Translational Science Interagency Fellowship Projects and Mentors

FDA Mentor Names

Huixiao Hong, Ph.D.

Ru Chen

Position and Organizational Affiliation

Huixiao Hong: SBRBPAS Expert / Branch Chief, Division of Bioinformatics and Biostatistics, NCTR

Ru Chen: Staff Fellow, Office of Translational Sciences, CDER

Contact Information (email/telephone)

Huixiao.Hong@fda.hhs.gov / 870-543-7296

Ru.Chen@fda.hhs.gov/240-402-0302

NCATS Mentor Names

Menghang Xia, Ph.D.

Ruili Huang, Ph.D.

Position and Organizational Affiliation

Menghang Xia: Tox21 Biology Team Lead, DPI

Ruili Huang: Tox21 Informatics Team Lead, DPI

Contact Information (email/telephone)

mxia@mail.nih.gov /301-827-5359

huangru@mail.nih.gov /301-827-0944

Research Project Summary

Many nitrosamines have been found to be carcinogenic and mutagenic and have been identified as impurities existing in drug products, casting doubt on the safety of these products. The FDA has published a guidance for industry on the control of nitrosamine impurities in clinical used drugs for preparing initial risk assessments. Thus, assessing the potential carcinogenicity and mutagenicity of nitrosamines is vital for facilitating safety evaluation of drug products in regulatory science. Evaluation of numerous nitrosamines using animals for their carcinogenicity and mutagenicity is not feasible. Therefore, alternative methods such as in vitro assays and machine learning for assessing the potential carcinogenicity and mutagenicity of nitrosamines are urgently needed to assist safety evaluation of drug products. This proposal will use machine learning combined with in vitro genotoxicity assays to assess the potential carcinogenicity and mutagenicity of nitrosamines present in drug products. The outcomes from this project will help FDA to evaluate the potential carcinogenicity and mutagenicity of nitrosamine impurities in a timely fashion and to ultimately improve risk assessment of drug products.

Proposed Project for TSIF Fellow

We will develop machine learning models and validate the models with in vitro assays for assessing potential carcinogenicity and mutagenicity of nitrosamines in drug products. At FDA, the fellow will collect nitrosamines and their toxicological effects from FDA’s regulatory documents, public databases, and literature, develop predictive models of carcinogenicity and mutagenicity using machine learning algorithms such as decision forest [1] based on Mold2 descriptors [2] using chemicals curated from public databases and literature as the training set, and predict the potential carcinogenicity and mutagenicity of the curated nitrosamines using the developed models. At NCATS, the fellow will test carcinogenicity and mutagenicity using various in vitro cell-based qHTS assays [3] for the collected nitrosamines and will assess potential carcinogenicity and mutagenicity of nitrosamines in drug products by combining the results of machine learning model predictions and in vitro genotoxicity assays.

Relevant Publications

1. Tong W, Hong H, Fang H, Xie Q, Perkins R. Decision forest: combining the predictions of multiple independent decision tree models. J Chem Inf Comput Sci. 2003 Mar-Apr;43(2):525-31. doi: 10.1021/ci020058s. PMID: 12653517.
2. Hong H, Xie Q, Ge W, Qian F, Fang H, Shi L, Su Z, Perkins R, Tong W. Mold2, molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics. J Chem Inf Model. 2008 Jul;48(7):1337-44. doi: 10.1021/ci800038f. Epub 2008 Jun 20. PMID: 18564836.
3. Hsieh J, Smith-Roe S, Huang R, Sedykh A, Shockley K, Auerbach S, Merrick B, Xia M, Tice R, Witt K (2019) Identifying Compounds with Genotoxicity Potential Using Tox21 High Throughput Screening Assays. Chemical Research in Toxicology 32:1384-1401

FDA Mentor Name

Daniela Verthelyi, M.D., Ph.D.

Position and Organizational Affiliation

Chief, Laboratory of Immunology, CDER

Contact Information (email/telephone)

daniela.verthelyi@fda.hhs.gov / 240-402-7450 

NCATS Mentor Name

Mark Henderson, Ph.D.

Position and Organizational Affiliation

Biology Group Leader, Early Translation Branch, DPI

Contact Information (email/telephone)

hendersonmj@mail.nih.gov / 301-827-1769

Research Project Summary

The last five years have seen a rapid increase in the number of nucleic acid-based therapeutics under development, in clinical trials, or approved for human use. This class of therapeutics includes antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), and messenger RNAs (mRNAs). Nucleic acids have been reported to elicit off-target effects on innate immune cells via binding to pattern recognition receptors (PRRs), which can trigger inflammatory signaling cascades, and in some instances has been associated with fever-like symptoms or thrombocytopenia in clinical trials. These can be due to unintended effects of the oligonucleotides or impurities in the product. We propose to investigate and develop cell-based reporters of immune cell activation that can be utilized to better characterize nucleic acid-based therapeutics. Macrophages, which express PRRs and can recognize nucleic acids, are an essential component of the innate immune system that can rapidly respond to their environment. This project proposes to engineer iPSCs CRISPR/Cas9 technology and differentiate these cells to macrophage lineage to create bioreporters of inflammatory signaling, interferon inducible responses, and oxidative stress (e.g. heme oxygenase 1).

Proposed Project for TSIF Fellow

First, the fellow would train at FDA/CDER, where (s)he would learn about drug product immunogenicity in the Verthelyi lab. The fellow will gain an understanding of current strategies to assess immune responses to active pharmaceutical ingredients and product impurities for new molecular entities and generic nucleic acid products. 

Second, the fellow would train at NCATS/DPI, where (s)he would continue learning about assay development and engage in optimization and implementation of the iPSC-derived macrophage assays. PRR activation will be investigated by comparing current assay technologies (immortalized cells, e.g. THP-1 RAW264.7, HEK293) with the newly generated reporter cells that are differentiated into macrophages (M0, M1, or M2 phenotype). The effects of nucleic acid therapeutics will be examined, with a focus on optimizing assay robustness and reproducibility. Key results would be validated in primary monocytes/macrophages from healthy blood donors. 

Overall, the goals of the proposed project are: 1) to pursue new strategies to predict innate immune responses to nucleic acid therapeutics (approved and investigational), and 2) to determine whether the toolset has predictive validity and provides utility for the examination of future clinical candidates.

FDA Mentor Names

Markham Luke, M.D., Ph.D.

Liang Zhao, Ph.D.

Silvana Borges, M.D.

Position and Organizational Affiliation

Markham Luke: Director, Division of Therapeutic Performance 1, CDER

Liang Zhao: Director, Division of Quantitative Methods and Modeling, CDER

Silvana Borges: Deputy Director, Division of Therapeutic Performance, CDER

Contact Information (email/telephone)

markham.luke@fda.hhs.gov / 301-796-5556

liang.zhao@fda.hhs.gov / 240-402-4468

silvana.borges@fda.hhs.gov /301-796-0963

NCATS Mentor Name

Jessica Binder, Ph.D.

Position and Organizational Affiliation

Biomedical Data Scientist, DPI

Contact Information (email/telephone)

jessica.binder@nih.hhs.gov / 301-402-8953

Research Project Summary

FDA uses Real World Data (RWD) and Evidence (RWE) to monitor postmarket safety and adverse events and to make regulatory decisions. The health care community is using these data to support coverage decisions and to develop guidelines and decision support tools for use in clinical practice. Medical product developers are using RWD and RWE to support clinical trial designs (e.g., large simple trials, pragmatic clinical trials) and observational studies to generate innovative, new treatment approaches.

A generic drug is a medication created to be the same as an already marketed brand-name drug in dosage form, safety, strength, route of administration, quality, performance characteristics, and intended use. These similarities help to demonstrate bioequivalence, which means that a generic medicine works in the same way and provides the same clinical benefit as the brand-name medicine. In other words, you can take a generic medicine as an equal substitute for its brand-name counterpart.

While the impact of generic drugs may seem relatively obvious from potential cost-savings, the actual benefit to health care outcome for a given healthcare need may be less observable and complicated by the US healthcare delivery system and reimbursement plans. We anticipate that thru the use of RWD and RWE available to HHS, including FDA, CMS, and NIH that we may be able to discern the impact of certain generic drugs on health care outcomes.

Proposed Project for TSIF Fellow

We propose funding a fellow to help initiate and coordinate research on use of RWD to measure the impact of certain generic drug availabilities on health care outcomes. Such a fellow would be versed or very interested in econometrics and have an interest in drug access and supply. Three possible prongs to the project are listed below.

• Research report on generic drug utility and value added/subtracted in various healthcare areas
  1. Does patient access to prescribed medications generally improve, or improve in specific areas?
  2. Do health outcomes concomitantly improve because a greater proportion of the patients can now afford to take certain medications? Are health outcomes maintained, or degraded?
• Identify areas that might have some controversies or clinical doubt about generic drug use – e.g. thyroid medications, inhaled drug products, topical drugs, anti-obesity peptide drugs?
  1. Explore whether RWE data can help us understand differential uptake of generic drugs, e.g. where prescribers instruct pharmacists to “dispense as written” or where patients feel that they are not responding the same way to a generic?
  2. Why do some patients use the brand when the generic is available? Managed care, pharmacy benefit management (PBM issues) vs. prescriber habit?
• Compare two drugs in similar clinical situation, but one with generic access and another without?

Relevant Publications

1. A new paradigm for topical generic drug products: Impact on therapeutic access - PubMed (nih.gov)
2. Medication Cost-Savings and Utilization of Generic Inhaled Corticosteroid (ICS) and Long-Acting Beta-Agonist (LABA) Drug Products in the USA - PubMed (nih.gov)
3. Patents And Regulatory Exclusivities On Inhalers For Asthma And COPD, 1986–2020 | Health Affairs
4. Frontiers | Integrating Real-World Evidence in the Regulatory Decision-Making Process: A Systematic Analysis of Experiences in the US, EU, and China Using a Logic Model | Medicine (frontiersin.org)
5. Real world evidence (RWE) – a disruptive innovation or the quiet evolution of medical evidence generation? - PMC (nih.gov)
6. JCI - Opportunities and challenges in using real-world data for health care
7. Comparative Effectiveness and Safety of Generic Versus Brand-Name Fluticasone–Salmeterol to Treat Chronic Obstructive Pulmonary Disease | Annals of Internal Medicine (acpjournals.org)

FDA Mentor Name

Nirjal Bhattarai, Ph.D.

Position and Organizational Affiliation

Lab Chief, TVBB/DC2/OCTHT/OTP, CBER

Contact Information (email/telephone)

Nirjal.Bhattarai@fda.hhs.gov / 240-402-6834

NCATS Mentor Names

Elizabeth Ottinger, Ph.D.

Venkata Mangalampalli, Ph.D.

Position and Organizational Affiliation

Elizabeth Ottinger: Acting Director of the Therapeutics Development Branch, DPI

Venkata Mangalampalli: Staff Scientist of the Therapeutics Development Branch, DPI

Contact Information (email/telephone)

elizabeth.ottinger@nih.gov / 301-827-0969

venkata.mangalampalli@nih.gov /301-761-6957

Research Project Summary

Adeno-associated virus (AAV) vector-based gene therapies have shown great potential to treat many human diseases. Although AAV gene therapy has improved over the last decade, challenges in vector manufacturing and issues with unwanted immune responses to the AAV vectors themselves remain. The goal of this project is to develop novel manufacturing strategies to improve AAV vector quality, purity, and yield, while simultaneously reducing immunogenicity.

Proposed Project for TSIF Fellow

In this project, the fellow will work on one of these focus areas to improve AAV vector-based gene therapy.

1. Focus Area 1: Characterization of host cell factors and improvement of AAV vector production         
   The HEK293 cell line is commonly used for AAV vector production. While significant improvements have been made in vector design to improve production, very little is understood about impact of the host cell factors on AAV production. Previous studies have shown activation of antiviral and inflammatory factors in HEK293 cells during AAV production; however, their impact on vector production is unknown. In this project, the fellow will perform comprehensive assessment of factors present in HEK293 cells that affect vector quality, potency, and yield. Using a high-throughput chemical screening method that takes advantage of libraries of small molecule inhibitors, HEK293 factors that affect vector production will be identified. Once these factor(s) are identified, CRISPR/Cas system will be used to engineer a novel HEK293 cell line with these factor(s) knocked out for improved AAV vector production.
2. Focus Area 2: Rational design of AAV capsids to reduce immunogenicity and anti-drug-antibody response        
   Host immune responses to AAV vectors can cause adverse events such as compliment activation and organ toxicities as well as reduce efficacy of AAV vector-mediated gene therapy. Developing AAV vectors with reduced immunogenicity profiles, without affecting potency, would significantly improve the potential applications for AAV in gene therapies. In this project, the fellow will develop novel strategies to design AAV capsids to inhibit host immune responses. For example, fellow will perform studies to identify novel immune-inhibitory peptide(s) from other human viruses that are known to evade immune responses to cause persistent infection. Next, the fellow will engineer novel AAV capsids with these immune-inhibitory peptide(s) incorporated into the capsid. Fellow will perform studies to assess structure of novel capsids using computational and experimental methods. The immunogenicity, tropism and potency of newly designed capsids will be studied using primary human cells and 3D cellular models such as organoids in vitro and mouse models in vivo. In vivo assessment will include measurement of anti-AAV capsid T cell responses, antibodies against AAV capsids, and release of inflammatory cytokines in the serum following AAV administration.
3. Focus Area 3: Development of stable HEK293 cell line for improved AAV vector production        
   Currently, AAV vectors are produced in HEK293 cells by transient transfection of three plasmids: a) a helper plasmid that expresses adenovirus helper genes required for AAV packaging; b) a helper plasmid that expresses AAV Rep and Cap genes, which are required for genome synthesis and capsid formation; and c) a plasmid that expresses the payload (gene of interest). This method is inherently variable, a significant issue in the manufacturing process that contributes to lot-to-lot inconsistencies in vector production. To minimize the variability of transient transfection, the fellow will work on developing a variant HEK293 cell line that stably expresses either one or both of the helper plasmids required for AAV production. The fellow will then test the new cell line for AAV vector production and assess vector quality, purity, and potency. The fellow will also characterize the resulting cell line(s) by performing comprehensive “Omic” profiling of clones that are high vector producers and identify factors that impact productivity.

Relevant Publications

1. A short hepatitis C virus NS5A peptide expression by AAV vector modulates human T cell activation and reduces vector immunogenicity. Gene Therapy. 2021. PMID: 34759330
2. The platform vector gene therapies project: increasing the efficiency of adeno-associated virus gene therapy clinical trial startup. Hum Gene Ther. 2020. PMID: 32993373

FDA Mentor Name

Kang Chen

Position and Organizational Affiliation

Research Chemist, CDER

Contact Information (email/telephone)

Kang.Chen@fda.hhs.gov / 240-402-5550

NCATS Mentor Names

Christopher LeClair, Ph.D.

Dingyin Tao, Ph.D.

Position and Organizational Affiliation

Christopher LeClair: Director, Analytical Chemistry Core, DPI

Dingyin Tao: Lead, Mass Spectrometry Team, Analytical Chemistry Core, DPI

Contact Information (email/telephone)

leclairc@mail.nih.gov / 301-480-9941

dingyin.tao@nih.gov / 301-827-7176

Research Project Summary

As of March 2020, drug applications for certain biological products previously regulated under section 505 of the FD&C Act are now assessed and licensed under the 351(a/k) BLA pathway of the PHS Act. This regulatory transition enabled the possibility of new biosimilar applications for these products, which if approved, could reduce direct patient cost. Included in these regulated biological products are growth hormone drugs composed of the individual proteins or protein mixtures of human chorionic gonadotrophin (hCG), follicle stimulating hormone (FSH), luteinizing hormone (LH), human growth hormone (hGH) and human thyroid stimulating hormone (hTSH), which are naturally sourced from human urine or recombinantly expressed in various host cells. Biosimilar applicants need to provide appropriate data to demonstrate the protein higher order structure (HOS), oligomerization, glycosylation pattern, and bioassay results are of sufficient similarity between the biosimilar product and the innovator product. This necessitates developing modern analytical methods for successful analysis of complex protein mixtures specifically related to human growth hormones. The current proposal will evaluate similar growth hormone drug products with varied sources of production and formulation. Chemical, structural, and biological activity results will be analyzed holistically to assess correlations among them and identify characteristics of process features. Both the agency and biosimilar drug developers will benefit from these modern analytical approaches that would foster approval of future biosimilar hormone mixtures.

Proposed Project for TSIF Fellow

Under the guidance of mentors at the FDA and NCATS, the fellow will develop analytical methods for the analysis of human growth hormones, which are an important category of biological products. This will be achieved using various techniques and technology that include but is not limited to (i) fast protein liquid chromatography (FPLC), (ii) nuclear magnetic resonance (NMR), (iii) dynamics light scattering (DLS), (iv) mass spectrometry (MS), and (v) in vitro cell based bioassay. The fellow will conduct analysis and gather data on chemical and structural modifications (e.g., protein glycosylation, higher order structure, and oligomerization) and their effect in the bioassay of hormone drugs. The implementation of applicable biological product analysis in the drug regulatory field will offer greater assurance of drug quality and minimize potential adverse effects introduced through the use of biosimilar versions or changes to the manufacturing process. This research will provide CMC reviewers the necessary information, especially glycan and structural variation reflected in MS and NMR spectral data, to effectively evaluate physiochemical differences. The application of state-of-the-art analytical techniques at the FDA and NCATS for drug product quality characterization will be a unique regulatory research and development experience not available from other programs. Research results will be disseminated through professional meetings, peer-reviewed publications, and potential regulatory guidance.

Relevant Publications

1. Chen K., Long D., Lute S., Levy M., Brorson K. & Keire D. Simple NMR methods for evaluating higher order structures of monoclonal antibody therapeutics with quinary structure. J. Pharm. Biomed. Anal. 2016 128, 398-407.
2. Patil S., Keire D. & Chen K. Comparison of NMR and Dynamic Light Scattering for measuring diffusion coefficients of formulated insulin: implications for particle size distribution measurements in drug products. AAPS Journal 2017 19, 1760-1766.
3. Peng J, Patil S., Keire D. & Chen K. Chemical Structure and Composition of Major Glycans Covalently Linked to Therapeutic Monoclonal Antibodies by Middle-Down Nuclear Magnetic Resonance. Anal. Chem. 2018 90, 11016-11024
4. Xie T. et al. The ELISA Detectability and Potency of Pegfilgrastim Decrease in Physiological Conditions: Key Roles for Aggregation and Individual Variability, Scientific Report, 2020 10, 2476.
5. Zhuo Y., Keire D. & Chen K. Minor N-glycan Mapping of monoclonal Antibody Therapeutics using Middle-down NMR Spectroscopy, Mol. Pharm. 2021 18, 441.
6. Biel, T. et al, An etanercept O-glycovariant with heightened potency, Molecular Therapy - Methods & Clinical Development 2022 124, 135.
7. Shipman J., Sommers C., Keire, D., Chen. K. & Zhu, H., Comprehensive N-Glycan Mapping using Parallel Reaction Monitoring LC-MS/MS, Pharm. Res. 2023 40, 1399.
8. Wang, K. & Chen, K. Direct Assessment of Oligomerization of Chemically Modified Peptides and Proteins in Formulations using DLS and DOSY-NMR. Pharm. Res. 2023 40, 1329.
9. Qiao X, Tao D, Qu Y, Sun L, Gao L, Zhang X, Liang Z, Zhang L, Zhang Y. Large-scale N-glycoproteome map of rat brain tissue: simultaneous characterization of insoluble and soluble protein fractions. Proteomics. 2011, 11(21):4274-8.
10. Yan W, Zhong Y, Hu X, Xu T, Zhang Y, Kales S, Qu Y, Talley DC, Baljinnyam B, LeClair CA, Simeonov A, Polster BM, Huang R, Ye Y, Rai G, Henderson MJ, Tao D, Fang S. Auranofin targets UBA1 and enhances UBA1 activity by facilitating ubiquitin trans-thioesterification to E2 ubiquitin-conjugating enzymes. Nat Commun. 2023, 14(1):4798.
11. Burns AP, Zhang YQ, Xu T, Wei Z, Yao Q, Fang Y, Cebotaru V, Xia M, Hall MD, Huang R, Simeonov A, LeClair CA, Tao D. A Universal and High-Throughput Proteomics Sample Preparation Platform. Anal Chem. 2021, 93(24):8423-8431.

FDA Mentor Names

John Talpos, Ph.D.

Hector Rosas Hernandez, Ph.D.

Position and Organizational Affiliation

John Talpos: Director of Division of Neurotoxicology, NCTR

Hector Rosas Hernandez: Staff Fellow, NCTR

Contact Information (email/telephone)

john.talpos@fda.hhs.gov / 870-543-7329

hector.rosas-hernandez@fda.hhs.gov / 870-543-7440

NCATS Mentor Name

Emily Lee, Ph.D.

Position and Organizational Affiliation

Staff Scientist, Team Lead, DPI

Contact Information (email/telephone)

emily.lee@nih.gov / 301-480-7702

Research Project Summary

There is a need to integrate the use of functional neural models together with blood-brain-barrier assays to help predict toxic effects of compounds in healthy and disease brains. NCATS has previously established a method for generating functional neural spheroids with differentiated human induced pluripotent stem cell (hiPSC)-derived neurons and astrocytes, at cell type compositions mimicking specific regions of the human brain.

We have demonstrated that these neural spheroids display spontaneous synchronous calcium oscillations, as measured with fluorescence biosensors or calcium dyes, with patterns that depend on the neuronal-type composition. We have also developed neural spheroids incorporating neurons genetically engineered with CRISPR-induced alleles associated with Alzheimer’s (AD; APOE4 and APP A673V) and Parkinson’s disease (PD; A53T SNCA) and shown that inclusion of neurons with these disease mutations changes calcium activity. FDA/NCTR has developed models of the blood-brain-barrier (BBB) and studied the effects of amyloid β-peptide (Aβ) on BBB function.

Here, we propose to integrate the use of neural spheroids from NCATS and BBB chip models from FDA/NCTR to 1) investigate whether poly-substance exposures, including heavy metals, affect neuronal activity, neurotoxicity, and development of AD and PD disease relevant phenotypes, in healthy and diseased neural spheroid mimicking different brain regions (e.g. SN, PFC, and HPC) and containing immune cells like microglia; and 2) determine how this toxicity may be altered by incorporating the effects of selective compound passage or clearance measured in a BBB tissue chip microfluidics system, with or without AD and PD disease relevant perturbations.

Proposed Project for the Fellow

The TSIF Fellow will directly lead this project, as well as design and execute experiments, with mentorship from Dr. Emily Lee (NCATS), Dr. John Talpos (NCTR/FDA), and Dr. Hector Rosas Hernandez.

At NCATS, the TSIF Fellow, he/she will be trained by Dr. Emily Lee (Team Lead) and Dr. Jiajing Zhang (current postdoctoral fellow). He/she will be trained to make neural spheroids and on high-throughput screening including small molecule screening and phenotypic assays, disease modeling, automation technologies, and data processing. We expect that the TSIF Fellow will utilize existing functional neural activity read-outs and develop novel, disease relevant assays that will be used to measure effects of chemical substances on neuronal activity and disease progression in the AD/PD neural spheroid models, including production/accumulation of Aβ, Tau, -synuclein, neuroinflammatory markers such as reactive oxygen species (ROS), and cell death.

At NCTR/FDA, the TSIF Fellow will train on the development of a BBB models on a chip by Dr. Hector Rosas Hernandez. The TSIF fellow will also gain additional experience in developing assays related to neuronal viability and inflammation in BBB microphysiological systems, including the use of confocal microscopy, differentiation of lineage-specific cells from hiPSCs and performing toxicological research.

The project outcomes will include the understanding of poly-substance exposure on neuronal activity, neurotoxicity and the development of neurodegenerative disease assay models, as well as validating their use as predictive platforms for preclinical drug testing. We anticipate at least 2 publications to result from this work.

Relevant Publications

1. Strong, C.E., Kundu, S., Boutin, M., Chen, Y.-C., Wilson, K., *Lee, E., and *Ferrer, M. (2022). Functional brain region-specific neural spheroids for modeling neurological diseases and therapeutics screening BioRxiv: The Preprint Server for Biology, May 4, 2022.      
   Currently resubmitted to Comms Bio after peer-reviewed revisions
2. Boutin, M.E., Strong, C.E., Van Hese, B., Hu, X., Itkin, Z., Chen, Y.-C., LaCroix, A., Gordon, R., Guicherit, O., Carromeu, C., Kundu, S., Lee, EM, Ferrer M. (2022). A multiparametric calcium signal screening platform using iPSC-derived cortical neural spheroids. SLAS Discovery S2472555222000089. https://doi.org/10.1016/j.slasd.2022.01.003.
3. Rosas-Hernandez, H., Cuevas, E., Lantz, S. M., Paule, M. G., & Ali, S. F. (2018). Isolation and culture of brain microvascular endothelial cells for in vitro blood-brain barrier studies. Neurotrophic Factors: Methods and Protocols, 315-331.
4. Cuevas, E., Rosas-Hernandez, H., Burks, S. M., Ramirez-Lee, M. A., Guzman, A., Imam, S. Z., ... & Sarkar, S. (2019). Amyloid Beta 25–35 induces blood-brain barrier disruption in vitro. Metabolic brain disease, 34, 1365-1374.

FDA Mentor Names

Sara Brenner, M.D., M.P.H.

Keith Campbell, M.D., Ph.D.

Position and Organizational Affiliation

Sara Brenner: Chief Medical Officer; Associate Director for Medical Affairs; Director, Diagnostic Data Program, CDRH

Keith Campbell: Director, FDA SHIELD Program, CDRH

Contact Information (email/telephone)

Sara.Brenner@fda.hhs.gov / (240) 402-7533

Keith.Campbell@fda.hhs.gov / (541) 977-7771

NCATS Mentor Names

Sam Michael

Marc Ferrer, Ph.D.

Position and Organizational Affiliation

Sam Michael: Chief, Information Technology Resources Branch (ITRB), OAM

Marc Ferrer: Senior Scientist, Director, 3D Tissue Bioprinting Lab, ETB, DPI

Contact Information (email/telephone)

michaelsg@mail.nih.gov / (301) 827-7796

marc.ferrer@nih.gov / (301) 480-9845

Research Project Summary

The FDA Diagnostic Data (DxD) Program is a collaborative enterprise supporting FDA’s mission-critical priorities, including:

1) Developing innovative approaches for capture, harmonization, transmission, and analysis of diagnostic data originating from over the counter (OTC), point-of-care (POC), and lab-based diagnostic tests

2) Expanding the quality, functionality, and utility of the diagnostic data ecosystem across multiple stakeholders and agencies

3) Providing enhanced regulatory support and guidance to ensure that safe, effective, and accurate diagnostics from emerging and convergent technologies are first to market in the U.S.

We are seeking a TSIF Fellow to join this exciting team and contribute to research and project development studying and deploying data analytics and creative new approaches to support innovation within FDA and with NIH NCATS. An important part of this work is a new program: Diagnostics Data & Evidence Ecosystem Platform (DEEP). It is an agile inter-agency program to build a regulatory sandbox for diagnostic data using leading edge technologies.

The DxD Program serves as a model for how high-quality data from both conventional and unconventional sources, including real-world data (RWD), can be used to support regulatory decision-making across other medical product spaces. Executing on this visionary program of wide breadth and scale requires the support of diverse and talented group of people who are enthusiastic about taking a future-oriented approach to supporting FDA and CDRH’s mission. The members of the DxD Program bring together expertise in IVDs, microbiology, virology, medicine, public health, software, digital health, cybersecurity, information technology, and research and development.

Proposed Project for TSIF Fellow

The FDA Diagnostic Data (DxD) Program established a new, first-of-its-kind technology program at FDA with full-time staffing and significant funding with two specific focus areas – Digital Diagnostics [OTC/POC] and Semantic Harmonization and Interoperability Enhancement for Laboratory Data [SHIELD] – aimed at improving the quality, interoperability, portability, and utility of OTC, POC, and laboratory-based diagnostic data within and between institutions and individuals.

The TSIF Fellow will primarily focus on DEEP a currently funded joint FDA-NIH NCATS project. The first deliverable for this project is building a functional EUA to 510(k) conversion module for regulatory submissions. DEEP will enable IVD device reviewers to leverage real-world evidence and data as part of the EUA to 510(k) conversion process for clearing COVID-related IVDs. We aim to reduce reviewer burden and improve review performance and quality by leveraging high quality data supplied by sponsors along with a variety of high-quality diagnostic data sources from DxD program partners and other federal agencies. These relationships with industry, academia, and federal agencies will create a robust network of powerful connections for the selected fellow and provide many opportunities for current and future learning, career, and research opportunities.

DEEP is being built on the Palantir Foundry platform using proven and leading-edge capabilities including semantic search and machine learning. This enables us to move fast and deliver solid capabilities. It will pull together elements of the OTC/POC and SHIELD programs. We expect close partnership with NCATS for developing inter-agency programs and for their expertise in Palantir.

Relevant Publications

FDA

Encoding laboratory testing data: case studies of the national implementation of HHS requirements and related standards in five laboratories | Journal of the American Medical Informatics Association | Oxford Academic (oup.com)

Diagnostic Data Program | FDA

Diagnostic Data Exchange (FDA) | The Opportunity Project (census.gov)

Clinical Genomic and Genetic Testing: Towards Data Standards for Analysis and Exchange 

NCATS

De-black-boxing health AI: demonstrating reproducible machine learning computable phenotypes using the N3C-RECOVER Long COVID model in the All of Us data repository.

Vaccination Against SARS-CoV-2 Decreases Risk of Adverse Events in Patients who Develop COVID-19 Following Cancer Surgery.

Metformin is Associated with Reduced COVID-19 Severity in Patients with Prediabetes.

Issues with Variability in EHR Data About Race and Ethnicity: A Descriptive Analysis of the National COVID Cohort Collaborative Data Enclave.

Assessing Disparities in COVID-19 Testing Using National COVID Cohort Collaborative.

Higher hospitalization and mortality rates among SARS-CoV-2-infected persons in rural America.

Multilevel determinants of racial/ethnic disparities in severe maternal morbidity and mortality in the context of the COVID-19 pandemic in the USA: protocol for a concurrent triangulation, mixed-methods study.

Identifying who has long COVID in the USA: a machine learning approach using N3C data.

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

FDA Mentor Names

Heather Stone, M.P.H.

Suranjan De, M.S., M.B.A.

Position and Organizational Affiliation

Heather Stone: Health Science Policy Analyst (CURE ID Team Lead), Office of Medical Policy/Center for Drug Evaluation and Research (OMP/CDER)

Suranjan De: Deputy Director, Regulatory Science Staff, Office of Surveillance and Epidemiology, Center for Drug Evaluation and Research (OSE/CDER)

Contact Information (email/telephone)

heather.stone@fda.hhs.gov / 301-283-1682

Suranjan.de@fda.hhs.gov / 240-402-0498

NCATS Mentor Name

Ewy Mathé, Ph.D.

Position and Organizational Affiliation

Director of Informatics, DPI

Contact Information (email/telephone)

ewy.mathe@nih.gov

Research Project Summary

CURE ID is an FDA-NCATS collaboration that collects real-world drug repurposing information on rare diseases in case report forms (CRFs). The information is subsequently made publicly visible on an NCATS site through the CURE ID web and mobile applications (cure.ncats.io/). Many diseases, such as Balamuthia and angiosarcoma, are difficult to study and lack approved treatments. Analyzing aggregated treatment data for such diseases may help generate efficacy signals. The fellow will participate in the following CURE ID projects:

1. Automate Manual Extraction – Currently, published cases from the literature are manually extracted into a CRF. This project will build tools that automate the extraction using Natural Language Processing and Machine Learning technologies (NLP/ML).
2. Adverse Events CRF – The FDA adverse event reporting tool is not user-friendly and has not kept up with technological advancements (e.g., mobile apps) and there is interest from OSE in building off the CURE ID infrastructure to capture AEs.
3. Modify the EDGE Tool - The EDGE tool has exponentially augmented the data extraction capacity of CURE ID by automatically extracting COVID-19 cases from electronic health records (EHR) into a CRF. This project will work with partners to modify the EDGE tool for use in sepsis, meningitis, and hyperemesis gravidarum.
4. Explore and pilot a Hybrid CRF – The goal for this project is to combine the existing patient, clinician, and EHR extracted CRFs into one where data extracted from EHRs is supplemented with patient’s review and physician feedback, when possible, for incorporation into a hybrid CRF.

Proposed Project for TSIF Fellow

The outlined projects will require the fellow to apply their knowledge, learn new skills, generate data, and conduct various analyses:

Automate Manual Extraction - The fellow will use informatics and clinical knowledge to explore existing tools and develop methods to identify and extract information from case reports in literature databases, then populate the CRF. They will analyze any gathered data to identify promising drugs for the targeted disease, enrich the CURE ID database with information about the drug, and investigate mechanisms of action. This may culminate in designing in vitro studies to be conducted at NCATS.

Adverse Events CRF - The fellow will collaborate with FDA to design this CRF and alongside NCATS informatics, will implement it. Analysis of data gathered has potential to improve drug safety.

Modify the EDGE Tool - The fellow will bridge the clinical and informatics sides of this project. The fellow would also have an opportunity to work with the Hopkins team to further develop the EDGE tool by identifying variables to be extracted for sepsis, meningitis, and hyperemesis gravidarum.

Explore and pilot a Hybrid CRF – The fellow will help design and develop a hybrid CRF. They will investigate implementation of a Global Unique Identifier (GUID) to link EHR, patient-provided, and physician-provided information together while ensuring minimal identifiability.

Importantly, all projects aim to expand the data being collected as part of CURE ID. For each project, landscape and use case-focused data analysis will be performed by the scholar to exemplify the utility of the data.

Relevant Publications

The data from automation of manual extraction will provide the fellow with sufficient data to conduct analysis on disease(s) of their choosing. This data can also be combined with the clinician submitted, and patient submitted case reports on CURE ID for larger studies and publication.

The fellow will be a significant part of creating new data infrastructure and informatics processes while modifying the EDGE tool and developing a hybrid CRF. They will have the opportunity to author several publications outlining the informatics structure of these projects and lessons learnt from developing novel tools.

Prior publications related to the project include:

1. Charles R, Milani B, Dagne DA, Oliver N, Ali B, Stone HA, Schito M, Tirupathi, R. Landscape Analysis to Identify Effective Drug Repurposing Candidates for the Treatment of Implantation Mycoses: Comparison of World Health Organization Survey Treatment Data and Published Case Reports on CURE ID. Poster Presentation at IDWeek 2023. Boston, MA. October 11-15, 2023.
2. Farid T, Charles R, Tumas K, Stone HA, Tirupathi R. The landscape of infections caused by rare bacterial pathogens. Poster Presentation at IDWeek 2023. Boston, MA. October 11-15, 2023.
3. Milani B, Dagne DA, Choi HL, Schito M, Stone HA. Diagnostic capacities and treatment practices on implantation mycoses: Results from the 2022 WHO global online survey. PLOS Neglected Tropical Diseases 2023 17(6): e0011443. https://doi.org/10.1371/journal.pntd.0011443
4. Heavner, Smith F. PhD, RN1,2; Anderson, Wesley PhD3; Kashyap, Rahul MBBS, MBA4,5; Dasher, Pamela BA1; Mathé, Ewy A. PhD6; Merson, Laura7; Guerin, Philippe J. MD, PhD8,9; Weaver, Jeff MBA10; Robinson, Matthew MD11; Schito, Marco PhD1; Kumar, Vishakha K. MD, MBA12; Nagy, Paul PhD13. A Path to Real-World Evidence in Critical Care Using Open-Source Data Harmonization Tools. Critical Care Explorations 5(4):p e0893, April 2023. | DOI: 10.1097/CCE.0000000000000893
5. Adhikari SD, Chaudhuri S, Boodman C, Gupta M, Schito M, Stone H, Gupta N. Fosfomycin for Non-Urinary Tract Infections: a systematic review. Infez Med. 2023 Jun 1;31(2):163-173. doi: 10.53854/liim-3102-4. PMID: 37283634; PMCID: PMC10241401.
6. Reema Charles, MBBS, MD and others (Stone H), 627. CURE ID as a Tool for Curating and Analyzing Drugs Used in COVID-19 Clinical Trials, Open Forum Infectious Diseases, Volume 8, Issue Supplement_1, November 2021, Pages S417–S418, https://doi.org/10.1093/ofid/ofab466.825
7. Mili Duggal, MPH, PhD and others (Stone H), 546. Capturing Clinician’s Experiences Repurposing Drugs to Inform Future Studies During COVID-19, Open Forum Infectious Diseases, Volume 7, Issue Supplement_1, October 2020, Page S339, https://doi.org/10.1093/ofid/ofaa439.740
8. Stone H. and others, 1380. Safety of Repurposed Drugs for Multidrug-Resistant and Extensively Drug-Resistant Tuberculosis: An Analysis of Adverse Events Reported in the Literature, Open Forum Infectious Diseases, Volume 6, Issue Supplement_2, October 2019, Page S501, https://doi.org/10.1093/ofid/ofz360.1244
9. Stone H, Paul P. Exploring the Range of Clinical Efforts to Identify Repurposed Drugs for Neglected Infectious Diseases, America Journal of Tropical Medicine and Hygiene, Volume 101, January 201, Page 349-349.
10. Stone H. and others, Collaborative Use Repurposing Engine (CURE): FDA-NCATS/NIH Effort to Capture the Global Clinical Experience of Drug Repurposing to Facilitate Development of New Treatments for Neglected and Emerging Infectious Diseases, Oral Abstract and Poster Presentation at IDWeek San Diego, CA, 2017. Open Forum Infectious Diseases, Volume 4, Issue suppl_1, Fall 2017, Page S12, https://doi.org/10.1093/ofid/ofx162.030
11. Sacks L, Stone H, Callahan L, et al. (NTD-RD Working Group of FDA and NCATS). Database of Repurposed Drugs to Treat Neglected Tropical Diseases: An FDA-NCATS Collaboration. Abstract and Poster Presentation at the American Society for Tropical Medicine and Hygiene (ASTMH) 163rd Annual Conference, Washington DC. 2013.

FDA Mentor Names

Sangeeta Khare, M.S., Ph.D.

Kuppan Gokulan, Ph.D.

Position and Organizational Affiliation

Sangeeta Khare: Principal Investigator/Research Microbiologist, Division of Microbiology, NCTR

Kuppan Gokulan: Principal Investigator/Research Microbiologist, Division of Microbiology, NCTR

Contact Information (email/telephone)

sangeeta.khare@fda.hhs.gov / 870.543.7519

Kuppan.gokulan@fda.hhs.gov / 870.543.7467

NCATS Mentor Names

Xin Xu, Ph.D.

Elias Carvalho Padilha, Ph.D.

Position and Organizational Affiliation

Xin Xu: Sr. Scientist, Director, Drug Metabolism and Pharmacokinetics (DMPK) Core, DPI

Elias Carvalho Padilha: Staff Scientist, DMPK Core, DPI

Contact Information (email/telephone)

xin.xu3@nih.gov / 301.480.9844

elias.padilha@nih.gov / 301.827.1813

Research Project Summary

Transepithelial electrical resistance (TEER) is an in vitro method to measure the barrier function of cellular monolayers that has been widely utilized in biological research such as drug screening and more 1-5. The NCATS DMPK Core in partnership with Applied Biophysics developed the automated TEER96 device (https://www.biophysics.com/teer96.php) to increase the throughput of TEER measurements. The device also allows for the continuous detection of TEER values over time in a sterile and temperature-controlled environment. Given the gained functionality, a unique opportunity is presented to utilize this technology to live-monitor the impact of chemicals to cell monolayers cultured in transwell systems. The DMPK Core has conducted a screening of orally available toxins from the Tox21 library in Caco-2 intestinal cell monolayers while monitoring TEER over 72 hours (collaboration with Dr. Menghang Xia of NCATS). Preliminary data showed that several compounds caused concentration dependent monolayer disruptions measured by TEER; however, the mechanisms involved in this barrier disruption remain elusive. This project aims to expand the TEER screening of oral toxins to the intestinal monolayer model and elucidate barrier disruption mechanisms with the goal of developing a new gut toxicity screening paradigm.

The project will leverage the NCATS expertise with the TEER96, high-throughput screening, and automation and, at the NCTR, the project will benefit from Dr. Khare’s expertise in gut biology and toxicology to unveil the mechanistic features of the gut barrier disruption by orally available environmental toxins. The data generated from this project will provide valuable information for FDA regulation and public health.

Proposed Project for TSIF Fellow

The selected Fellow will participate in developing a new gut toxicity screening paradigm. The Fellow will lead the development of high-throughput assay for the intestinal barrier monitoring using TEER and further investigate the molecular mechanism of the food grade toxins involved in the disruption of the intestinal epithelial layer. The Fellow will work 50% time at the NCATS and 50% time at the NCTR/FDA. The proposed work will be as follows:

NCATS: Test the potential intestinal toxicity of compounds from the Tox21 10K compound library that may be orally ingested from food or water (collaboration with Dr. Menghang Xia of NCATS Tox21 Program). These test compounds include pesticides, antibiotics, fragrances, food coloring compounds that are usually present in food or water.

NCATS will perform TEER96 screening in human epithelial (Caco-2) cells and share the data of TEER results with NCTR Collaborator. Samples (cell extracts) will be sent to NCTR for gene expression analysis and (supernatants) cytotoxicity measurement. After gene expression analysis at NCTR.

NCTR: Complete cell extraction and perform gene expression on samples related to cell monolayer disruption, cell death, and other relevant mechanisms which can influence the observed TEER profile. Cytotoxicity measurements will be measured from supernatants. Data will be shared with NCATS.

The Fellow will present experiment results at the monthly meeting and share the data with NCATS and FDA mentors. The Fellow will participate in data interpretation and writing scientific report(s) with TEER profiles and gene expression information to be considered for publication in a scientific journal.

Relevant Publications

1. Gokulan K, Kolluru P, Cerniglia CE, Khare S. Dose-Dependent Effects of Aloin on the Intestinal Bacterial Community Structure, Short Chain Fatty Acids Metabolism and Intestinal Epithelial Cell Permeability. Frontiers in Microbiology 2019;10.
2. Gokulan K, Kumar A, Lahiani MH, Sutherland VL, Cerniglia CE, Khare S. Differential Toxicological Outcome of Corn Oil Exposure in Rats and Mice as Assessed by Microbial Composition, Epithelial Permeability, and Ileal Mucosa-Associated Immune Status. Toxicological Sciences 2021;180:89-102.
3. Hao HH, Gokulan K, Pineiro SA, et al. Effects of Acute and Chronic Exposure to Residual Level Erythromycin on Human Intestinal Epithelium Cell Permeability and Cytotoxicity. Microorganisms 2019;7.
4. Orr SE, Gokulan K, Boudreau M, Cerniglia CE, Khare S. Alteration in the mRNA expression of genes associated with gastrointestinal permeability and ileal TNF- secretion due to the exposure of silver nanoparticles in Sprague-Dawley rats. Journal of Nanobiotechnology 2019;17.
5. Williams KM, Gokulan K, Cerniglia CE, Khare S. Size and dose dependent effects of silver nanoparticle exposure on intestinal permeability in an in vitro model of the human gut epithelium. Journal of Nanobiotechnology 2016;14.
6. Siramshetty V, Williams J, Nguyen T, et al. Validating ADME QSAR Models Using Marketed Drugs. Slas Discovery 2021;26:1326-1336.
7. Williams J, Siramshetty V, Nguyen DT, et al. Using in vitro ADME data for lead compound selection: An emphasis on PAMPA pH 5 permeability and oral bioavailability. Bioorganic & Medicinal Chemistry 2022;56.
8. Gokulan K, Mathur A, Kumar A, Vanlandingham MM, Khare S. Route of Arsenic Exposure Differentially Impacts the Expression of Genes Involved in Gut-Mucosa-Associated Immune Responses and Gastrointestinal Permeability. International Journal of Molecular Sciences 2023;24.
9. Parajuli P, Gokulan K, Khare S. Preclinical In Vitro Model to Assess the Changes in Permeability and Cytotoxicity of Polarized Intestinal Epithelial Cells during Exposure Mimicking Oral or Intravenous Routes: An Example of Arsenite Exposure. International Journal of Molecular Sciences 2022;23.

Skrzydlewski P, Twaruzek M, Grajewski J. Cytotoxicity of Mycotoxins and Their Combinations on Different Cell Lines: A Review. Toxins 2022;14.