ABSTRACT
We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or â¼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.
Subject(s)
Genome , Primates , Animals , Humans , Base Sequence , Primates/classification , Primates/genetics , Biological Evolution , Sequence Analysis, DNA , Genomic Structural VariationABSTRACT
Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1 retrotransposition; 80% of the larger inversions are balanced and affect twice as many nucleotides as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons. Since flanking repeats promote non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7 × 10-4 per locus per generation. Recurrent inversions exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes specific haplotypes to disease-causing CNVs.
Subject(s)
Chromosome Inversion , Segmental Duplications, Genomic , Chromosome Inversion/genetics , DNA Copy Number Variations/genetics , Genome, Human , Genomics , HumansABSTRACT
Human immunodeficiency virus (HIV) cure efforts are increasingly focused on harnessing CD8+ T cell functions, which requires a deeper understanding of CD8+ T cells promoting HIV control. Here we identifiy an antigen-responsive TOXhiTCF1+CD39+CD8+ T cell population with high expression of inhibitory receptors and low expression of canonical cytolytic molecules. Transcriptional analysis of simian immunodeficiency virus (SIV)-specific CD8+ T cells and proteomic analysis of purified CD8+ T cell subsets identified TOXhiTCF1+CD39+CD8+ T cells as intermediate effectors that retained stem-like features with a lineage relationship with terminal effector T cells. TOXhiTCF1+CD39+CD8+ T cells were found at higher frequency than TCF1-CD39+CD8+ T cells in follicular microenvironments and were preferentially located in proximity of SIV-RNA+ cells. Their frequency was associated with reduced plasma viremia and lower SIV reservoir size. Highly similar TOXhiTCF1+CD39+CD8+ T cells were detected in lymph nodes from antiretroviral therapy-naive and antiretroviral therapy-suppressed people living with HIV, suggesting this population of CD8+ T cells contributes to limiting SIV and HIV persistence.
Subject(s)
CD8-Positive T-Lymphocytes , Lymph Nodes , Simian Acquired Immunodeficiency Syndrome , Simian Immunodeficiency Virus , Simian Immunodeficiency Virus/immunology , CD8-Positive T-Lymphocytes/immunology , Animals , Simian Acquired Immunodeficiency Syndrome/immunology , Simian Acquired Immunodeficiency Syndrome/virology , Lymph Nodes/immunology , Humans , Macaca mulatta , HIV Infections/immunology , HIV Infections/virology , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolismABSTRACT
The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.
Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/metabolism , Drug Evaluation, Preclinical/methods , Pneumonia, Viral/metabolism , Proteomics/methods , A549 Cells , Angiotensin-Converting Enzyme 2 , Animals , Antiviral Agents/pharmacology , COVID-19 , Caco-2 Cells , Casein Kinase II/antagonists & inhibitors , Casein Kinase II/metabolism , Chlorocebus aethiops , Coronavirus Infections/virology , Cyclin-Dependent Kinases/antagonists & inhibitors , Cyclin-Dependent Kinases/metabolism , HEK293 Cells , Host-Pathogen Interactions , Humans , Pandemics , Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Phosphoinositide-3 Kinase Inhibitors/pharmacology , Phosphorylation , Pneumonia, Viral/virology , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins/antagonists & inhibitors , Proto-Oncogene Proteins/metabolism , Receptor Protein-Tyrosine Kinases/antagonists & inhibitors , Receptor Protein-Tyrosine Kinases/metabolism , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/metabolism , Vero Cells , p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors , p38 Mitogen-Activated Protein Kinases/metabolism , Axl Receptor Tyrosine KinaseABSTRACT
We have developed a platform for quantitative genetic interaction mapping using viral infectivity as a functional readout and constructed a viral host-dependency epistasis map (vE-MAP) of 356 human genes linked to HIV function, comprising >63,000 pairwise genetic perturbations. The vE-MAP provides an expansive view of the genetic dependencies underlying HIV infection and can be used to identify drug targets and study viral mutations. We found that the RNA deadenylase complex, CNOT, is a central player in the vE-MAP and show that knockout of CNOT1, 10, and 11 suppressed HIV infection in primary T cells by upregulating innate immunity pathways. This phenotype was rescued by deletion of IRF7, a transcription factor regulating interferon-stimulated genes, revealing a previously unrecognized host signaling pathway involved in HIV infection. The vE-MAP represents a generic platform that can be used to study the global effects of how different pathogens hijack and rewire the host during infection.
Subject(s)
Epistasis, Genetic , HIV Infections/genetics , Interferon Regulatory Factor-7/genetics , Transcription Factors/genetics , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/pathology , HIV Infections/immunology , HIV Infections/pathology , HIV Infections/virology , HIV-1/genetics , HIV-1/pathogenicity , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/immunology , Humans , Immunity, Innate/genetics , Interferons/genetics , Mutation , Signal Transduction/geneticsABSTRACT
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3-5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome.
Subject(s)
Evolution, Molecular , Genome/genetics , Genomics , Pan paniscus/genetics , Phylogeny , Animals , Eukaryotic Initiation Factor-4A/genetics , Female , Genes , Gorilla gorilla/genetics , Molecular Sequence Annotation/standards , Pan troglodytes/genetics , Pongo/genetics , Segmental Duplications, Genomic , Sequence Analysis, DNAABSTRACT
The electronic properties of moiré heterostructures depend sensitively on the relative orientation between layers of the stack. For example, near-magic-angle twisted bilayer graphene (TBG) commonly shows superconductivity, yet a TBG sample with one of the graphene layers rotationally aligned to a hexagonal Boron Nitride (hBN) cladding layer provided experimental observation of orbital ferromagnetism. To create samples with aligned graphene/hBN, researchers often align edges of exfoliated flakes that appear straight in optical micrographs. However, graphene or hBN can cleave along either zig-zag or armchair lattice directions, introducing a [Formula: see text] ambiguity in the relative orientation of two flakes. By characterizing the crystal lattice orientation of exfoliated flakes prior to stacking using Raman and second-harmonic generation for graphene and hBN, respectively, we unambiguously align monolayer graphene to hBN at a near-[Formula: see text], not [Formula: see text], relative twist angle. We confirm this alignment by torsional force microscopy of the graphene/hBN moiré on an open-face stack, and then by cryogenic transport measurements, after full encapsulation with a second, nonaligned hBN layer. This work demonstrates a key step toward systematically exploring the effects of the relative twist angle between dissimilar materials within moiré heterostructures.
ABSTRACT
In a stack of atomically thin van der Waals layers, introducing interlayer twist creates a moiré superlattice whose period is a function of twist angle. Changes in that twist angle of even hundredths of a degree can dramatically transform the system's electronic properties. Setting a precise and uniform twist angle for a stack remains difficult; hence, determining that twist angle and mapping its spatial variation is very important. Techniques have emerged to do this by imaging the moiré, but most of these require sophisticated infrastructure, time-consuming sample preparation beyond stack synthesis, or both. In this work, we show that torsional force microscopy (TFM), a scanning probe technique sensitive to dynamic friction, can reveal surface and shallow subsurface structure of van der Waals stacks on multiple length scales: the moirés formed between bi-layers of graphene and between graphene and hexagonal boron nitride (hBN) and also the atomic crystal lattices of graphene and hBN. In TFM, torsional motion of an Atomic Force Microscope (AFM) cantilever is monitored as it is actively driven at a torsional resonance while a feedback loop maintains contact at a set force with the sample surface. TFM works at room temperature in air, with no need for an electrical bias between the tip and the sample, making it applicable to a wide array of samples. It should enable determination of precise structural information including twist angles and strain in moiré superlattices and crystallographic orientation of van der Waals flakes to support predictable moiré heterostructure fabrication.
ABSTRACT
Studies of two-dimensional electron systems in a strong magnetic field revealed the quantum Hall effect1, a topological state of matter featuring a finite Chern number C and chiral edge states2,3. Haldane4 later theorized that Chern insulators with integer quantum Hall effects could appear in lattice models with complex hopping parameters even at zero magnetic field. The ABC-trilayer graphene/hexagonal boron nitride (ABC-TLG/hBN) moiré superlattice provides an attractive platform with which to explore Chern insulators because it features nearly flat moiré minibands with a valley-dependent, electrically tunable Chern number5,6. Here we report the experimental observation of a correlated Chern insulator in an ABC-TLG/hBN moiré superlattice. We show that reversing the direction of the applied vertical electric field switches the moiré minibands of ABC-TLG/hBN between zero and finite Chern numbers, as revealed by large changes in magneto-transport behaviour. For topological hole minibands tuned to have a finite Chern number, we focus on quarter filling, corresponding to one hole per moiré unit cell. The Hall resistance is well quantized at h/2e2 (where h is Planck's constant and e is the charge on the electron), which implies C = 2, for a magnetic field exceeding 0.4 tesla. The correlated Chern insulator is ferromagnetic, exhibiting substantial magnetic hysteresis and a large anomalous Hall signal at zero magnetic field. Our discovery of a C = 2 Chern insulator at zero magnetic field should open up opportunities for discovering correlated topological states, possibly with topological excitations7, in nearly flat and topologically nontrivial moiré minibands.
ABSTRACT
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
ABSTRACT
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
Subject(s)
Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Coronavirus Infections/metabolism , Drug Repositioning , Molecular Targeted Therapy , Pneumonia, Viral/drug therapy , Pneumonia, Viral/metabolism , Protein Interaction Maps , Viral Proteins/metabolism , Animals , Antiviral Agents/classification , Antiviral Agents/pharmacology , Betacoronavirus/genetics , Betacoronavirus/metabolism , Betacoronavirus/pathogenicity , COVID-19 , Chlorocebus aethiops , Cloning, Molecular , Coronavirus Infections/immunology , Coronavirus Infections/virology , Drug Evaluation, Preclinical , HEK293 Cells , Host-Pathogen Interactions/drug effects , Humans , Immunity, Innate , Mass Spectrometry , Pandemics , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Protein Binding , Protein Biosynthesis/drug effects , Protein Domains , Protein Interaction Mapping , Receptors, sigma/metabolism , SARS-CoV-2 , SKP Cullin F-Box Protein Ligases/metabolism , Vero Cells , Viral Proteins/genetics , COVID-19 Drug TreatmentABSTRACT
Anisotropic hopping in a toy Hofstadter model was recently invoked to explain a rich and surprising Landau spectrum measured in twisted bilayer graphene away from the magic angle. Suspecting that such anisotropy could arise from unintended uniaxial strain, we extend the Bistritzer-MacDonald model to include uniaxial heterostrain and present a detailed analysis of its impact on band structure and magnetotransport. We find that such strain strongly influences band structure, shifting the three otherwise-degenerate van Hove points to different energies. Coupled to a Boltzmann magnetotransport calculation, this reproduces previously unexplained nonsaturating [Formula: see text] magnetoresistance over broad ranges of density near filling [Formula: see text] and predicts subtler features that had not been noticed in the experimental data. In contrast to these distinctive signatures in longitudinal resistivity, the Hall coefficient is barely influenced by strain, to the extent that it still shows a single sign change on each side of the charge neutrality point-surprisingly, this sign change no longer occurs at a van Hove point. The theory also predicts a marked rotation of the electrical transport principal axes as a function of filling even for fixed strain and for rigid bands. More careful examination of interaction-induced nematic order versus strain effects in twisted bilayer graphene could thus be in order.
ABSTRACT
Responding effectively to external stress is crucial for neurons. Defective stress granule dynamics has been hypothesized as one of the pathways that renders motor neurons in amyotrophic lateral sclerosis (ALS) more prone to early death. Specifically, it is thought that stress granules seed the cytoplasmic TDP-43 inclusions that are observed in the neurons of most ALS patients, as well as ~50% of all frontotemporal dementia (FTD) patients. In this study, we tested this hypothesis in an intact mammalian nervous system. We established an in vivo heat stress paradigm in mice that effectively triggers the eIF2α pathway and the formation of stress granules in the CNS. In non-transgenic mice, we report an age-dependent decline in the formation of heat-induced stress granules, with 18-month-old animals showing a significant impairment. Furthermore, although neuronal stress granules were robustly observed in non-transgenic mice and SOD1G93A mice, they were largely absent in age-matched TDP-43M337V animals. The observed defect in stress granule formation in TDP-43M337V mice correlated with deficits in expression of key protein components typically required for phase separation. Lastly, while TDP-43 was not localized to stress granules, we observed complete nuclear depletion of TDP-43 in a subset of neurons, with the highest proportion being in the TDP-43M337V mice. Overall, our results indicate that mutant TDP-43 expression is associated with defective stress granule assembly and increased TDP-43 nuclear depletion in the mammalian nervous system, which could be relevant to ALS/FTD pathogenesis.
Subject(s)
Amyotrophic Lateral Sclerosis , Frontotemporal Dementia , Mice , Animals , Amyotrophic Lateral Sclerosis/metabolism , Frontotemporal Dementia/pathology , Stress Granules , Motor Neurons/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Mammals/metabolismABSTRACT
Understanding the mechanism of high-transition-temperature (high-Tc) superconductivity is a central problem in condensed matter physics. It is often speculated that high-Tc superconductivity arises in a doped Mott insulator1 as described by the Hubbard model2-4. An exact solution of the Hubbard model, however, is extremely challenging owing to the strong electron-electron correlation in Mott insulators. Therefore, it is highly desirable to study a tunable Hubbard system, in which systematic investigations of the unconventional superconductivity and its evolution with the Hubbard parameters can deepen our understanding of the Hubbard model. Here we report signatures of tunable superconductivity in an ABC-trilayer graphene (TLG) and hexagonal boron nitride (hBN) moiré superlattice. Unlike in 'magic angle' twisted bilayer graphene, theoretical calculations show that under a vertical displacement field, the ABC-TLG/hBN heterostructure features an isolated flat valence miniband associated with a Hubbard model on a triangular superlattice5,6 where the bandwidth can be tuned continuously with the vertical displacement field. Upon applying such a displacement field we find experimentally that the ABC-TLG/hBN superlattice displays Mott insulating states below 20 kelvin at one-quarter and one-half fillings of the states, corresponding to one and two holes per unit cell, respectively. Upon further cooling, signatures of superconductivity ('domes') emerge below 1 kelvin for the electron- and hole-doped sides of the one-quarter-filling Mott state. The electronic behaviour in the ABC-TLG/hBN superlattice is expected to depend sensitively on the interplay between the electron-electron interaction and the miniband bandwidth. By varying the vertical displacement field, we demonstrate transitions from the candidate superconductor to Mott insulator and metallic phases. Our study shows that ABC-TLG/hBN heterostructures offer attractive model systems in which to explore rich correlated behaviour emerging in the tunable triangular Hubbard model.
ABSTRACT
Congenital heart disease (CHD) is a common group of birth defects with a strong genetic contribution to their etiology, but historically the diagnostic yield from exome studies of isolated CHD has been low. Pleiotropy, variable expressivity, and the difficulty of accurately phenotyping newborns contribute to this problem. We hypothesized that performing exome sequencing on selected individuals in families with multiple members affected by left-sided CHD, then filtering variants by population frequency, in silico predictive algorithms, and phenotypic annotations from publicly available databases would increase this yield and generate a list of candidate disease-causing variants that would show a high validation rate. In eight of the nineteen families in our study (42%), we established a well-known gene/phenotype link for a candidate variant or performed confirmation of a candidate variant's effect on protein function, including variants in genes not previously described or firmly established as disease genes in the body of CHD literature: BMP10, CASZ1, ROCK1 and SMYD1. Two plausible variants in different genes were found to segregate in the same family in two instances suggesting oligogenic inheritance. These results highlight the need for functional validation and demonstrate that in the era of next-generation sequencing, multiplex families with isolated CHD can still bring high yield to the discovery of novel disease genes.
Subject(s)
Exome , Heart Defects, Congenital , Bone Morphogenetic Proteins/genetics , DNA-Binding Proteins/genetics , Exome/genetics , Gene Frequency , Genetic Association Studies , Heart Defects, Congenital/genetics , Humans , Infant, Newborn , Pedigree , Transcription Factors/genetics , Exome Sequencing , rho-Associated Kinases/geneticsABSTRACT
SignificanceWhen two sheets of graphene are twisted to the magic angle of 1.1∘, the resulting flat moiré bands can host exotic correlated electronic states such as superconductivity and ferromagnetism. Here, we show transport properties of a twisted bilayer graphene device at 1.38∘, far enough above the magic angle that we do not expect exotic correlated states. Instead, we see several unusual behaviors in the device's resistivity upon tuning both charge carrier density and perpendicular magnetic field. We can reproduce these behaviors with a surprisingly simple model based on Hofstadter's butterfly. These results shed light on the underlying properties of twisted bilayer graphene.
ABSTRACT
Rhombohedral polytype transition metal dichalcogenide (TMDC) multilayers exhibit non-centrosymmetric interlayer stacking, which yields intriguing properties such as ferroelectricity, a large second-order susceptibility coefficient χ(2), giant valley coherence, and a bulk photovoltaic effect. These properties have spurred significant interest in developing phase-selective growth methods for multilayer rhombohedral TMDC films. Here, we report a confined-space, hybrid metal-organic chemical vapor deposition method that preferentially grows 3R-WS2 multilayer films with thickness up to 130 nm. We confirm the 3R stacking structure via polarization-resolved second-harmonic generation characterization and the 3-fold symmetry revealed by anisotropic H2O2 etching. The multilayer 3R WS2 shows a dendritic morphology, which is indicative of diffusion-limited growth. Multilayer regions with large, stepped terraces enable layer-resolved evaluation of the optical properties of 3R-WS2 via Raman, photoluminescence, and differential reflectance spectroscopy. These measurements confirm the interfacial quality and suggest ferroelectric modification of the exciton energies.
ABSTRACT
Idiopathic pulmonary fibrosis (IPF) is an incurable interstitial lung disease characterized by fibrosis. Two FDA-approved drugs, pirfenidone and nintedanib, only modestly prolong survival. In this study, we asked whether levels of select circulating biomarkers in patients with IPF demonstrated changes in response to treatment over time and whether treatment with pirfenidone and nintedanib led to differential biomarker expression. Serial plasma samples from 48 patients with IPF on usual treatment and six healthy volunteers were analyzed to identify differentially expressed blood protein. Hypothesis-driven potential biomarker selection was based on recent literature, internal preclinical data, and the PROLIFIC Consortium (Schafer P. 6th Annual IPF Summit. Boston, MA, 2022) proposed biomarkers of pulmonary fibrosis. We compared our findings to public databases to provide insights into relevant signaling pathways in IPF. Of the 26 proteins measured, we found that 11 (SP-D, TIMP1, MMP7, CYFRA21-1, YKL40, CA125, sICAM, IP-10, MDC, CXCL13) were significantly elevated in patients with IPF compared with healthy volunteers but their levels did not significantly change over time. In the IPF samples, seven proteins were elevated in the treatment group compared with the no-treatment group. However, protein profiles were not distinguishable between patients on pirfenidone versus nintedanib. We demonstrated that most proteins differentially detected in our samples were predicted to be secreted from the lung epithelial or interstitial compartments. However, a significant minority of the proteins are not known to be transcriptionally expressed by lung cells, suggesting an ongoing systemic response. Understanding the contributions of the systemic response in IPF may be important as new therapeutics are developed.NEW & NOTEWORTHY In this study, we confirmed protein expression differences in only a subset of predicted biomarkers from IPF and control subjects. Most differentially expressed proteins were predicted to be secreted from lung cells. However, a significant minority of the proteins are not known to be transcriptionally expressed by lung cells, suggesting an ongoing systemic response. The contributions of the systemic response in IPF may be important as new therapeutics are developed.
Subject(s)
Antigens, Neoplasm , Idiopathic Pulmonary Fibrosis , Keratin-19 , Humans , Idiopathic Pulmonary Fibrosis/pathology , Lung/metabolism , Fibrosis , BiomarkersABSTRACT
PURPOSE: Data on treatments for male breast cancer patients are limited owing to rarity and underrepresentation in clinical trials. The real-world POLARIS study gathers data on palbociclib use for the treatment of hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2-) advanced breast cancer (ABC) in female and male patients. This sub-analysis describes real-world palbociclib treatment patterns, clinical outcomes, and quality of life (QoL) in male patients. METHODS: POLARIS is a prospective, noninterventional, multicenter, real-world study of patients with HR+/HER2- ABC receiving palbociclib. Assessments included medical record reviews, patient QoL questionnaires (European Organisation for Research and Treatment of Cancer Quality-of-Life Questionnaire-Core 30), site characteristics questionnaires, and physician treatment selection surveys. Variables included demographics, disease history, global health status/QoL, clinical assessments and adverse events. Analyses were descriptive in nature. For clinical outcomes, real-world tumor responses and progression were determined by physician assessment in routine clinical practice. Real-world progression-free survival (rwPFS) was described using the Kaplan-Meier method. RESULTS: At data cutoff, 15 male patients were enrolled (median age, 66 years). Nine patients received palbociclib as a first-line treatment and 6 as a second-line or later treatment. Patients received a median of 20 cycles of palbociclib. Neutropenia was experienced by 2 patients and grade ≥ 3 adverse events were reported in 11 patients. Global health status/QoL scores remained generally consistent during the study. One patient (6.7%) achieved a complete tumor response, 4 (26.7%) a partial response, and 8 (53.3%) stable disease. Median rwPFS was 19.8 months (95% CI, 7.4-38.0). Median follow-up duration was 24.7 months (95% CI, 20.0-35.7). CONCLUSION: This real-world analysis showed that palbociclib was well tolerated and provides preliminary data on treatment patterns and outcomes with palbociclib in male patients with HR+/HER2- ABC, helping inform the use of palbociclib in this patient subgroup. TRIAL IDENTIFIER: NCT03280303.
Subject(s)
Breast Neoplasms , Piperazines , Pyridines , Aged , Humans , Male , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Breast Neoplasms/pathology , Prospective Studies , Quality of Life , Receptor, ErbB-2/metabolismABSTRACT
Differentiation blockade is a hallmark of acute myeloid leukemia (AML). A strategy to overcome such a blockade is a promising approach against the disease. The lack of understanding of the underlying mechanisms hampers development of such strategies. Dysregulated ribonucleotide reductase (RNR) is considered a druggable target in proliferative cancers susceptible to deoxynucleoside triphosphate (dNTP) depletion. Herein, we report an unanticipated discovery that hyperactivating RNR enables differentiation and decreases leukemia cell growth. We integrate pharmacogenomics and metabolomics analyses to identify that pharmacologically (eg, nelarabine) or genetically upregulating RNR subunit M2 (RRM2) creates a dNTP pool imbalance and overcomes differentiation arrest. Moreover, R-loop-mediated DNA replication stress signaling is responsible for RRM2 activation by nelarabine treatment. Further aggravating dNTP imbalance by depleting the dNTP hydrolase SAM domain and HD domain-containing protein 1 (SAMHD1) enhances ablation of leukemia stem cells by RRM2 hyperactivation. Mechanistically, excessive activation of extracellular signal-regulated kinase (ERK) signaling downstream of the imbalance contributes to cellular outcomes of RNR hyperactivation. A CRISPR screen identifies a synthetic lethal interaction between loss of DUSP6, an ERK-negative regulator, and nelarabine treatment. These data demonstrate that dNTP homeostasis governs leukemia maintenance, and a combination of DUSP inhibition and nelarabine represents a therapeutic strategy.