The rockefeller university

In mammalian cells, gene copy number is controlled to maintain gene expression and genome stability. However, a common molecular feature across cancer types is oncogene amplification, increasing the copy number and expression of tumor-promoting genes and thus promoting cancer progression. For example, in tyrosine kinase inhibitor (TKI)-resistant lung adenocarcinoma (LUAD), oncogene amplification is frequent. Despite the prevalence of oncogene amplification in TKI-resistant tumors, the underlying mechanisms are not fully understood. Here, we find that LUADs exhibit a unique chromatin signature demarcated by strong CTCF and cohesin deposition in drug-naive tumors, which correlates with the boundaries of oncogene amplicons in TKI-resistant LUAD cells. We identify a global chromatin-priming effect during the acquisition of TKI resistance, marked by a dynamic increase of H3K27Ac, cohesin loading and inter-TAD interactions, which occur before the onset of oncogene amplification. Furthermore, we show that METTL7A, reported to localize to the endoplasmic reticulum and inner nuclear membrane, has a chromatin regulatory function by binding to amplified loci and regulating cohesin recruitment and inter-TAD interactions. METTL7A appears to remodel the chromatin landscape prior to large-scale copy number gains. Although METTL7A depletion exerts little phenotypical effects on drug-naive cells, its depletion prevents the formation and maintenance of TKI resistant-clones, showcasing its role as cells become resistant. In summary, we unveil a mechanism required for the acquisition of TKI resistance regulated by an unexpected chromatin function of METTL7A.

Rapid molecular assays guiding treatment of methicillin-resistant Staphylococcus aureus detect SCCmec (Xpert) or the SCCmec-orfX junction (BCID2). Sequence variation in this region can disrupt primer binding, yielding false-negative results. Investigation of a missed bloodstream infection linked escape to a CRISPR-Cas-associated SCCmec variant, leading to identification of 64 variants from 45 patients-2% of 2432 screened. Misdiagnosis was restricted to clonal complex 5, a hospital-associated lineage; 11 of 40 SCCmec/junctions evaded detection by BCID2 or Xpert. Variants had mecA instability and circulated in healthcare settings. Our findings reveal a unique escape mechanism and underscore a threat to diagnostic accuracy. This study identifies methicillin-resistant Staphylococcus aureus clones carrying a CRISPR-Cas-linked SCCmec variant that escapes detection by rapid, point-of-care molecular diagnostics that are routinely used to guide antimicrobial therapy of bloodstream infections; the work has implications for clinical management.

Adult stem cells balance self-renewal and differentiation to build, maintain and repair tissues. The role of signalling pathways and transcriptional networks in controlling stem cell function has been extensively studied, but there is increasing appreciation that mechanical forces also have a crucial regulatory role. Mechanical forces, signalling pathways and transcriptional networks must be coordinated across diverse length and timescales to maintain tissue homeostasis and function. Such coordination between stem cells and neighbouring cells dictates when cells divide, migrate and differentiate. Recent advances in measuring and manipulating the mechanical forces that act upon and are produced by stem cells are providing new insights into development and disease. In this Review, we discuss the mechanical forces involved when epithelial stem cells construct their microenvironment and what happens in cancer when stem cell niche mechanics are disrupted or dysregulated. As the skin has evolved to withstand the harsh mechanical pressures from the outside environment, we often use the stem cells of mammalian skin epithelium as a paradigm for adult stem cells shaping their surrounding tissues.

Life is invasive, occupying all physically accessible scales, stretching between almost nothing (protons, electrons, and photons) and almost everything (the whole biosphere). Motivated by seventeenth-century insights into this infinity, this paper proposes a language to discuss life as an infinite double cascade of machines making machines. Using this simplified language, we first discuss the micro-cascade proposed by Leibniz, which describes how the self-reproducing machine of the cell is built of smaller submachines down to the atomic scale. In the other direction, we propose that a macro-cascade builds from cells larger, organizational machines, up to the scale of the biosphere. The two cascades meet at the critical point of 103 s in time and 1 micron in length, the scales of a microbial cell. We speculate on how this double cascade evolved once a self-replicating machine emerged in the salty water of prebiotic earth.

The larvae of ants are essential for colony organization and growth, yet knowledge of their internal anatomy is sparse, and the homologies of many larval structures remain uncertain. We therefore used synchrotron-radiation micro-computed tomography (SR-mu -CT) and scanning electron microscopy (SEM) to investigate, respectively, the internal and external morphology of the larva of the clonal raider ant, Ooceraea biroi (FOREL, 1907), a model species for experimental biology. The documented characters are compared with conditions found in other Formicidae and Hymenoptera, and more broadly with features of larvae of other orders of Holometabola. As in other groups of Aculeata (and Orussidae), the body of Ooceraea is grub-like and depigmented, with distinctly reduced cephalic structures, and a weakly sclerotized, strongly simplified, sausage-like postcephalic body. This larval pattern reflects a distinct simplification compared with immature stages in the symphytan grade, with completely reduced eyes, antennae, and extrinsic labral muscles, vestigial palps, and missing thoracic legs and abdominal prolegs. Despite a simplified and largely uniform body configuration in apocritan larvae, including ants, there is considerable variation. Larvae of Formicidae vary distinctly in external features, especially in the general body shape, setation, and mandibular teeth. We therefore summarize eight morphological characters from previous studies to contextualize our findings, highlighting the often-underestimated diversity of larval morphology, which provides fertile ground for future study. Our study extends the knowledge of the external and internal morphology of ant larvae by taking a multi-modal approach to phenotype sampling, particularly via mu -CT. These methods have the potential of rapidly increasing the knowledge of previously neglected larval morphology, facilitating deeper investigations of evolutionary transformations in immature stages and providing a more complete picture of the evolution of an ecologically paramount group of insects.

Purpose: Curative therapies remain a significant unmet need for advanced human colorectal cancer (CRC). The aim of this study was to establish a 3-step 225Ac-DOTA pretargeted radioimmunotherapy (PRIT) system for human CRC, targeting two individual antigens: glycoprotein A33 (GPA33) and human epidermal growth factor receptor 2 (HER2). Methods: In vitro cellular uptake and internalization assays, as well as survival assays (colony forming) were performed in GPA33-and HER2-positive SW1222 human CRC cells. In vivo biodistribution and therapy studies were performed with two human CRC xenograft mouse models. Results: For both antigens, treatment with up to 74 kBq 225Ac-DOTA-PRIT in SW1222-tumored mice significantly enhanced overall survival in comparison to controls, including histologic cures. The uptake of 225Ac at the tumor correlated with antigen expression (antigen expression for GPA33:HER2 is 5:1). Cellular assays showed no significant differences in internalized fraction or nucleus-associated radioactivity between the two targets. GPA33 had a higher absorbed dose to the nucleus (1.3 Gy vs. 0.65 Gy for HER2), resulting in reduced clonogenic survival. A single cycle of either GPA33 or HER2 DOTA-PRIT (37 kBq; 193.31 Gy and 113.91 Gy (relative biological effectiveness [RBE] = 5), respectively) was equally effective. No chronic nephrotoxicity was seen at <= 20 Gy (RBE = 5). The efficacy of GPA33-directed 225Ac-DOTA-PRIT was also confirmed in a patient-derived xenograft model. Conclusion: In summary, 225Ac-DOTA-PRIT to GPA33 or HER2 was highly effective and safe in preclinical models of human CRC. Tumor response to treatment could not be predicted by nuclear absorbed dose alone, highlighting the importance of comprehensive micro-and macro-dosimetry.

Microglia, the innate immune cells of the brain, play a defining role in the progression of Alzheimer's disease (AD)1. The microglial response to amyloid plaques in AD can range from neuroprotective to neurotoxic2. Here we show that the protective function of microglia is governed by the transcription factor PU.1, which becomes downregulated following microglial contact with plaques. Lowering PU.1 expression in microglia reduces the severity of amyloid disease pathology in mice and is linked to the expression of immunoregulatory lymphoid receptor proteins, particularly CD28, a surface receptor that is critical for T cell activation3,4. Microglia-specific deficiency in CD28, which is expressed by a small subset of plaque-associated PU.1low microglia, promotes a broad inflammatory microglial state that is associated with increased amyloid plaque load. Our findings indicate that PU.1low CD28-expressing microglia may operate as suppressive microglia that mitigate the progression of AD by reducing the severity of neuroinflammation. This role of CD28 and potentially other lymphoid co-stimulatory and co-inhibitory receptor proteins in governing microglial responses in AD points to possible immunotherapy approaches for treating the disease by promoting protective microglial functions.

Objective To evaluate the relationship of skin fibroblast CD34 and alpha-smooth muscle actin (alpha-SMA) and immune cell infiltration with disease duration in diffuse cutaneous systemic sclerosis (dcSSc) and identify predictors of improvement. Methods Skin biopsies and clinical data were analyzed from patients with dcSSc enrolled in lenabasum (n = 79), belimumab (n = 18), or nilotinib (n = 8) trials. CD34 and alpha-SMA were scored semiquantitatively. Immune cells (CD20+, CD3+, and CD123+) were counted. Clinical and histologic features were compared between those with early (<18 months) versus later disease (>= 18 months). Clinical improvement was defined as >5-point decrease in modified Rodnan skin score (mRSS) at 52 weeks. An Akaike's information criterion-optimal multiple logistic regression model for clinical improvement among 68 mycophenolate mofetil (MMF) users was developed. Fibroblast spatial organization was visualized using imaging mass cytometry (IMC) in a representative sample. Results Despite similar baseline mRSS, early disease was associated with lower CD34, higher alpha-SMA, increased B cells, and greater mRSS improvement compared with later SSc. IMC demonstrated regions of CD34+ fibroblasts in superficial dermis and alpha-SMA+ fibroblasts in deeper, collagen-dense regions. Among MMF users, high CD34 and alpha-SMA predicted improvement in early SSc; however, high alpha-SMA predicted lower odds of improvement in later SSc. The probability of improvement was lowest in early SSc with alpha-SMA(low)/CD34(low) immunophenotype and later SSc with alpha-SMA(high). In later SSc, B cells were higher in alpha-SMA(high) versus alpha-SMA(low) skin. Conclusion Fibroblast immunophenotype varied by baseline disease duration and improved model performance for identifying those with improvement on MMF. Skin biopsies may be useful for refining prognosis and guiding patient management decisions.

Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks.

The inclusive jet cross section is measured as a function of jet transverse momentum p(T) and rapidity y. The measurement is performed using proton-proton collision data at root s = 5.02 TeV, recorded by the CMS experiment at the LHC, corresponding to an integrated luminosity of 27.4 pb(-1). The jets are reconstructed with the anti-k(T) algorithm using a distance parameter of R = 0.4, within the rapidity interval |y| < 2, and across the kinematic range 0.06 < p(T)< 1 TeV. The jet cross section is unfolded from detector to particle level using the determined jet response and resolution. The results are compared to predictions of perturbative quantum chromodynamics, calculated at both next-to-leading order and next-to-next-to-leading order. The predictions are corrected for nonperturbative effects, and presented for a variety of parton distribution functions and choices of the renormalization/factorization scales and the strong coupling alpha(S).