Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly with limited therapeutic options. Here, we report on a study of >12 million variants including 163,714 directly genotyped, most rare, protein-altering variant. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5×10–8) distributed across 34 loci. While wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first signal specific to wet AMD, near MMP9 (difference-P = 4.1×10–10). Very rare coding variants (frequency < 0.1%) in CFH, CFI, and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Abstract. We develop results for the use of Lasso and Post-Lasso methods to form first-stage predictions and estimate optimal instruments in linear instrumental variables (IV) models with many instruments, p. Our results apply even when p is much larger than the sample size, n. We show that the IV estimator based on using Lasso or Post-Lasso in the first stage is root-n consistent and asymptotically normal when the first-stage is approximately sparse; i.e.when the conditional expectation of the endogenous variables given the instruments can be wellapproximated by a relatively small set of variables whose identities may be unknown. We also show the estimator is semi-parametrically efficient when the structural error is homoscedastic.Notably our results allow for imperfect model selection, and do not rely upon the unrealistic "beta-min" conditions that are widely used to establish validity of inference following model selection. In simulation experiments, the Lasso-based IV estimator with a data-driven penalty performs well compared to recently advocated many-instrument-robust procedures. In an empirical example dealing with the effect of judicial eminent domain decisions on economic outcomes, the Lasso-based IV estimator outperforms an intuitive benchmark.Optimal instruments are conditional expectations. In developing the IV results, we establish a series of new results for Lasso and Post-Lasso estimators of nonparametric conditional expectation functions which are of independent theoretical and practical interest. We construct a modification of Lasso designed to deal with non-Gaussian, heteroscedastic disturbances which uses a data-weighted 1-penalty function. By innovatively using moderate deviation theory for self-normalized sums, we provide convergence rates for the resulting Lasso and Post-Lasso estimators that are as sharp as the corresponding rates in the homoscedastic Gaussian case under the condition that log p = o(n 1/3 ). We also provide a data-driven method for choosing the penalty level that must be specified in obtaining Lasso and Post-Lasso estimates and establish its asymptotic validity under non-Gaussian, heteroscedastic disturbances.

We present an integrated analysis of the clinical measurements, immune cells and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.

The Arabidopsis photoreceptor cryptochrome 2 (CRY2) was previously used as an optogenetic module, allowing spatiotemporal control of cellular processes with light. Here we report the development of a new CRY2-derived optogenetic module, ‘CRY2olig’, which induces rapid, robust, and reversible protein oligomerization in response to light. Using this module, we developed a novel protein interaction assay, LINC (Light Induced Co-clustering) that can be used to interrogate protein interaction dynamics in live cells. In addition to use probing protein interactions, CRY2olig can also be used to induce and reversibly control diverse cellular processes with spatial and temporal resolution. Here, we demonstrate disrupting clathrin-mediated endocytosis and promoting Arp2/3-mediated actin polymerization with light. These new CRY2-based approaches expand the growing arsenal of optogenetic strategies to probe cellular function.

The human lens is comprised largely of crystallin proteins assembled into a highly ordered, interactive macro-structure essential for lens transparency and refractive index. Any disruption of intra- or inter-protein interactions will alter this delicate structure, exposing hydrophobic surfaces, with consequent protein aggregation and cataract formation. Cataracts are the most common cause of blindness worldwide, affecting tens of millions of people, and currently the only treatment is surgical removal of cataractous lenses. The precise mechanisms by which lens proteins both prevent aggregation and maintain lens transparency are largely unknown. Lanosterol is an amphipathic molecule enriched in the lens. It is synthesized by lanosterol synthase (LSS) in a key cyclization reaction of a cholesterol synthesis pathway. Here we identify two distinct homozygous LSS missense mutations (W581R and G588S) in two families with extensive congenital cataracts. Both of these mutations affect highly conserved amino acid residues and impair key catalytic functions of LSS. Engineered expression of wild-type, but not mutant, LSS prevents intracellular protein aggregation of various cataract-causing mutant crystallins. Treatment by lanosterol, but not cholesterol, significantly decreased preformed protein aggregates both in vitro and in cell-transfection experiments. We further show that lanosterol treatment could reduce cataract severity and increase transparency in dissected rabbit cataractous lenses in vitro and cataract severity in vivo in dogs. Our study identifies lanosterol as a key molecule in the prevention of lens protein aggregation and points to a novel strategy for cataract prevention and treatment.

SUMMARY HIV-infected individuals are living longer on antiretroviral therapy, but many patients display signs that in some ways resemble premature aging. To investigate and quantify the impact of chronic HIV infection on aging, we report a global analysis of the whole blood DNA methylomes of 137 HIV+ individuals under sustained therapy along with 44 matched HIV− individuals. First, we develop and validate epigenetic models of aging that are independent of blood cell composition. Using these models, we find that both chronic and recent HIV infection lead to an average aging advancement of 4.9 years, increasing expected mortality risk by 19%. In addition, sustained infection results in global deregulation of the methylome across >80,000 CpGs and specific hypomethylation of the region encoding the human leukocyte antigen locus (HLA). We find that decreased HLA methylation is predictive of lower CD4/CD8 T cell ratio, linking molecular aging, epigenetic regulation and disease progression.

There has been much research over the past two decades with the aim of engineering cartilage constructs for repairing or restoring damaged cartilage. To engineer healthy neocartilage, the constructs must have mechanical properties matching those of native cartilage as well as appropriate for the loading conditions of the joint. This article discusses the mechanical behavior of native cartilage and surveys different types of tensile, compressive, and shear tests with their limitations. It also comprehensively reviews recent work and achievements in developing the mathematical models representing the mechanical properties of both native and engineered cartilage. Different methods for enhancing the mechanical properties of engineered cartilage are also discussed, including scaffold design, mechanical stimulation, and chemical stimulation. This article concludes with recommendations for future research aimed at achieving engineered cartilage with mechanical properties matching those found in native cartilage.

For all the significant ps reported in this article, p rep > .979. Volume 18-Number 6 499 S. Yamaguchi et al.