

Friday, September 15, 2023

8:30-9:00        Dr. Michael Surace (AstraZeneca)

Overview Presentation

9:00-10:00      Dr. Janis Taube (Johns Hopkins)

“Multiplex IF/IHC assays: From Discovery to Development”

• • • AstroPath Platform for mIF Biomarker Discovery
    • Inter- and Intra-institutional Reproducibility Studies for mIF Assays
    • Development of SITC Best-Practice Guidelines and Checklist for mIF/IHC

10:00-11:00     Mark Landers (Akoya)

“Bringing Spatial Biology to the Clinic”

• • • Spatial Biology Signatures have Continued to Demonstrate Clinical Utility in Translational Studies.
    • Robust, Reproducible Solutions are Needed to Bring Spatial Biology to the Clinic to Better Serve Patients.
    • Akoya is Building a Platform for Clinical Test and CDx Development to Accelerate Clinical Adoption of Spatial Biology.

11:00-12:00     Dr. Kurt Schalper (Yale University School of Medicine)

“Decoding the Role of the Tumor Microenvironment in Immune Evasion and Therapeutic Sensitivity of Non-small Cell Lung Cancer”

• • • Non-small Cell Lung Cancer
    • Immune Evasion:
    • Immunotherapy Resistance:
    • Spatial Biomarkers

Lunch – 12:00-1:00

1:00-1:45        Dr. James Denegre (Lunaphore)

“Lunaphore COMET: Spatial Cell Profiling with Hyperplex Immunofluorescence”

• • • Employ Standard, “off-the-shelf” Reagents
    • Panel Development and Optimization in Days
    • Robust Segmentation and Phenotyping
    • High Throughput Coupled with High Reproducibility

1:50-2:45        Dr. Salil Bhate (Broad Institute)

“Tissue semantics: from data to rules of organization and development”

• • • The Need for Tissue Semantics: different ways to think about the components of tissues and their spatial and functional relationships
    • Mapping Rules of Tissue Organization and Changes Across Disease Conditions
    • Using Time Course Spatial Data Alongside AI to Map Rules of Development

2:45-3:00        Coffee Break

3:00-3:50        Dr. Justin Lee (PathAI)

“Making machine learning models work across inter-lab variabilities: state-of-the-art domain generalization methods / Bypassing trichrome and Sirius Red stain variabilities: a novel method for collagen characterization and quantification from H&E whole-slide images.”

3:55-4:50        S. Chakra Chennubhotla, PhD (University of Pittsburgh)

Next generation spatial analytics to unravel the hidden circuitries of the tumor microenvironment

• • • Deriving functional cell phenotypes on a continuum from spatial biomarker data
    • Quantifying spatial intra-tumor heterogeneity with pointwise mutual information
    • Identifying outcome-correlated spatial configurations of functional phenotypes
    • Inferring the emergent microdomain-specific signaling networks driving patient outcomes

4:50 - 5:45      Tullia Bruno, PhD (University of Pittsburgh Medical Center)

Leveraging Spatial Imaging and Transcriptomics to Interrogate B-T Cell Cross Talk in Cancer.

5:45 - 6:30      Panel Discussion (Dr. Kurt Schalper, Dr. Salil Bhate, Dr. Justin Lee, Dr. Chennubhotla , Dr. Tullia Bruno)

6:30 - 8:00      Reception

Saturday, September 16, 2023

9:00-10:00      Dr. Denis Schapiro (Heidelberg University Hospital, Germany) – Via Zoom

“From Oncology to Cardiology: Spatial Omics Technologies for Topographic Biomarker Discovery”.

• • • Spatial omics and highly-multiplexed imaging
    • Data analysis and workflows
    • Cardiology
    • Oncology
    • Experimental design

10:05-11:05    Dr. Christian M. Schürch, (Institute of Pathology, University Hospital Tübingen, Germany) – via Zoom

"Deconstructing Disease Mechanisms, Therapy Responses and Patient Outcomes by Highly Multiplexed Tissue Imaging"

• • • Introduction to highly multiplexed tissue imaging methods, especially CODEX
    • Identification of a Spatial Score of immune cell interactions that is associated with immunotherapy outcomes in cutaneous T cell lymphoma
    • Spatial immune cell rearrangement and biomarker expression changes in glioblastoma tissue explants cultured in bioreactors under immunotherapy
    • Sex-specific responses to TNF inhibitor therapy in patients with inflammatory bowel disease

11:10-12:10    Dr. Angela Vasaturo (Ultivue)

"Deciphering the Tumor Microenvironment Using Fast and Robust Custom mIF Panels and Spatial Tissue Analysis"

12:10-1:10      Lunch

1:10-2:10        Dr. Jared Burks (MD Anderson)

“Technological Pathways:  Spatial Whole Omics Approaches”

• • • Integrating multimodality imaging
    • Maximizing tissue usage
    • Looking at the unexpected

2:10-2:30        Coffee/Snacks

2:30-3:30        TBA

3:30-4:00        Dr. Michael Surace (AstraZeneca) Symposium Wrap-up