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Driving the future of Medicine through disruptive convergent technologies
Science across, above and beyond with no boundaries

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Translating discoveries
into diagnostics
and therapeutics

Hand Organs

The main goal of the Center for Transcriptional Medicine is to catalyze the generation of a novel approach to reprogram chronically injured tissues and organs. This program integrates the best-in-class pipeline and teams of experts for the analysis, identification of master regulators, rapid synthesis and testing of targets and effective delivery to the target tissues in all-human experimental systems obtained from explanted organs with end-stage disease.

Our Approach

  • 1

    The workflow of the Center starts with the identification of master regulators of functional identity of specialize epithelial cells using a pipeline that integrates capturing and processing human explanted organs (livers, kidneys, lungs, hearts) with end-stage failure in close collaboration with the Transplant teams at UPMC and the Department of Surgery.

  • 2

    Human explanted tissues and processed cells are then computationally analyzed (e.g., transcriptomics, proteomics, metabolomics) to identify a framework that integrates patients’ orthogonal metabolic signatures and transcriptomes with clinical metadata for identifying and dissecting specific metabolic signatures and phenotypes that define end-stage organ failure.

  • 3

    Once transcription factors that work as master regulators are identified, nuclei acid-based medicines are manufactured and tested for efficiency and delivery in close collaboration with Nobel Prize winner Drew Weissman RNA Institute at UPENN to modify transcriptional programs and networks that affect functional phenotypes.

Pipeline

Coordinating the complex choreography of gene function

Lab scientist with syringe

Convergent Science Motivation

Transcription Factors

Transcription Factors are DNA-binding proteins that can activate or repress DNA transcription and control gene expression and function.

protein-coding genes

There are about 20,000 protein-coding genes in the Human Genome but only about 1,600 Transcription Factors to regulate them.

Transcriptional Reprogramming

Transcriptional Reprogramming is capable to manipulate cell fate by altering the transcriptomic and epigenetic landscapes of a target cell and controlling gene regulatory networks.

Liver Therapy

By systematically studying chronically injured and functionally impaired livers, looking for genetic and cellular mechanisms of action that contribute to end-stage disease; our teams have identified disrupted transcriptional networks and master regulators, that serve as a main control panel to regulate much of the gene expression and function in liver cells. And by applying transcriptional therapy—liver function came back online.

mRNA-based therapies

Dr. Drew Weissman the recent Nobel Laureate, discovered nucleoside base modifications that enabled the development of effective mRNA-based therapies that control protein production such transcription factors and have designed effective nanoparticles for specific delivery of nuclei-acid medicines.

The best People, the best science

Leadership

Alejandro Soto-Gutierrez, MD, PhD
Alejandro Soto-Gutierrez, MD, PhD
Leader

Professor in the Department of Pathology at the University of Pittsburgh.

Sarah Hainer, PhD
Sarah Hainer, PhD
Transcriptional Regulome Leader

Assistant Professor in the Department of Biological Sciences.

Website
Drew Weissman, MD, PhD
Drew Weissman, MD, PhD
Leader

Roberts Family Professor in Vaccine Research and Director of the Penn Institute for RNA Innovation. He is a Professor in the Department of Medicine and Director of Vaccine Research in the Infectious Diseases Division at the Perelman School of Medicine at the University of Pennsylvania.

Website
Deepak Nagrath, PhD
Deepak Nagrath, PhD
Metabolic Transcriptome Leader

Professor in the Department of Biomedical Engineering and Department of Chemical Engineering at the University of Michigan.

Website

Clinical Board

Timothy R. Billiar, MD
Timothy R. Billiar, MD

Executive Vice President & Chief Scientific Officer, UPMC
George Vance Foster Professor and Chair, Department of Surgery
Distinguished Professor of Surgery
Associate Senior Vice Chancellor For Clinical Academics, University of Pittsburgh

Abhinav Humar, MD
Abhinav Humar, MD

Chief, Division of Abdominal Transplantation Surgery
Clinical Director, Thomas E. Starzl Transplantation Institute
Thomas E. Starzl Professor in Transplantation Surgery

Liron Pantanowitz, MD, PhD, MHA
Liron Pantanowitz, MD, PhD, MHA

Chair of the Department of Pathology,
Maud L. Menten Professor of Pathology

Aatur D. Singhi, MD, PhD
Aatur D. Singhi, MD, PhD

Associate Professor of Pathology, Division of Anatomic Pathology
and Molecular Genomic Pathology, Director and Coordinator of Anatomic Pathology Research and Director of the UPMC Developmental Laboratory.

Martin N. Wijkstrom, MD
Martin N. Wijkstrom, MD, FACS

Associate Professor of Surgery
Director, Islet Cell Transplantation
Director, Abdominal Transplant Fellowship
University of Pittsburgh Medical Center

David A. Geller, MD, FACS
David A. Geller, MD, FACS

Director, UPMC Liver Cancer Center
Richard L. Simmons Professor of Surgery, University of Pittsburgh School of Medicine

Christopher Hughes, MD, FACS
Christopher Hughes, MD, FACS

Director of the UPMC Liver Transplant Program
Associate Professor of Surgery
University of Pittsburgh School of Medicine

Pablo G. Sanchez, MD, PhD, FACS
Pablo G. Sanchez, MD, PhD, FACS

Chief, Division of Lung Transplant and Lung Failure
Associate Professor of Cardiothoracic Surgery
Brack G. Hattler Endowed Professor of Cardiothoracic Transplantation
Vice Chair, Diversity, Equity and Inclusion
Director of Lung Transplant Research

Jaideep Behari, MD, PhD
Jaideep Behari, MD, PhD

Associate Professor,
Division of Gastroenterology, Hepatology, and Nutrition.
Director, FLOW Clinic (Fatty Liver, Obesity, and Wellness Clinic)
Associate Director, Pittsburgh Liver Research Center (PLRC)

Naudia L. Jonassaint, MD, MHS, MBA
Naudia L. Jonassaint, MD, MHS, MBA

Gastroenterology
Interim Chief, Division of Gastroenterology, Hepatology and Nutrition
Associate Dean for Clinical Affairs, School of Medicine
Vice Chair, Diversity, Equity, and Inclusion, Department of Medicine
Associate Professor of Medicine

Bishoy A. Gayed, MD
Bishoy A. Gayed, MD

Assistant Professor, University of Pittsburgh School of Medicine
Department of Urology
Genitourinary Oncology

Theodore S Lawrence, MD, PhD
Theodore S Lawrence, MD, PhD

Professor, Radiation Oncology
Radiosensitizers by metabolic and functional imaging Laboratory
University of Michigan Health

Bassem S. Hendawy, MD
Bassem S. Hendawy, MD

Assistant Professor of Pathology,
Division of Transplantation Pathology (Kidney)
University of Pittsburgh Medical Center

Gabriel Sica, MD, PhD
Gabriel Sica, MD, PhD

Professor of Pathology, Division of Anatomic Pathology
Lung Pathology
University of Pittsburgh Medical Center

Tomoharu Yoshizumi, MD, PhD, FACS
Tomoharu Yoshizumi, MD, PhD, FACS

Professor, Department of Surgery and Science,
Graduate School of Medical Sciences,
Kyushu University

Shennen A. Mao, MD
Shennen A. Mao, MD

Assistant Professor
Department of Surgery
Transplant Center
Mayo Clinic Jacksonville

Connectors

Stephen Rennard, MD
Stephen Rennard, MD

Professor, Pulmonary, Critical Care & Sleep Medicine Division
Department of Internal Medicine
University of Nebraska Medical Center

Ira J. Fox, MD
Ira J. Fox, MD

Professor of Surgery and Clinical and Translational Science
Department of Surgery
Department of Pediatrics
University of Pittsburgh

Hooman H. Rashidi MD, MS, FCAP

Executive Director of CPACE (Computational Pathology & AI Center of Excellence)
Associate Dean of AI in Medicine, University of Pittsburgh School of Medicine
Professor & Endowed Chair of Lombardi-Shinozuka Experimental Pathology Research
Executive Vice Chair of Computational Pathology, Department of Pathology

Mohamad-Gabriel Alameh, Ph.D.
Mohamad-Gabriel Alameh, Ph.D.

Assistant Professor of Pathology and Laboratory Medicine
Director, Engineered mRNA and Targeted Nanomedicine Core
Department of Pathology and Laboratory Medicine
University of Pennsylvania
Leader of the Medicine Design and Delivery Medicine Boards

Science Board

Yoram Vodovotz, Ph.D.
Yoram Vodovotz, Ph.D.

Director, Center for Inflammation and Regeneration Modeling
Professor of Surgery, Immunology, Computational and Systems Biology, Clinical and Translational Science, and Communication Science and Disorders
University of Pittsburgh

Cigall Kadoch, PhD
Cigall Kadoch, PhD

Associate Professor, Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School
Investigator, Howard Hughes Medical Institute
Institute Member and Epigenomics Program Co-Director, Broad Institute of MIT and Harvard
Founder, Foghorn Therapeutics (NASDAQ: FHTX)

Vladimir R. Muzykantov, MD, Ph.D
Vladimir R. Muzykantov, MD, Ph.D

Founders Professor in Nanoparticle Research
Vice-Chair for Faculty Development,
Systems Pharmacology and Translational Therapeutics
Department of Pharmacology, University of Pennsylvania

Sofia Diana Merajver, MD, PhD
Sofia Diana Merajver, MD, PhD

Professor, Medical Oncology, Internal Medicine
Breast Oncology Clinic | Rogel Cancer Center
University of Michigan Health

Jacob S Brenner, MD, PhD
Jacob S Brenner, MD, PhD

Assistant Professor & Attending Physician,
Penn Pulmonary & Critical Care and Systems
Departments of Medicine & Pharmacology
University of Pennsylvania

Melanie Königshoff, MD, PhD, ATSF, FERS
Melanie Königshoff, MD, PhD, ATSF, FERS

Professor of Medicine
Associate Chief of Research
Pulmonary, Allergy and Critical Care Medicine
University of Pittsburgh

Hamideh Parhiz, PharmD, Ph.D.
Hamideh Parhiz, PharmD, Ph.D.

Research Assistant Professor
Division of Infectious Diseases, Perelman School of Medicine
University of Pennsylvania

Divay Chandra, MD MSc
Divay Chandra, MD MSc

Assistant Professor of Medicine
Director, Electronic Cigarette Research Initiative
Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
University of Pittsburgh Medical Center

Edward (Ted) Kreider, MD, PhD
Edward (Ted) Kreider, MD, PhD

Division of Infectious Diseases,
Department of Medicine
University of Pennsylvania Perelman School of Medicine
University of Pennsylvania

Dhivyaa Rajasundaram, PhD
Dhivyaa Rajasundaram, PhD

Research Assistant Professor of Pediatrics
Director, Bioinformatics Core at UPMC Children’s Hospital of Pittsburgh

Elena N. Atochina-Vasserman, MD, Ph.D
Elena N. Atochina-Vasserman, MD, Ph.D

Research Assistant Professor of Medicine,
Division of Infectious Diseases, University of Pennsylvania Perelman School of Medicine,
University of Pennsylvania

Kathryn Whitehead, Ph.D.
Kathryn Whitehead, Ph.D.

Professor
Dept. of Chemical Engineering
Carnegie Mellon University

Ruben Zamora, PhD
Ruben Zamora, PhD

Research Professor of Surgery
Department of Surgery
University of Pittsburgh

Hatice Ulku Osmanbeyoglu, PhD
Hatice Ulku Osmanbeyoglu, PhD

Assistant Professor
Department of Biomedical Informatics
Department of Bioengineering
UPMC Hillman Cancer Center
University of Pittsburgh

Special Teams Boards

Organ Processing
John Sembrat

John Sembrat

Lanuza Faccioli, PhD

Lanuza Faccioli, PhD

Zhiping Hu, MD

Zhiping Hu, MD

Functional Epigenomics
Santana Lardo

Santana Lardo

Medicine Design Board
Garima Dwivedi, Ph.D

Garima Dwivedi, Ph.D

Yi-Kan Pan, Ph.D

Yi-Kan Pan, Ph.D

Laurent Giovanni Bartolo, PhD

Laurent Giovanni Bartolo, PhD

Delivery Medicine
Amira Mbarek, Ph.D

Amira Mbarek, Ph.D

Tong Wu, Ph.D

Tong Wu, Ph.D

Omar Banda, PhD

Omar Banda, PhD

METABOLIC SYSTEM BIOLOGY
Olamide Animasahun

Olamide Animasahun

Leyla Nurcihan Altay

Leyla Nurcihan Altay

Strategic Creative Writing and Project Management
Annalisa Baratta, PhD

Annalisa Baratta, PhD

Lawrence Paul

Lawrence Paul

STEM Training and Education for next generation Pioneers (STEPs)

STEPs is an interdisciplinary biomedical research training program for scientists at all levels

STEP Opportunities for All Members

  • Cross disciplinary research opportunities
  • Networking and scientific advancement across multiple labs
  • Mentoring from multiple expert scientists
  • Opportunities for internships and summer research experiences

Postdoctoral Researchers

  1. Intensive training in one of four labs
  2. Bimonthly meetings with cross disciplinary expert scientists and clinicians
  3. Internship opportunities
  4. Mentoring experience

Submit applications via email

Graduate Students

  1. Intensive training in one of four labs
  2. Cross lab training and research experiences
  3. Bimonthly meetings with cross disciplinary expert scientists and clinicians
  4. Undergraduate mentoring experience

Apply to PhD programs at Pitt:

Undergraduate Researchers

  1. Summer training program at Pitt in year 1, with continued research through the academic year
  2. In year 2, summer experience at with University of Michigan or UPenn
  3. Tiered mentoring program with faculty, postdocs, and grad students
  4. Team building activities and experiences

Applications accepted annually from January 1 to March 31

Catalyzing collaborations in new interdisciplinary medical fields

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