Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution

Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. This software can be run interactively on the worldwide web at https://www.pxengineering.org/. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization, and, for two of these three proteins, the construct with the largest number of KR substitutions exhibits significantly enhanced crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from Bulk KR-substituted domains show the engineered arginine residues frequently make hydrogen-bonds across crystal-packing interfaces. We thus demonstrate that Bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve crystallization.

Principles for Health Information Collection, Sharing, and Use: A Policy Statement From the American Heart Association

The evolution of the electronic health record, combined with advances in data curation and analytic technologies, increasingly enables data sharing and harmonization. Advances in the analysis of health-related and health-proxy information have already accelerated research discoveries and improved patient care. This American Heart Association policy statement discusses how broad data sharing can be an enabling driver of progress by providing data to develop, test, and benchmark innovative methods, scalable insights, and potential new paradigms for data storage and workflow. Along with these advances come concerns about the sensitive nature of some health data, equity considerations about the involvement of historically excluded communities, and the complex intersection of laws attempting to govern behavior. Data-sharing principles are therefore necessary across a wide swath of entities, including parties who collect health information, funders, researchers, patients, legislatures, commercial companies, and regulatory departments and agencies. This policy statement outlines some of the key equity and legal background relevant to health data sharing and responsible management. It then articulates principles that will guide the American Heart Association's engagement in public policy related to data collection, sharing, and use to continue to inform its work across the research enterprise, as well as specific examples of how these principles might be applied in the policy landscape. The goal of these principles is to improve policy to support the use or reuse of health information in ways that are respectful of patients and research participants, equitable in impact in terms of both risks and potential benefits, and beneficial across broad and demographically diverse communities in the United States.

Exclusion cycles: Reinforcing disparities in medicine

Clinical practice, data collection, and medical AI constitute self-reinforcing and interacting cycles of exclusion.

Open-Source Clinical Machine Learning Models: Critical Appraisal of Feasibility, Advantages, and Challenges

Machine learning applications promise to augment clinical capabilities and at least 64 models have already been approved by the US Food and Drug Administration. These tools are developed, shared, and used in an environment in which regulations and market forces remain immature. An important consideration when evaluating this environment is the introduction of open-source solutions in which innovations are freely shared; such solutions have long been a facet of digital culture. We discuss the feasibility and implications of open-source machine learning in a health care infrastructure built upon proprietary information. The decreased cost of development as compared to drugs and devices, a longstanding culture of open-source products in other industries, and the beginnings of machine learning–friendly regulatory pathways together allow for the development and deployment of open-source machine learning models. Such tools have distinct advantages including enhanced product integrity, customizability, and lower cost, leading to increased access. However, significant questions regarding engineering concerns about implementation infrastructure and model safety, a lack of incentives from intellectual property protection, and nebulous liability rules significantly complicate the ability to develop such open-source models. Ultimately, the reconciliation of open-source machine learning and the proprietary information–driven health care environment requires that policymakers, regulators, and health care organizations actively craft a conducive market in which innovative developers will continue to both work and collaborate.

Respecting Autonomy And Enabling Diversity: The Effect Of Eligibility And Enrollment On Research Data Demographics

Many promising advances in precision health and other Big Data research rely on large data sets to analyze correlations among genetic variants, behavior, environment, and outcomes to improve population health. But these data sets are generally populated with demographically homogeneous cohorts. We conducted a retrospective cohort study of patients at a major academic medical center during 2012-19 to explore how recruitment and enrollment approaches affected the demographic diversity of participants in its research biospecimen and data bank. We found that compared with the overall clinical population, patients who consented to enroll in the research data bank were significantly less diverse in terms of age, sex, race, ethnicity, and socioeconomic status. Compared with patients who were recruited for the data bank, patients who enrolled were younger and less likely to be Black or African American, Asian, or Hispanic. The overall demographic diversity of the data bank was affected as much (and in some cases more) by which patients were considered eligible for recruitment as by which patients consented to enroll. Our work underscores the need for systemic commitment to diversify data banks so that different communities can benefit from research.

Collaboration in times of crisis: A study on COVID-19 vaccine R&D partnerships

Collaboration is central for initiatives and efforts in the race to fight COVID-19, with particular focus on fostering rapid development of safe and effective COVID-19 vaccines. We investigated the types of partnerships that have emerged during the pandemic to develop these products. Using the World Health Organization’s list of COVID-19 vaccine developments, we found nearly one third of all vaccine candidates were developed by partnerships, which tended to use next-gen vaccine platforms more than solo efforts. These partnerships vary substantially between materials-transfer partnerships and knowledge-sharing partnerships. The difference is important: The type of sharing between partners not only shapes the collaboration, but also bears implications for knowledge and technology development in the field and more broadly. Policies promoting fair and effective collaboration and knowledge-sharing are key for public health to avoid stumbling blocks for vaccine development, deployment, and equitable access, both for COVID-19 and expected future pandemics.

Regulatory oversight, causal inference, and safe and effective health care machine learning

In recent years, the applications of Machine Learning (ML) in the health care delivery setting have grown to become both abundant and compelling. Regulators have taken notice of these developments and the U.S. Food and Drug Administration (FDA) has been engaging actively in thinking about how best to facilitate safe and effective use. Although the scope of its oversight for software-driven products is limited, if FDA takes the lead in promoting and facilitating appropriate applications of causal inference as a part of ML development, that leadership is likely to have implications well beyond regulated products.

Big data and black-box medical algorithms

New machine-learning techniques entering medicine present challenges in validation, regulation, and integration into practice.

Privacy in the age of medical big data

Big data has become the ubiquitous watch word of medical innovation. The rapid development of machine-learning techniques and artificial intelligence in particular has promised to revolutionize medical practice from the allocation of resources to the diagnosis of complex diseases. But with big data comes big risks and challenges, among them significant questions about patient privacy. Here, we outline the legal and ethical challenges big data brings to patient privacy. We discuss, among other topics, how best to conceive of health privacy; the importance of equity, consent, and patient governance in data collection; discrimination in data uses; and how to handle data breaches. We close by sketching possible ways forward for the regulatory system.

Promoting healthcare innovation on the demand side

Innovation policy often focuses on fortifying the incentives of firms that develop and sell new products by offering them lucrative rights to exclude competitors from the market. Regulators also rely on these same firms-and on similar incentives-to develop information about the effects of their products in patients, despite their obvious conflict of interest. The result may be a distorted understanding that leads to overuse of expensive new medical technologies. Recent technological advances have put healthcare payers in an excellent position to play a larger role in future innovation to improve healthcare and reduce its costs. Insurance companies and integrated healthcare providers have custody of treasure troves of data about healthcare provision and outcomes that can yield valuable insights about the effects of medical treatment without the need to conduct costly clinical trials. Some integrated healthcare systems have seized upon this advantage to make notable discoveries about the effects of particular products that have changed the standard of care. Moreover, to the extent that healthcare payers can profit from reducing costs, they will seek to avoid inappropriate use of costly technologies. Greater involvement of payers in healthcare innovation thus offers a potential counterweight to the incentives of product sellers to promote excessive use of costly new products. In recent years, the federal government has sought to promote innovation through analysis of healthcare records in a series of initiatives; some picture insurers as passive data repositories, while others provide opportunities for insurers to take a more active role in innovation. In this paper, we examine the role of health insurers in developing new knowledge about the provision and effects of healthcare-what we call 'demand-side innovation'. We address the contours of this underexplored area of innovation and describe the behavior of participating firms. We examine the effects of current legal rules on demand-side innovation, including insurance regulation, intellectual property rules, privacy protections, and FDA regulation of new healthcare technologies. Throughout, we highlight many policy tools that government can use and is using to facilitate payer innovation outside the traditional toolkit of patents and exclusive rights.

The Need for a Privacy Standard for Medical Devices That Transmit Protected Health Information Used in the Precision Medicine Initiative for Diabetes and Other Diseases

Privacy is an important concern for the Precision Medicine Initiative (PMI) because success of this initiative will require the public to be willing to participate by contributing large amounts of genetic/genomic information and sensor data. This sensitive personal information is intended to be used only for specified research purposes. Public willingness to participate will depend on the public's level of trust that their information will be protected and kept private. Medical devices may constantly provide information. Therefore, assuring privacy for device-generated information may be essential for broad participation in the PMI. Privacy standards for devices should be an important early step in the development of the PMI.

Regulating Black-Box Medicine

Data drive modern medicine. And our tools to analyze those data are growing ever more powerful. As health data are collected in greater and greater amounts, sophisticated algorithms based on those data can drive medical innovation, improve the process of care, and increase efficiency. Those algorithms, however, vary widely in quality. Some are accurate and powerful, while others may be riddled with errors or based on faulty science. When an opaque algorithm recommends an insulin dose to a diabetic patient, how do we know that dose is correct? Patients, providers, and insurers face substantial difficulties in identifying high-quality algorithms; they lack both expertise and proprietary information. How should we ensure that medical algorithms are safe and effective? Medical algorithms need regulatory oversight, but that oversight must be appropriately tailored. Unfortunately, the Food and Drug Administration (FDA) has suggested that it will regulate algorithms under its traditional framework, a relatively rigid system that is likely to stifle innovation and to block the development of more flexible, current algorithms. This Article draws upon ideas from the new governance movement to suggest a different path. FDA should pursue a more adaptive regulatory approach with requirements that developers disclose information underlying their algorithms. Disclosure would allow FDA oversight to be supplemented with evaluation by providers, hospitals, and insurers. This collaborative approach would supplement the agency's review with ongoing real-world feedback from sophisticated market actors. Medical algorithms have tremendous potential, but ensuring that such potential is developed in high-quality ways demands a careful balancing between public and private oversight, and a role for FDA that mediates--but does not dominate--the rapidly developing industry.

Models of consent to return of incidental findings in genomic research

Genomic research-including whole genome sequencing and whole exome sequencing-has a growing presence in contemporary biomedical investigation. The capacity of sequencing techniques to generate results that go beyond the primary aims of the research-historically referred to as "incidental findings"-has generated considerable discussion as to how this information should be handled-that is, whether incidental results should be returned, and if so, which ones.Federal regulations governing most human subjects research in the United States require the disclosure of "the procedures to be followed" in the research as part of the informed consent process. It seems reasonable to assume-and indeed, many commentators have concluded-that genomic investigators will be expected to inform participants about, among other procedures, the prospect that incidental findings will become available and the mechanisms for dealing with them. Investigators, most of whom will not have dealt with these issues before, will face considerable challenges in framing meaningful disclosures for research participants.To help in this task, we undertook to identify the elements that should be included in the informed consent process related to incidental findings. We did this by surveying a large number of genomic researchers (n = 241) and by conducting in-depth interviews with a smaller number of researchers (n = 28) and genomic research participants (n = 20). Based on these findings, it seems clear to us that routine approaches to informed consent are not likely to be effective in genomic research in which the prospect of incidental findings exists. Ensuring that participants' decisions are informed and meaningful will require innovative approaches to dealing with the consent issue. We have identified four prototypical models of a consent process for return of incidental findings.

Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data

Crystallization is the most serious bottleneck in high-throughput protein-structure determination by diffraction methods. We have used data mining of the large-scale experimental results of the Northeast Structural Genomics Consortium and experimental folding studies to characterize the biophysical properties that control protein crystallization. This analysis leads to the conclusion that crystallization propensity depends primarily on the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. We identify specific sequence features that correlate with crystallization propensity and that can be used to estimate the crystallization probability of a given construct. Analyses of entire predicted proteomes demonstrate substantial differences in the amino acid-sequence properties of human versus eubacterial proteins, which likely reflect differences in biophysical properties, including crystallization propensity. Our thermodynamic measurements do not generally support previous claims regarding correlations between sequence properties and protein stability.