Divergent role of Mitochondrial Amidoxime Reducing Component 1 (MARC1) in human and mouse.

Recent human genome-wide association studies have identified common missense variants in MARC1, p.Ala165Thr and p.Met187Lys, associated with lower hepatic fat, reduction in liver enzymes and protection from most causes of cirrhosis. Using an exome-wide association study we recapitulated earlier MARC1 p.Ala165Thr and p.Met187Lys findings in 540,000 individuals from five ancestry groups. We also discovered novel rare putative loss of function variants in MARC1 with a phenotype similar to MARC1 p.Ala165Thr/p.Met187Lys variants. In vitro studies of recombinant human MARC1 protein revealed Ala165Thr substitution causes protein instability and aberrant localization in hepatic cells, suggesting MARC1 inhibition or deletion may lead to hepatoprotection. Following this hypothesis, we generated Marc1 knockout mice and evaluated the effect of Marc1 deletion on liver phenotype. Unexpectedly, our study found that whole-body Marc1 deficiency in mouse is not protective against hepatic triglyceride accumulation, liver inflammation or fibrosis. In attempts to explain the lack of the observed phenotype, we discovered that Marc1 plays only a minor role in mouse liver while its paralogue Marc2 is the main Marc family enzyme in mice. Our findings highlight the major difference in MARC1 physiological function between human and mouse.

A cellular and molecular spatial atlas of dystrophic muscle.

Asynchronous skeletal muscle degeneration/regeneration is a hallmark feature of Duchenne muscular dystrophy (DMD); however, traditional -omics technologies that lack spatial context make it difficult to study the biological mechanisms of how asynchronous regeneration contributes to disease progression. Here, using the severely dystrophic D2-mdx mouse model, we generated a high-resolution cellular and molecular spatial atlas of dystrophic muscle by integrating spatial transcriptomics and single-cell RNAseq datasets. Unbiased clustering revealed nonuniform distribution of unique cell populations throughout D2-mdx muscle that were associated with multiple regenerative timepoints, demonstrating that this model faithfully recapitulates the asynchronous regeneration observed in human DMD muscle. By probing spatiotemporal gene expression signatures, we found that propagation of inflammatory and fibrotic signals from locally damaged areas contributes to widespread pathology and that querying expression signatures within discrete microenvironments can identify targetable pathways for DMD therapy. Overall, this spatial atlas of dystrophic muscle provides a valuable resource for studying DMD disease biology and therapeutic target discovery.

Activin E-ACVR1C cross talk controls energy storage via suppression of adipose lipolysis in mice.

Body fat distribution is a heritable risk factor for cardiovascular and metabolic disease. In humans, rare Inhibin beta E (INHBE, activin E) loss-of-function variants are associated with a lower waist-to-hip ratio and protection from type 2 diabetes. Hepatic fatty acid sensing promotes INHBE expression during fasting and in obese individuals, yet it is unclear how the hepatokine activin E governs body shape and energy metabolism. Here, we uncover activin E as a regulator of adipose energy storage. By suppressing ß-agonist-induced lipolysis, activin E promotes fat accumulation and adipocyte hypertrophy and contributes to adipose dysfunction in mice. Mechanistically, we demonstrate that activin E elicits its effect on adipose tissue through ACVR1C, activating SMAD2/3 signaling and suppressing PPARG target genes. Conversely, loss of activin E or ACVR1C in mice increases fat utilization, lowers adiposity, and drives PPARG-regulated gene signatures indicative of healthy adipose function. Our studies identify activin E-ACVR1C as a metabolic rheostat promoting liver-adipose cross talk to restrain excessive fat breakdown and preserve fat mass during prolonged fasting, a mechanism that is maladaptive in obese individuals.

In-Depth Mass Spectrometry Analysis Reveals the Plasma Proteomic and N-Glycoproteomic Impact of an Amish-Enriched Cardioprotective Variant in B4GALT1.

B4GALT1 encodes ß-1,4-galactosyltransferase 1, an enzyme that plays a major role in glycan synthesis in the Golgi apparatus by catalyzing the addition of terminal galactose. Studies increasingly suggest that B4GALT1 may be involved in the regulation of lipid metabolism pathways. Recently, we discovered a single-site missense variant Asn352Ser (N352S) in the functional domain of B4GALT1 in an Amish population, which decreases the level of LDL-cholesterol (LDL-c) as well as the protein levels of ApoB, fibrinogen, and IgG in the blood. To systematically evaluate the effects of this missense variant on protein glycosylation, expression, and secretion, we developed a nano-LC-MS/MS-based platform combined with TMT-labeling for in-depth quantitative proteomic and glycoproteomic analyses in the plasma of individuals homozygous for the B4GALT1 missense variant N352S versus non-carriers (n = 5 per genotype). A total of 488 secreted proteins in the plasma were identified and quantified, 34 of which showed significant fold changes in protein levels between N352S homozygotes and non-carriers. We determined N-glycosylation profiles from 370 glycosylation sites in 151 glycoproteins and identified ten proteins most significantly associated with decreased galactosylation and sialyation in B4GALT1 N352S homozygotes. These results further support that B4GALT1 N352S alters the glycosylation profiles of a variety of critical target proteins, thus governing the functions of these proteins in multiple pathways, such as those involved in lipid metabolism, coagulation, and the immune response.

Gate-Controlled Anyon Generation and Detection in Kitaev Spin Liquids.

Reliable manipulation of non-Abelian Ising anyons supported by Kitaev spin liquids may enable intrinsically fault-tolerant quantum computation. Here, we introduce a standalone scheme for both generating and detecting individual Ising anyons using tunable gate voltages in a heterostructure containing a non-Abelian Kitaev spin liquid and a monolayer semiconductor. The key ingredients of our setup are a Kondo coupling to stabilize an Ising anyon in the spin liquid around each electron in the semiconductor, and a large charging energy to allow control over the electron numbers in distinct gate-defined regions of the semiconductor. In particular, a single Ising anyon can be generated at a disk-shaped region by gate tuning its electron number to one, while it can be interferometrically detected by measuring the electrical conductance of a ring-shaped region around it whose electron number is allowed to fluctuate between zero and one. We provide concrete experimental guidelines for implementing our proposal in promising candidate materials like α-RuCl_{3}.

Vacancy Spectroscopy of Non-Abelian Kitaev Spin Liquids.

Spin vacancies in the non-Abelian Kitaev spin liquid are known to harbor Majorana zero modes, potentially enabling topological quantum computing at elevated temperatures. Here, we study the spectroscopic signatures of such Majorana zero modes in a scanning tunneling setup where a non-Abelian Kitaev spin liquid with a finite density of spin vacancies forms a tunneling barrier between a tip and a substrate. Our key result is a well-defined peak close to zero bias voltage in the derivative of the tunneling conductance whose voltage and intensity both increase with the density of vacancies. This "quasi-zero-voltage peak" is identified as the closest analog of the zero-voltage peak observed in topological superconductors that additionally reflects the fractionalized nature of spin-liquid-based Majorana zero modes. We further highlight a single-fermion Van Hove singularity at a higher voltage that reveals the energy scale of the emergent Majorana fermions in the Kitaev spin liquid. Our proposed signatures are within reach of current experiments on the candidate material α-RuCl_{3}.

Light-induced photodissociation in the lowest three electronic states of the NaH molecule.

It has been known that electronic conical intersections in a molecular system can also be created by laser light even in diatomics. The direct consequence of these light-induced degeneracies is the appearance of a strong mixing between the electronic and vibrational motions, which has a strong fingerprint on the ultrafast nuclear dynamics. In the present work, pump and probe numerical simulations are performed with the NaH molecule involving the first three singlet electronic states (X1Σ+(X), A1Σ+(A) and B1Π(B)) and several light-induced degeneracies in the numerical description. To demonstrate the impact of the multiple light-induced non-adiabatic effects together with the molecular rotation on the dynamical properties of the molecule, the dissociation probabilities, kinetic energy release spectra (KER) and the angular distributions of the photofragments were calculated by discussing the role of the permanent dipole moment as well.

Coupling polyatomic molecules to lossy nanocavities: Lindblad vs Schrödinger description.

The use of cavities to impact molecular structure and dynamics has become popular. As cavities, in particular plasmonic nanocavities, are lossy and the lifetime of their modes can be very short, their lossy nature must be incorporated into the calculations. The Lindblad master equation is commonly considered an appropriate tool to describe this lossy nature. This approach requires the dynamics of the density operator and is thus substantially more costly than approaches employing the Schrödinger equation for the quantum wave function when several or many nuclear degrees of freedom are involved. In this work, we compare numerically the Lindblad and Schrödinger descriptions discussed in the literature for a molecular example where the cavity is pumped by a laser. The laser and cavity properties are varied over a range of parameters. It is found that the Schrödinger description adequately describes the dynamics of the polaritons and emission signal as long as the laser intensity is moderate and the pump time is not much longer than the lifetime of the cavity mode. Otherwise, it is demonstrated that the Schrödinger description gradually fails. We also show that the failure of the Schrödinger description can often be remedied by renormalizing the wave function at every step of time propagation. The results are discussed and analyzed.

Nematically Templated Vortex Lattices in Superconducting FeSe.

New pathways to controlling the morphology of superconducting vortex lattices─and their subsequent dynamics─are required to guide and scale vortex world-lines into a computing platform. We have found that the nematic twin boundaries align superconducting vortices in the adjacent terraces due to the incommensurate potential between vortices surrounding twin boundaries and those trapped within them. With the varying density and morphology of twin boundaries, the vortex lattice assumes several distinct structural phases, including square, regular, and irregular one-dimensional lattices. Through concomitant analysis of vortex lattice models, we have inferred the characteristic energetics of the twin boundary potential and furthermore predicted the existence of geometric size effects as a function of increasing confinement by the twin boundaries. These findings extend the ideas of directed control over vortex lattices to intrinsic topological defects and their self-organized networks, which have direct implications for the future design and control of strain-based topological quantum computing architectures.

Emergent Magnetism with Continuous Control in the Ultrahigh-Conductivity Layered Oxide PdCoO2.

The current challenge to realizing continuously tunable magnetism lies in our inability to systematically change properties, such as valence, spin, and orbital degrees of freedom, as well as crystallographic geometry. Here, we demonstrate that ferromagnetism can be externally turned on with the application of low-energy helium implantation and can be subsequently erased and returned to the pristine state via annealing. This high level of continuous control is made possible by targeting magnetic metastability in the ultrahigh-conductivity, nonmagnetic layered oxide PdCoO2 where local lattice distortions generated by helium implantation induce the emergence of a net moment on the surrounding transition metal octahedral sites. These highly localized moments communicate through the itinerant metal states, which trigger the onset of percolated long-range ferromagnetism. The ability to continuously tune competing interactions enables tailoring precise magnetic and magnetotransport responses in an ultrahigh-conductivity film and will be critical to applications across spintronics.

Glutaminase 2 knockdown reduces hyperammonemia and associated lethality of urea cycle disorder mouse model.

Amino acids, the building blocks of proteins in the cells and tissues, are of fundamental importance for cell survival, maintenance, and proliferation. The liver plays a critical role in amino acid metabolism and detoxication of byproducts such as ammonia. Urea cycle disorders with hyperammonemia remain difficult to treat and eventually necessitate liver transplantation. In this study, ornithine transcarbamylase deficient (Otcspf-ash ) mouse model was used to test whether knockdown of a key glutamine metabolism enzyme glutaminase 2 (GLS2, gene name: Gls2) or glutamate dehydrogenase 1 (GLUD1, gene name: Glud1) could rescue the hyperammonemia and associated lethality induced by a high protein diet. We found that reduced hepatic expression of Gls2 but not Glud1 by AAV8-mediated delivery of a short hairpin RNA in Otcspf-ash mice diminished hyperammonemia and reduced lethality. Knockdown of Gls2 but not Glud1 in Otcspf-ash mice exhibited reduced body weight loss and increased plasma glutamine concentration. These data suggest that Gls2 hepatic knockdown could potentially help alleviate risk for hyperammonemia and other clinical manifestations of patients suffering from defects in the urea cycle.

Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney.

BACKGROUND: Microscopic analysis of urine sediment is probably the most commonly used diagnostic procedure in nephrology. The urinary cells, however, have not yet undergone careful unbiased characterization. METHODS: Single-cell transcriptomic analysis was performed on 17 urine samples obtained from five subjects at two different occasions, using both spot and 24-hour urine collection. A pooled urine sample from multiple healthy individuals served as a reference control. In total 23,082 cells were analyzed. Urinary cells were compared with human kidney and human bladder datasets to understand similarities and differences among the observed cell types. RESULTS: Almost all kidney cell types can be identified in urine, such as podocyte, proximal tubule, loop of Henle, and collecting duct, in addition to macrophages, lymphocytes, and bladder cells. The urinary cell-type composition was subject specific and reasonably stable using different collection methods and over time. Urinary cells clustered with kidney and bladder cells, such as urinary podocytes with kidney podocytes, and principal cells of the kidney and urine, indicating their similarities in gene expression. CONCLUSIONS: A reference dataset for cells in human urine was generated. Single-cell transcriptomics enables detection and quantification of almost all types of cells in the kidney and urinary tract.

Humanized C3 Mouse: A Novel Accelerated Model of C3 Glomerulopathy.

BACKGROUND: C3 glomerulopathy (C3G) is characterized by the alternative-pathway (AP) hyperactivation induced by nephritic factors or complement gene mutations. Mice deficient in complement factor H (CFH) are a classic C3G model, with kidney disease that requires several months to progress to renal failure. Novel C3G models can further contribute to understanding the mechanism behind this disease and developing therapeutic approaches. METHODS: A novel, rapidly progressing, severe, murine model of C3G was developed by replacing the mouse C3 gene with the human C3 homolog using VelociGene technology. Functional, histologic, molecular, and pharmacologic assays characterize the presentation of renal disease and enable useful pharmacologic interventions in the humanized C3 (C3hu/hu) mice. RESULTS: The C3hu/hu mice exhibit increased morbidity early in life and die by about 5-6 months of age. The C3hu/hu mice display elevated biomarkers of kidney dysfunction, glomerulosclerosis, C3/C5b-9 deposition, and reduced circulating C3 compared with wild-type mice. Administration of a C5-blocking mAb improved survival rate and offered functional and histopathologic benefits. Blockade of AP activation by anti-C3b or CFB mAbs also extended survival and preserved kidney function. CONCLUSIONS: The C3hu/hu mice are a useful model for C3G because they share many pathologic features consistent with the human disease. The C3G phenotype in C3hu/hu mice may originate from a dysregulated interaction of human C3 protein with multiple mouse complement proteins, leading to unregulated C3 activation via AP. The accelerated disease course in C3hu/hu mice may further enable preclinical studies to assess and validate new therapeutics for C3G.

Signatures of light-induced nonadiabaticity in the field-dressed vibronic spectrum of formaldehyde.

Nonadiabatic coupling is absent between the electronic ground X and first excited (singlet) A states of formaldehyde. As laser fields can induce conical intersections between these two electronic states, formaldehyde is particularly suitable for investigating light-induced nonadiabaticity in a polyatomic molecule. The present work reports on the spectrum induced by light-the so-called field-dressed spectrum-probed by a weak laser pulse. A full-dimensional ab initio approach in the framework of Floquet-state representation is applied. The low-energy spectrum, which without the dressing field would correspond to an infrared vibrational spectrum in the X-state, and the high-energy spectrum, which without the dressing field would correspond to the X → A spectrum, are computed and analyzed. The spectra are shown to be highly sensitive to the frequency of the dressing light allowing one to isolate different nonadiabatic phenomena.

Nonadiabatic phenomena in molecular vibrational polaritons.

Nonadiabatic phenomena are investigated in the rovibrational motion of molecules confined in an infrared cavity. Conical intersections (CIs) between vibrational polaritons, similar to CIs between electronic polaritonic surfaces, are found. The spectral, topological, and dynamic properties of the vibrational polaritons show clear fingerprints of nonadiabatic couplings between molecular vibration, rotation, and the cavity photonic mode. Furthermore, it is found that for the investigated system, composed of two rovibrating HCl molecules and the cavity mode, breaking the molecular permutational symmetry, by changing 35Cl to 37Cl in one of the HCl molecules, the polaritonic surfaces, nonadiabatic couplings, and related spectral, topological, and dynamic properties can deviate substantially. This implies that the natural occurrence of different molecular isotopologues needs to be considered when modeling realistic polaritonic systems.

The potassium channel Kcne3 is a VEGFA-inducible gene selectively expressed by vascular endothelial tip cells.

Angiogenesis is largely driven by motile endothelial tip-cells capable of invading avascular tissue domains and enabling new vessel formation. Highly responsive to Vascular Endothelial Growth-Factor-A (VEGFA), endothelial tip-cells also suppress angiogenic sprouting in adjacent stalk cells, and thus have been a primary therapeutic focus in addressing neovascular pathologies. Surprisingly, however, there remains a paucity of specific endothelial tip-cell markers. Here, we employ transcriptional profiling and a lacZ reporter allele to identify Kcne3 as an early and selective endothelial tip-cell marker in multiple angiogenic contexts. In development, Kcne3 expression initiates during early phases of angiogenesis (E9) and remains specific to endothelial tip-cells, often adjacent to regions expressing VEGFA. Consistently, Kcne3 activation is highly responsive to exogenous VEGFA but maintains tip-cell specificity throughout normal retinal angiogenesis. We also demonstrate endothelial tip-cell selectivity of Kcne3 in several injury and tumor models. Together, our data show that Kcne3 is a unique marker of sprouting angiogenic tip-cells and offers new opportunities for investigating and targeting this cell type.

Robust field-dressed spectra of diatomics in an optical lattice.

The absorption spectra of the cold Na2 molecule dressed by a linearly polarized standing laser wave is investigated with a theoretical model incorporating translational, electronic, vibrational as well as rotational degrees of freedom. In such a situation a light-induced conical intersection (LICI) can be formed (J. Phys. B: At. Mol. Opt. Phys., 2008, 41, 221001). To measure the spectra a weak field is used whose propagation direction is perpendicular to the direction of the dressing field but has identical polarization direction. Although LICIs are present in our model, the simulations demonstrate a very robust absorption spectrum, which is insensitive to the intensity and the wavelength of the dressing field and which does not reflect clear signatures of light-induced nonadiabatic phenomena related to the strong mixing between the electronic, vibrational, rotational and translational motions. However, by widening artificially the very narrow translational energy level gaps, the fingerprint of the LICI appears to some extent in the spectrum.

Quantum light-induced nonadiabatic phenomena in the absorption spectrum of formaldehyde: Full- and reduced-dimensionality studies.

The coupling of a molecule to a cavity can induce conical intersections of the arising polaritonic potential energy surfaces. Such intersections give rise to the strongest possible nonadiabatic effects. By choosing an example that does not possess nonadiabatic effects in the absence of the cavity, we can study, for the first time, the emergence of these effects in a polyatomic molecule due to its coupling with the cavity taking into account all vibrational degrees of freedom. The results are compared with those of reduced-dimensionality models, and the shortcomings and merits of the latter are analyzed.

Defining the Activated Fibroblast Population in Lung Fibrosis Using Single-Cell Sequencing.

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disorder driven by unrelenting extracellular matrix deposition. Fibroblasts are recognized as the central mediators of extracellular matrix production in IPF; however, the characteristics of the underlying fibroblast cell populations in IPF remain poorly understood. Here, we use an unbiased single-cell RNA sequencing analysis of a bleomycin-induced pulmonary fibrosis model to characterize molecular responses to fibrotic injury. Lung cells were isolated on Day 11 to capture emerging fibrosis and gene expression was analyzed by three complementary techniques, which, together, generated a 49-gene signature that defined an activated subpopulation of fibroblasts. However, none of the identified genes were specific to the activated cells or to the disease setting, implying that the activated fibroblasts are not uniquely defined, but exhibit a similar, yet amplified, gene expression pattern to control cells. Our findings have important implications for fibrosis research, including: 1) defining myofibroblasts with any single marker will fail to capture much of the underlying biology; 2) fibroblast activation is poorly correlated with expression of transforming growth factor-ß pathway genes; 3) single-cell analysis provides insight into the mechanism of action of effective therapies (nintedanib); 4) early events in lung fibrosis need not involve significant changes in fibroblast number; populations that do increase in number, such as macrophages, dendritic cells, and proliferating myeloid cells, may merit closer examination for their role in pathogenesis.