Latest information on COVID-19

Stanford Pathology Research Centers

U19 Center: A vaccine design to induce protective B and T cell immunity against hepatitis C Virus (U19P)

PI: Steven Foung, MD

"The goal of this U19 project is the development of an HCV vaccine to prevent disease progression after virus exposure in a vaccinated host."

The CDC estimates that 3 million people are living with hepatitis C virus (HCV) infection in the United States and there is an annual infection rate of 34,000 new infections. A contributing factor is the consequence of an opioid epidemic that shows no signs of slowing down and is unfortunately associated with increased injection drug use as a major mode to consume illicit opioids. HCV is transmitted by mainly contaminated blood. Data from some states in areas struggling with this problem showed an astonishing 364% increase in infection amongst young adults. The U19 Program is to develop an HCV vaccine to prevent disease progression after virus exposure in a vaccinated individual. The projects focus on the development of a vaccine that will elicit broadly protective antibodies and cellular responses that are long-lasting.

Steven Foung, MD

Stanford Impact of Genomic Variation on Function Center (SIGVFC)

PI: Ansuman Satpathy, MD, PhD

"The mission of the Stanford Impact of Genomic Variation on Function Center is to create a high-quality, open-access, and single cell-resolution reference map of human gene expression and regulation in immune cells during human development, across organ systems in healthy adults, and in patient tissues from diverse immune-related diseases."

A comprehensive map of gene expression and gene regulation in human cells is critical to understand how genetic variation impacts human health and disease. Since gene regulation can be exquisitely cell type-, tissue-, and disease-specific, a comprehensive catalog of these elements has been limited by the lack of scalable single-cell methods that can be applied to diverse human tissues. The mission of the Stanford Impact of Genomic Variation on Function Center is to create a high-quality, open-access, and single cell-resolution reference map of human gene expression and regulation in immune cells during human development, across organ systems in healthy adults, and in patient tissues from diverse immune-related diseases.

The Stanford Impact of Genomic Variation on Function Center is part of a consortium: Impact-of-Genomic-Variation-on-Function-Consortium

Ansuman Satpathy, MD, PhD

Stanford U54: Mechanisms and Duration of Immunity to SARS-CoV-2
Serological Sciences Center of Excellence (SUSS-COE)

PI: Scott Boyd, MD, PhD

"We propose the Stanford U54 SARS-CoV-2 Serological Sciences Center of Excellence (SUSS-COE) as a member of the SeroNet consortium gathered to address the urgent need for better understanding of human immune responses to the SARS-CoV-2 coronavirus pandemic that has engulfed the U.S. and the world."

We propose the Stanford U54 SARS-CoV-2 Serological Sciences Center of Excellence (SUSS-COE) as a member of the SeroNet consortium gathered to address the urgent need for better understanding of human immune responses to the SARS-CoV-2 coronavirus pandemic that has engulfed the U.S. and the world. We will emphasize deep mechanistic analysis of the adaptive immune responses of COVID-19 patients, spanning serological, B cell and T cell responses; analysis of immune responses in the blood as well as mucosal tissue sites; comparing immune responses induced by infection to those induced by candidate vaccines; and paying particular attention to the understanding the clinical needs and immune responses of underserved, underrepresented and at-risk patient populations. Within these parameters, we will attempt to determine the factors that result in effective and durable immunity to SARS-CoV-2 infection and provide useful knowledge and tools for physicians and patients.

The Stanford U54 SARS-CoV-2 Serological Sciences Center of Excellence is part of a consortium. For more information about SeroNet (SUSS-COE) please go to: Stanford SeroNet Center for Excellence. National Cancer Institute (NCI) description: Serological Sciences Centers of Excellence

Scott Boyd, MD, PhD

Stanford Mendelian Genomics Research Center (U01 HG011762-01)

PI: Stephen Montgomery, MD, PhD

"Discovering the genetic underpinnings of Mendelian disease to enable patient diagnosis and guide treatment is greatly facilitated by diverse genomics assays and computational methods."

Rapid advances in genomics have ushered in new opportunities for Mendelian disease discovery and diagnosis. In the last decade, exome and genome sequencing have moved from the research domain to clinical practice. These approaches have identified new disease genes and causative variants for ~30% of individuals suffering from a rare genetic disease. We believe that the systematic application of promising new genomics assays coupled with innovative computational approaches will foster discovery benefitting the 70% of symptomatic individuals without a genetic diagnosis. To this end we are applying long-read whole genome sequencing, RNA-sequencing, epigenomics assays, metabolomics and targeted in vitro and in vivo assays to evaluate a cohort of undiagnosed individuals suspected to have a Mendelian disorder. Our approach is augmented through the development and application of computational strategies enabling improved gene and phenotype matching, integrative multi-omics analysis, and variant interpretation. This work is expected to establish a new frontier in Mendelian disease discovery.

Stephen Montgomery,
MD, PhD

The Stanford Mendelian Genomics Research Center (MRGC) team has developed key prior expertise and leadership in the use of diverse state-of-the-art experimental and computational methods for the diagnosis and discovery of Mendelian disorders. We hypothesize that the next phase of Mendelian genomics research will be defined by assessing and deploying the most effective ‘omics’ strategies. We have proposed that ongoing and iterative integration of functional genomics data into the translational genomics toolkit will significantly increase discovery of new gene and variant disease associations beyond the capabilities of DNA-sequencing assays alone. Work at our site will potentiate the broad impact of the MGRC sites across the country by providing a platform for functional genomics research, validation and diagnosis in Mendelian disease.

Visit the main site at NIH (National Human Genome Research Institute) for more information: The GREGoR Consortium, genomcs research to elucidate the genetics of rare diseases

eDyNAmiC (extrachromosomal DNA in Cancer)
Cancer Grand Challenges

PI: Paul Mischel, MD

The Challange

"Extrachromosomal DNA: Understand the biology of ecDNA generation and action, and develop approaches to target these mechanisms in cancer."

Tackling the extrachromosomal (ecDNA) Cancer Grand Challenge has the potential to transform the care of up-to a third of all cancer patients. ecDNA doesn’t play by the normal “rules” of chromosomal inheritance, enabling tumors to achieve far higher levels of cancer-causing oncogenes than would otherwise be possible. ecDNA hides in plain sight, enabling tumors to be relentless beasts that are especially treatment resistant, adaptive, and aggressive resulting in patients with shorter survivals. Currently, cancer patients do not have a way of knowing whether their tumors have ecDNA, nor are there effective therapies including drugs, radiation, and surgery to address it. A new paradigm to find ecDNA cancer and effectively treat it is needed.

To meet this Grand Challenge, the eDyNAmiC programme brings forward the most comprehensive  strategic approach ever to understand ecDNA and create plans, tools, and capabilities to find it in patients, disarm it, and treat it with uniquely designed therapies. eDyNAmiC’s seven Work Packages (WPs) will advance toward their goals in parallel but also as one team synergising in real time.

Paul Mischel, MD

ecDNA is a different adversary than oncology has faced before. To be able to find it and attack it, we must first understand it. Two of the seven WPs are designed to do just that: WP1 learns how ecDNA forms and functions and WP2 identifies how the structure of ecDNA changes cancer-causing genes to become even more aggressive and resistant to treatment. WP3 and WP4 focus on the theme of finding ecDNA diagnostically through blood analysis, finding what gave rise to it in the first place, and finding vulnerabilities to target with therapies. WP5 and WP6 take on perhaps the toughest challenge—to figure out why ecDNA cancers are so resistant to treatment, adaptive to treatment, and why these tumors are less responsive than most to immuno-therapy. These two WPs will tell us a lot about whether we can take on ecDNA cancer with today’s arsenal of treatments. Finally, WP7 delivers hope by focusing on the development of new, novel classes of medicines designed to transform and cure these cancers. To make this WP realistic yet visionary, we will use advanced medicinal chemistry that is capable of building new molecules and adapting existing drugs to face the ecDNA challenge.

The combined scientific and patient advocacy team bring a uniquely integrated and complementary set of motivations, talents, and resources to this programme. We have the right group for this endeavor because of the leadership of the scientists who made the paradigm shifting discoveries of ecDNA driving cancer growth in the last decade. We are a team of committed people spanning essential disciplines for all WPs, who also add diversity of scientific perspective and offer proven track records of accomplishment and expertise essential for taking on this unprecedented challenge in cancer. Uniting researchers, patients, and patient advocates is a fierce commitment to patients, their families, and the personal experience with cancer in our own lives.