HHMI Research Articles

Assessing Experiential Learning at an HBCU

This paper will highlight the work at Delaware State University, an HBCU, on experiential education projects through a Howard Hughes Medical Institute (HHMI) Inclusive Excellence grant. It focuses on assessing experiential learning curriculum in individual courses as well as evaluating student growth from research and external opportunities. It highlights the preliminary outcomes of these projects with rubrics and survey data for assessing new experiential activities in course curriculum across campus as well as the Experiential STEM Lab Internship Program. As a component of Delaware State University’s strategic plan, these new programs have promoted student success as well as diversity, equity, and inclusion initiatives. The results will demonstrate positive benefits for faculty, students, and a culture of assessment.

An interview with Jared Rutter.

Jared Rutter's group studies the mechanisms by which cells sense their metabolic environment and integrate these signals to influence cell behaviors. Jared completed his PhD at the University of Texas Southwestern Medical Center, USA, where he stayed on to begin his independent research career as the first Sara and Frank McKnight Independent Fellow. He established his own lab at the University of Utah, USA, where he is now Distinguished Professor of Biochemistry and an HHMI Investigator. Jared is a Guest Editor for Development's special issue on Metabolic and Nutritional Control of Development and Regeneration. We caught up with him to find out more about his research, his experiences with translating this work to the clinic and the importance of placing metabolism research in the broader biological context.

Promoting Student Success and DE&I in Experiential Education at an HBCU: STEM Lab Internship Programs

Over the past four years, a Howard Hughes Medical Institute (HHMI) Inclusive Excellence grant supported Delaware State University (DSU) to increase student success and foster faculty development in the STEM (Science, Technology, Engineering, and Mathematics) fields. One component of this grant has provided students, particularly early sequence (freshman and sophomores), the opportunity to participate in a lab internship program. This program has provided students with access to vital research experience and removed some of the barriers for student opportunities, particularly for minority and first-generation students, in STEM fields. The internship program is rooted in principles of diversity, equity, and inclusion and is a cost-effective model for increasing experiential opportunities for STEM students. This paper will share the logistics and inclusive parameters of the program, survey data from student and faculty mentors, as well as highlight the benefits of incorporating an early experiential learning opportunity for students in STEM fields. The paper demonstrates the steps to create a low-cost lab program and how future internships experiences can be designed with diversity, equity, and inclusion as core principles.

Diagnostic and Therapeutic Challenges.

Reprint requests: Fang Lu, Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China; E-mail: [email protected] The authors report no conflict of interest, and funding received for this work from any of the following organizations: National Institutes of Health (NIH), Wellcome Trust, Howard Hughes Medical Institute (HHMI), and other(s). RETINA®, The Journal of Retinal and Vitreous Diseases, encourages readers to submit Diagnostic and Therapeutic Challenges to [email protected] Cases for the Diagnostic and Therapeutic Challenges section should include a detailed history of the patient, the diagnosis, the workup, the management, and, finally, the question or questions that the submitter wishes to have answered by the consultants.

Encouraging signs for a new generation of AAV-driven gene therapy

David McCall, Commissioning Editor of Cell & Gene Therapy Insights, speaks to Dr Katherine A High, President, Therapeutics, AskBio.Dr Katherine High trained in internal medicine, hematology, and molecular genetics, and began her faculty career at UNC-Chapel Hill. After moving to the University of Pennsylvania, she conducted pioneering bench-to-bedside studies of gene therapy for hemophilia. These led to a series of basic and clinical investigations that characterized the human immune response to AAV gene delivery vectors. Her work evolved to encompass clinical translation of genetic therapies for multiple inherited disorders. As the inaugural director of a Center at The Children’s Hospital of Philadelphia, where she was also an Investigator of the Howard Hughes Medical Institute (HHMI), Dr High assembled a multidisciplinary team of scientists and physicians to discover and develop new gene therapies for genetic diseases. In 2013, her Center at CHOP spun out as Spark Therapeutics, where she led the team that achieved the first FDA approval of a gene therapy for a genetic disease. After Spark was acquired by Roche in 2019, Dr High did a (virtual) sabbatical as a Visiting Professor at Rockefeller University, and in 2021 joined AskBio as President, Therapeutics. Dr High is an elected member of the National Academy of Medicine (US), the American Academy of Arts and Sciences, the Royal College of Physicians (London), and the National Academy of Sciences (US).

Isolation and characterization of the novel Mycobacterium smegmatis phage Dawnguard

Bacteriophages are the most ubiquitous organisms found within the biosphere, composed of an estimated 1031 particles worldwide. The evolutionary “arms‐race” between bacteriophages and bacteria have set the stage the natural selection process that has underpinned biological complexity. Because of the sheer volume of phage particles, it is practically impossible to identify every unique phage available; however, the combined power of laboratory techniques and computer prediction software has made the identification of a few of these phages possible. Under the guidance of the Howard Hughes Medical Institute (HHMI) Science Education Alliance‐Phage Hunters Advancing Genomics and Evolutionary Science (SEA‐PHAGES) isolation guide, solid and liquid samples from three locations across the Hampden‐Sydney College campus in central Virginia were tested for the presence of M. smegmatis phage. Although we were unable to isolate novel phages from these areas, we were successful in performing bioinformatic characterization of a phage previously isolated but not studied in detail. Using the computer programs DNA Master and Phage Evidence Collection and Annotation Network (PECAAN), we discovered a significant error in previous annotations done on the M. smegmatis phage Samcrothat we were able to correct prior to submission of the phage's gene annotation to GenBank for publication. The phage, renamed Dawnguard, possesses several genes of interest, including a glycosyltransferase, immunity repressors, and a resolvase, that may explain its unique adaptations to effective reproduction in M. smegmatis.

Making personalized, autologous cell therapies accessible: interview with Nabiha Saklayen and Marinna Madrid ofCellino Biotech Inc.

Nabiha Saklayen is CEO and Co-Founder of Cellino. Cellino's proprietary technology makesstem cell-derived therapies scalable for the first time. Nabiha was selected as a Pioneer in MIT Tech Review's 35 Innovators under 35 list for her patented inventions in cellular laser editing. She received her PhDin physics from Harvard University as a Howard Hughes Medical Institute (HHMI) International Fellow. She is also the inaugural Tory Burch Foundation Fellow in Genomics at the Innovative Genomics Institute led by Nobel laureate, DrJennifer Doudna. Nabiha is also a TED speaker and co-creator of I Am a Scientist, an educational program running in 50 states that inspires children to explore science. Marinna Madrid is Chief Product Officer and Co-Founder at Cellino. She received her MAandPhDin applied physics from Harvard University, where she co-invented laser-based intracellular delivery techniques. She received her BSc in biophysics from the University of California, Los Angeles, after transferring from Riverside Community College. She is the recipient of the Harvard Graduate Prize Fellowship, the Catalyst Accelerator Grant from Harvard Medical School, and was on the Forbes 30 Under 30listfor healthcare in 2019. She has several patents, peer-reviewed publicationsand wrote the first review paper on autologous induced pluripotent stem cell (iPSC)-based cell therapies. She is also passionate about access to education and the role the community college system plays in providing upward mobility for historically disadvantaged groups. The interview was conducted on February 8, 2022, by Alice Soteriou, Commissioning Editor of Regenerative Medicine.

Converting Access Microbiology to an open research platform: focus group and AI review tool research results

The Microbiology Society will be launching an open research platform in October 2021. Developed using funding from the Wellcome Trust and the Howard Hughes Medical Institute (HHMI), the platform will combine our current sound-science journal, Access Microbiology, with artificial intelligence (AI) review tools and many of the elements of a preprint server. In an effort to improve the rigour, reproducibility and transparency of the academic record, the Access Microbiology platform will host both preprints of articles and their Version of Record (VOR) publications, as well as the reviewer reports, Editor's decision, authors' response to reviewers and the AI review reports. To ensure the platform meets the needs of our community, in February 2020 we conducted focus group meetings with various stakeholders. Using articles previously submitted to Access Microbiology, we undertook testing of a range of potential AI review tools and investigated the technical feasibility and utility of including these tools as part of the platform. In keeping with the open and transparent ethos of the platform, we present here a summary of the focus group feedback and AI review tool testing.

Liver zonation

Liver zonation

HHMI to require immediate open access

Scientists who work for the Howard Hughes Medical Institute (HHMI) will make their research articles available to the public immediately and for free as of Jan. 1, 2022, . HHMI is also joining , th...

Stockpiling of Used Personal Protective Equipment Now for Future Decontamination and Reuse in the COVID-19 Pandemic.

Department of Radiology Vancouver General Hospital Vancouver, British Columbia, Canada [email protected] The authors disclose no conflict of interest. In particular, the author did not receive funding from any of the following organizations: National Institutes of Health (NIH), Wellcome Trust; Howard Hughes Medical Institute (HHMI), or other(s).

Eugenia Chiappe

Eugenia Chiappe

Review: Some Animals Are More Equal than Others: Keystone Species and Trophic Cascades and Exploring Earth's Keystone Species

At the beginning of every school year, many educators are asked to prepare lesson plans for each course they teach, to be used in the case of an emergency absence. Teachers struggle to find resources that are not only engaging, but also present relevant information in a way students can understand without a teacher being there to translate for them. The Howard Hughes Medical Institute (HHMI) BioInteractive website hosts a vast library of biology-related media resources, virtual labs, and simulations that can be used under these circumstances. Two lessons of note include the film entitled Some Animals Are More Equal than Others: Keystone Species and Trophic Cascades and a related Google Earth Voyager module called Exploring Earth's Keystone Species.The short film opens by explaining pioneering research by Robert Paine and James Estes into interactions between sea star, sea urchin, and sea otter populations and their effects on the local Washington State kelp forests. The key concepts covered encompass topics that link across the entire biology or environmental science content, including population dynamics, food webs, trophic structure, biodiversity, ecosystem stability, species interactions, and experimental design. Covering all of these topics makes the film appropriate to show at any point in the course curriculum. Moreover, the video is short, only 20 minutes, which leaves plenty of time for students to discuss and analyze the information and apply their understanding to activities. Students could discuss ideas such as causal loop modeling of a kelp forest, completing a claim-evidence-reasoning prompt, or making predictions related to a different ecosystem of study. The HHMI website has a pretty highly cognitively demanding set of prompts that could fill several class periods with deep discussions related to these areas.Moreover, HHMI has partnered with Google Earth to provide a Voyager module entitled Exploring Earth's Keystone Species to accompany the video that students will find especially interesting. In this module, students explore other keystone species from around the world, such as the gray wolf, Eurasian beaver, and African elephant. In each location, students are provided a slideshow with captivating imagery, a short description of the organism, and the ability to explore the animal's habitat in greater detail. Be sure to give students a time limit or they could get sucked in for hours! Adding this Google Earth activity to the video is a high-leverage teacher move, not only because it will prompt more detailed discussions and deeper connections to the topic, but also because it presents the content in a more culturally relevant manner. It provides a greater diversity of examples with which students can develop personal connections.Finally, when combined, these two resources provide a challenging, differentiated, and diverse set of learning tasks that engage students in authentic learning in a personally meaningful way. It challenges students to think beyond their classroom about keystone species and human impacts on these species from a more global perspective. This will hopefully lead the students to the place every biology teacher wants their students to go – having them be better stewards of their dynamic and fragile planet.

Tuning receptor signaling through ligand engineering

I will present the results of studies in our laboratory investigating the role of extracellular ligand‐receptor complex structure on the nature of signaling outputs in a range of systems. Most cell surface receptors are activated by some degree of ligand‐mediated clustering or oligomerization, but it is less clear to what degree the nature of the downstream signal induced by ligand can be ‘tuned’ or manipulated by natural or engineered ligands that engage the receptors with alternative geometries or binding parameters. Typically, ligands that elicit distinct pharmacologies through a single receptor have been observed GPCRs, but we have engineered ligands for T cell and cytokine receptors that exhibit partial agonism and inverse agonism. As one example, we have modulated cytokine receptor signaling by altering the orientation and proximity of a cytokine receptor dimer using diabodies and other synthetic designed scaffolds as surrogate ligands. We directly correlated the intact receptor dimer structures, determined crystallographically, with functional outcome and we find that indeed such systems are ‘tunable’ by remodeling dimer topology and distance. Thus, induced alterations in receptor dimer geometry can ‘tune’ signaling and extracellular ligands that enforce large receptor inter‐subunit distances can counteract intracellular oncogenic ligand‐independent receptor activation. The approach of modulating signaling output through receptors is important to overcoming the therapeutic limitations of cytokine pleiotropy. In my talk I will discuss recent results bearing on this topic.Support or Funding Information1Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA. 2Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA.

Watching a Fine‐tuned Molecular Machine at Work: Structural and Functional Studies of the 26S Proteasome

The degradation of ubiquitin‐tagged proteins by the 26S proteasome is a highly complex process with several well‐coordinated sub‐steps, including ubiquitin recognition, deubiquitination, substrate engagement by the AAA+ motor, mechanical unfolding, translocation, and proteolytic cleavage. Our recently developed FRET‐ and fluorescence‐based assays, relying on the labeling of proteasome‐incorporated unnatural amino acids, allow us to dissect the kinetics and coordination of individual processing steps, and study the coupled conformational changes of the proteasome. Single‐molecule measurements provide exciting details about the conformational dynamics of the proteasomal regulatory particle and how ubiquitin binding, substrate engagement by the AAA+ motor, or the presence of certain receptor subunits affect the switching between substrate‐free and substrate‐processing states, which are furthermore controlled through specific interactions between the ATPase hexamer and the proteasomal lid subcomplex.FRET‐based assays reveal how substrates are propelled through the central channel of the proteasome and progress through the various stages of degradation, including a translocation stall during deubiquitination and the backtracking of substrate upon failure to remove ubiquitin chains prior to substrate entry into the AAA+ motor. Our mutational studies thereby provide important new insight into the mechanisms of substrate engagement and the contributions of individual ATPase subunits depending on their position in the vertical spiral‐staircase arrangement of the AAA+ hexamer. By using substrates with various architectures, we also gained a better understanding of how a substrate’s geometry and ubiquitin modifications affect the degradation rate, and how the proteasome may prioritize its substrates in the cell.Support or Funding InformationHoward Hughes Medical Institute; NIH‐NIGMS (R01‐GM094497)

Fostering inclusion and diversity through research, teaching, mentoring, and outreach.

I am deeply humbled and honored to receive the American Society for Cell Biology (ASCB) Prize for Excellence in Inclusivity. Thank you to the ASCB for recognizing the contributions of faculty to inclusion and diversity in STEM and the importance of this for the advancement of science. Thank you to the Howard Hughes Medical Institute (HHMI) for your generous support of inclusivity. The prize money will be used to fund outreach activities aimed at increasing inclusion in science and to create research opportunities for students from underrepresented groups in the sciences. In this essay, I share bits of my life’s story that I hope will resonate with a broad audience, especially students from underrepresented groups in STEM, and that drive my passion for inclusion and diversity. I provide points of consideration for students to enhance their preparation for science careers and for faculty to improve the current landscape of inclusion and diversity in STEM.

185PD - Immunological differences between immune-rich estrogen receptor-positive and -negative breast cancers

BackgroundA subset of estrogen receptor-positive (ER+) breast cancers have significant tumor infiltrating lymphocytes (TILs), similar to triple-negative breast cancer (TNBC). We examined differences in the immune microenvironment of immune-rich ER+ and immune-rich TNBC to find out if similar or different immunotherapy strategies are appropriate for these distinct disease types. MethodsER+/HER2-negative and TNBC cases were obtained from The Cancer Genome Atlas (TCGA) (n=818 RNA Seq) and METABRIC (n=1465 microarray). An immune gene expression score, as surrogate for TILs, was calculated for each case (Danaher et al). Signature scores were correlated with histologic TILs (R=0.44, p<0.001) for available cases. All cases in the top 25% of signature scores were considered immune-rich. We compared 22 immune cell populations between immune-rich TNBC (n=86) and ER+(n=119) using CIBERSORT (Student’s t-test, FDR adjusted). We examined differential expression of 770 immune-related genes and 137 immuno-oncology (IO) drug targets. Macrophage abundance was measured by quantitative immunofluorescence (QIF) using pan-macrophage marker CD68 in 169 TNBC and 87 ER+ FFPE tissues. ResultsIn TCGA and METABRIC, CIBERSORT showed more M0 (p=0.015, p=0.0043) and M1 macrophages (p=9.4e-08, p=6.24e-11) in immune-rich TNBC compared to ER+. Mast cells (p=0.0093, p=4.09e-15) and M2 macrophages (p=4.4e-05, p=0.053) were more abundant in immune-rich ER+. QIF confirmed higher macrophage content in TNBC (p=0.0001). In both datasets, 36 IO targets were higher expressed in TNBC and 15 in ER+ cases (Table). Notably, coordinated high expression of TGFb pathway members TGFb3, TGFb-R2, and LRRC32 was seen in ER+ cancers and correlated positively with M2 and negatively with M1 macrophage content across all cases.Table185PDTablePotential ER+ Immuno- Oncology TargetsTNBC Mean ExpressionER+ Mean ExpressionFold-Change Mean Expressionp-valueFDR-adjustedIL6ST2,71711,8154.355.13E-212.32E-19TGF-b32,0854,7452.281.32E-248.97E-23CXCR1 (IL-8 receptor A)4399882.251.04E-097.46E-09CSF3R1,0502,0251.938.46E-127.67E-11RORC1,0081,8551.843.65E-082.26E-07ADORA2A2,1633,4421.596.18E-083.65E-07LRRC32 (TGFb activator)7,54911,1521.481.09E-075.31E-07TLR38801,3001.481.65E-055.92E-05CXCL121,0551,5351.458.44E-052.53E-04CLEC14A4927051.432.68E-059.11E-05TGFb-R27,5599,8451.302.08E-045.90E-04TNFSF147998721.092.94E-036.89E-03MICA3493741.077.54E-031.51E-29NLRP33,0153,1451.043.12E-037.20E-03JAK112,68313,0581.030.0190.035 ConclusionsIO drugs targeting TGFb, M2 macrophages and mast cells are attractive therapeutic candidates in immune-rich ER+ breast cancer based on the expression characteristics of these targets. Legal entity responsible for the studyThe authors. FundingHoward Hughes Medical Institute Medical Fellows Grant. DisclosureV. Pelenkanou: Full / Part-time employment: Sanofi, US. D. Rimm: Advisory / Consultancy: Amgen; Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Advisory / Consultancy: Agendia; Advisory / Consultancy: Biocept; Advisory / Consultancy: BMS; Advisory / Consultancy: Cell Signaling Technology; Advisory / Consultancy, Research grant / Funding (institution): Cepheid; Advisory / Consultancy: Daiichi Sankyo; Advisory / Consultancy: GSK; Advisory / Consultancy: InVicro/Konica/Minolta; Advisory / Consultancy: Merck; Advisory / Consultancy, Research grant / Funding (institution): NanoString; Advisory / Consultancy, Research grant / Funding (institution): Perkin Elmer; Advisory / Consultancy: PAIGE.AI; Advisory / Consultancy, Research grant / Funding (institution): Ventana; Advisory / Consultancy, Research grant / Funding (institution): Ultivue; Shareholder / Stockholder / Stock options: PixelGear; Research grant / Funding (institution): Navigate/Novartis; Research grant / Funding (institution): NextCure; Research grant / Funding (institution): Lilly. L. Pusztai: Honoraria (self), Advisory / Consultancy: Merck; Honoraria (self), Advisory / Consultancy: AstraZeneca; Honoraria (self), Advisory / Consultancy: Novartis; Honoraria (self), Advisory / Consultancy: Seattle Genetics; Honoraria (self), Advisory / Consultancy: Pfizer; Honoraria (self), Advisory / Consultancy: Almac. All other authors have declared no conflicts of interest.

The people behind the papers - Eduardo Leyva-Díaz and Oliver Hobert.

Transcriptional autoregulation occurs when transcription factors bind their own cis-regulatory sequences, ensuring their own continuous expression along with expression of other targets. During development, continued expression of identity-specifying transcription factors can be achieved by autoregulation, but until now formal evidence for a developmental requirement of autoregulation has been lacking. A new paper in Development provides this proof with the help of CRISPR/Cas9 gene editing in the C. elegans nervous system. We caught up with the paper's two authors: postdoc Eduardo Leyva-Díaz and his supervisor Oliver Hobert, Professor of Biological Sciences and HHMI Investigator at Columbia University, New York, to find out more about the work.

KFG Q&amp;A for HHMI

KFG Q&amp;A for HHMI

Machine-learning Prognostic Models from the 2014–16 Ebola Outbreak: Data-harmonization Challenges, Validation Strategies, and mHealth Applications

BackgroundEbola virus disease (EVD) plagues low-resource and difficult-to-access settings. Machine learning prognostic models and mHealth tools could improve the understanding and use of evidence-based care guidelines in such settings. However, data incompleteness and lack of interoperability limit model generalizability. This study harmonizes diverse datasets from the 2014–16 EVD epidemic and generates several prognostic models incorporated into the novel Ebola Care Guidelines app that provides informed access to recommended evidence-based guidelines. MethodsMultivariate logistic regression was applied to investigate survival outcomes in 470 patients admitted to five Ebola treatment units in Liberia and Sierra Leone at various timepoints during 2014–16. We generated a parsimonious model (viral load, age, temperature, bleeding, jaundice, dyspnea, dysphagia, and time-to-presentation) and several fallback models for when these variables are unavailable. All were externally validated against two independent datasets and compared to further models including expert observational wellness assessments. Models were incorporated into an app highlighting the signs/symptoms with the largest contribution to prognosis. FindingsThe parsimonious model approached the predictive power of observational assessments by experienced clinicians (Area-Under-the-Curve, AUC = 0.70–0.79, accuracy = 0.64–0.74) and maintained its performance across subcohorts with different healthcare seeking behaviors. Age and viral load contributed >5-fold the weighting of other features and including them in a minimal model had a similar AUC, albeit at the cost of specificity. InterpretationClinically guided prognostic models can recapitulate clinical expertise and be useful when such expertise is unavailable. Incorporating these models into mHealth tools may facilitate their interpretation and provide informed access to comprehensive clinical guidelines. FundingHoward Hughes Medical Institute, US National Institutes of Health, Bill & Melinda Gates Foundation, International Medical Corps, UK Department for International Development, and GOAL Global.