Sinu P. John, Ph.D.

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Signaling Systems Section
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Our research focuses primarily on identification of cell intrinsic factors (protein coding and non-coding genes) associated with regulation of macrophage signaling. We use high throughput genome-wide techniques such as RNAi screening, CRISPR screening, RNA-seq, ATAC-seq, etc. to identify and characterize the genes and gene-regulatory mechanisms that modulate the immune response in macrophage cells. In addition, we study the role of various external factors (environmental pollutants, drugs, diet, etc.) that modulate the immune response in macrophages with an emphasis to develop therapeutic candidates for the treatment of infectious and immune diseases. We use both bacterial and several emerging viral models such as HIV, Influenza, SARS-CoV-2, etc. to study the impact of immune regulation by various intrinsic and external factors.

Selected Publications

John SP, Singh A, Sun J, Pierre MJ, Alsalih L, Lipsey C, Traore Z, Balcom-Luker S, Bradfield CJ, Song J, Markowitz TE, Smelkinson M, Ferrer M, Fraser IDC. Small-molecule screening identifies Syk kinase inhibition and rutaecarpine as modulators of macrophage training and SARS-CoV-2 infection. Cell Rep. 2022 Oct 4;41(1):111441.

John SP, Sun J, Carlson RJ, Cao B, Bradfield CJ, Song J, Smelkinson M, Fraser IDC. IFIT1 Exerts Opposing Regulatory Effects on the Inflammatory and Interferon Gene Programs in LPS-Activated Human Macrophages. Cell Rep. 2018 Oct 2;25(1):95-106.e6.

John SP, Chin CR, Perreira JM, Feeley EM, Aker AM, Savidis G, Smith SE, Elia AE, Everitt AR, Vora M, Pertel T, Elledge SJ, Kellam P, Brass AL. The CD225 domain of IFITM3 is required for both IFITM protein association and inhibition of influenza A virus and dengue virus replication. J Virol. 2013 Jul;87(14):7837-52.

Zhu J, Gaiha GD, John SP, Pertel T, Chin CR, Gao G, Qu H, Walker BD, Elledge SJ, Brass AL. Reactivation of latent HIV-1 by inhibition of BRD4. Cell Rep. 2012 Oct 25;2(4):807-16.

Everitt AR, Clare S, Pertel T, John SP, Wash RS, Smith SE, Chin CR, Feeley EM, Sims JS, Adams DJ, Wise HM, Kane L, Goulding D, Digard P, Anttila V, Baillie JK, Walsh TS, Hume DA, Palotie A, Xue Y, Colonna V, Tyler-Smith C, Dunning J, Gordon SB; GenISIS Investigators; MOSAIC Investigators; Smyth RL, Openshaw PJ, Dougan G, Brass AL, Kellam P. IFITM3 restricts the morbidity and mortality associated with influenza. Nature. 2012 Mar 25;484(7395):519-23.

Brass AL, Huang IC, Benita Y, John SP, Krishnan MN, Feeley EM, Ryan BJ, Weyer JL, van der Weyden L, Fikrig E, Adams DJ, Xavier RJ, Farzan M, Elledge SJ. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell. 2009 Dec 24;139(7):1243-54.

Visit PubMed for a complete publication listing.

Major Areas of Research
  • Genes and epigenetic states modulating macrophage signaling and function
  • Identification and characterization of trained immunity stimuli
  • Applications of trained immunity in infectious and immune disease

Rachel Sparks, M.D.

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Lymphocyte Biology Section
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Dr. Sparks leads a multidisciplinary team of basic scientists, bioinformaticians, and clinical staff with the goal of using systems biology approaches to study the human immune system in health and disease. Her research focuses on (1) evaluation of both known and unknown immunological disorders to better understand the molecular underpinnings of these diseases, uncover correlates of disease subtypes to help improve diagnosis and prognosis, and identify potential novel treatment targets with the goal of therapeutic trials, and (2) using vaccination and systems immunology to probe the immune system of both healthy individuals and those with immunological disorders.

Clinical Studies

Sample collection from healthy volunteers for assay optimization (Principal Investigator; NCT03538600)

Systems analyses of the immune response to the seasonal influenza vaccine (Principal Investigator; NCT04025580)

Sample collection for systems evaluation of patients with unknown or incompletely characterized immune defects (Principal Investigator; NCT04408950)

A Phase 1/2 Open-label Study to Evaluate the Safety and Efficacy of Tofacitinib for Chronic Granulomatous Disease with Inflammatory Complications (Lead Associate Investigator: NCT05104723)

Selected Publications

Visit PubMed for a complete publication listing.

Major Areas of Research
  • Systems immunology approaches to investigate human immune dysregulation and immunodeficiency
  • Using multi-omics data to design targeted drug therapy trials
  • Understanding vaccine response variation in different immunological backgrounds

Rachel Sparks, M.D.

Specialty(s): Allergy and Immunology, Internal Medicine
Provides direct clinical care to patients at NIH Clinical Center

Education:

M.D., The University of Washington

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New $17 Million Grant Establishes LJI as Global Hub for Immunology Data Curation and Analysis

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La Jolla Institute for Immunology
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New $17 Million Grant Establishes LJI as Global Hub for Immunology Data Curation and Analysis
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Novel Study Model Reveals New Understanding of Fatal Familial Insomnia

NIAID Now |

Novel Study Model Reveals New Understanding of Fatal Familial Insomnia
Cerebral Organoids Show NIAID Investigators Disease Characteristics

Fatal familial insomnia (FFI) is a little-known yet horrific disease in which people die from lack of sleep. A protein mutation in the brain prevents sleep, and the body gradually deteriorates. Fortunately, the disease is extremely rare. Fewer than 1,000 people in the United States are estimated to have FFI, according to the NIH’s Genetic and Rare Diseases Information Center. Unfortunately for those with the disease, it can be hereditary – thus the “familial” aspect in the name and importance of developing diagnostic tests and treatments. 

FFI is among a group of unusual neurologic conditions known as prion diseases – those caused by normally harmless prion protein that can malfunction and kill brain cells. Because FFI is found in the brain (suspected origin is the thalamus) studying its spread is not possible until a patient has died. But at that point, valuable disease information is not available because the brain no longer functions. Likewise, studies in rodents and laboratory glassware only have provided limited information.

In a new study published in PLOS Genetics, scientists from the National Institute of Allergy and Infectious Diseases (NIAID) developed a cerebral organoid model to study the exact protein mutation that causes FFI. Human cerebral organoids are small balls of brain cells ranging in size from a poppy seed to a pea; scientists use human skin cells to create organoids. Cerebral organoids have organization, structure, and electrical signaling systems similar to human brain tissue. Because they can survive in a controlled environment for months to years, cerebral organoids also are ideal for studying nervous system diseases over lengthy periods of time.

In the new study using the FFI organoids, NIAID scientists working at Rocky Mountain Laboratories in Hamilton, Mont., compared cell functions – primarily in neurons – between the FFI model and organoids without the FFI protein mutation, making several important observations about the mutation’s effect on brain cells.

They believe the abnormalities likely are features of asymptomatic FFI that may lead to disease.

They surprisingly did not observe spontaneous change in shape or spread of the FFI protein to additional prion protein. Such spread typically is a trademark of prion disease – changing prion protein throughout the brain from the normal shape to the malfunctioning folded shape.

“Our findings show that the mutation causes brain cells to dysfunction without the need for misfolding,” the study states. “We could confirm that most changes were caused by the presence of the mutation” rather than interacting with prion protein lacking the mutation.

Further, the group found that neurons in the FFI organoid model were impaired because of damaged mitochondria – which typically produce energy to keep the brain cells healthy. In future studies they hope to establish a relationship between impaired mitochondria function and the mutated FFI prion protein, and whether neurons attempt to stay healthy and avoid harm from the mutated FFI prion protein by switching from mitochondria as an energy source.

They also plan to explore relationships between the mutated FFI prion protein and neurons associated with “wakefulness,” sleep and rapid eye movement in the brain.

Reference:
S Foliaki et al. Altered energy metabolism in Fatal Familial Insomnia cerebral organoids is associated with astrogliosis and neuronal dysfunction. PLOS Genetics DOI: (2023).


 

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