Cell-cycle inhibition and immune microenvironment in breast cancer treated with ribociclib and letrozole or chemotherapy

In this study, we performed genomic analyses of cell cycle and tumor microenvironment changes during and after ribociclib and letrozole or chemotherapy in the CORALLEEN trial. 106 women with untreated PAM50-defined Luminal B early breast cancers were randomly assigned to receive neoadjuvant ribociclib and letrozole or standard-of-care chemotherapy. Ki67 immunohistochemistry, tumor-infiltrating lymphocytes quantification, and RNA sequencing were obtained from tissue biopsies pre-treatment, on day 14 of treatment, and tumor specimens from surgical resection. Results showed that at surgery, Ki67 and the PAM50 proliferation scores were lower after ribociclib compared to chemotherapy. However, consistent reactivation of tumor cell proliferation from day 14 to surgery was only observed in the ribociclib arm. In tumors with complete cell cycle arrest (CCCA) at surgery, PAM50 proliferation scores were lower in the ribociclib arm compared to chemotherapy (p < 0.001), whereas the opposite was observed with tumor cellularity (p = 0.002). Gene expression signatures (GES) associated with antigen-presenting cells (APCs) and innate immune system activity showed increased expression post-chemotherapy but decreased expression post-ribociclib. Interferon-associated GES had decreased expression with CCCA and increased expression with non-CCCA. Our findings suggest that while both treatment strategies decreased proliferation, the depth and the patterns over time differed by treatment arm. Immunologically, ribociclib was associated with downregulated GES associated with APCs and the innate immune system in Luminal B tumors, contrary to existing preclinical data. Further studies are needed to understand the effect of CDK4/6 inhibition on the tumor cells and microenvironment, an effect which may vary according to tumor subtypes

COOL-LAMPS III: Discovery of a 25".9 Separation Quasar Lensed by a Merging Galaxy Cluster

In the third paper from the COOL-LAMPS Collaboration, we report the discovery of COOL J0542-2125, a gravitationally lensed quasar at $z=1.84$, observed as three images due to an intervening massive galaxy cluster at $z=0.61$. The lensed quasar images were identified in a search for lens systems in recent public optical imaging data and have separations on the sky up to 25".9, wider than any previously known lensed quasar. The galaxy cluster acting as a strong lens appears to be in the process of merging, with two sub-clusters separated by $\sim 1$ Mpc in the plane of the sky, and their central galaxies showing a radial velocity difference of $\sim 1000$ km/s. Both cluster cores show strongly lensed images of an assortment of background sources, as does the region between them. A preliminary strong lens model implies masses of $M(<250\ \rm{kpc}) = 1.79^{+0.16} _{-0.01} \times 10^{14} M_{\odot}$and$M(<250\ \rm{kpc}) = 1.48^{+0.04}_{-0.10} \times 10^{14} M_{\odot}$ for the East and West sub-clusters, respectively. This line of sight is also coincident with a ROSAT ALL-sky Survey source, centered between the two confirmed cluster halos reminiscent of other major cluster-scale mergers.Comment: 13 pages, 6 figures. Submitted to Ap

COOL-LAMPS. IV. A Sample of Bright Strongly Lensed Galaxies at 3 < z < 4

We report the discovery of five bright, strong gravitationally lensed galaxies at 3 < z < 4: COOL J0101+2055 (z = 3.459), COOL J0104−0757 (z = 3.480), COOL J0145+1018 (z = 3.310), COOL J0516−2208 (z = 3.549), and COOL J1356+0339 (z = 3.753). These galaxies have magnitudes of rAB, zAB < 21.81 mag and are lensed by galaxy clusters at 0.26 < z < 1. This sample nearly doubles the number of known bright lensed galaxies with extended arcs at 3 < z < 4. We characterize the lensed galaxies using ground-based grz/giy imaging and optical spectroscopy. We report model-based magnitudes and derive stellar masses, dust content, and star formation rates via stellar population synthesis modeling. Building lens models based on ground-based imaging, we estimate source magnifications ranging from ∼29 to ∼180. Combining these analyses, we derive demagnified stellar masses in the range ${\mathrm{log}}_{10}({M}_{* }/{M}_{\odot })\sim 9.69-10.75$ and star formation rates in the youngest age bin in the range ${\mathrm{log}}_{10}(\mathrm{SFR}/({M}_{\odot }\,{\mathrm{yr}}^{-1}))\sim 0.39-1.46$, placing the sample galaxies on the massive end of the star-forming main sequence in this redshift interval. In addition, three of the five galaxies have strong Lyα emissions, offering unique opportunities to study Lyα emitters at high redshift in future work

Strong Interaction Physics at the Luminosity Frontier with 22 GeV Electrons at Jefferson Lab

This document presents the initial scientific case for upgrading the Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab (JLab) to 22 GeV. It is the result of a community effort, incorporating insights from a series of workshops conducted between March 2022 and April 2023. With a track record of over 25 years in delivering the world's most intense and precise multi-GeV electron beams, CEBAF's potential for a higher energy upgrade presents a unique opportunity for an innovative nuclear physics program, which seamlessly integrates a rich historical background with a promising future. The proposed physics program encompass a diverse range of investigations centered around the nonperturbative dynamics inherent in hadron structure and the exploration of strongly interacting systems. It builds upon the exceptional capabilities of CEBAF in high-luminosity operations, the availability of existing or planned Hall equipment, and recent advancements in accelerator technology. The proposed program cover various scientific topics, including Hadron Spectroscopy, Partonic Structure and Spin, Hadronization and Transverse Momentum, Spatial Structure, Mechanical Properties, Form Factors and Emergent Hadron Mass, Hadron-Quark Transition, and Nuclear Dynamics at Extreme Conditions, as well as QCD Confinement and Fundamental Symmetries. Each topic highlights the key measurements achievable at a 22 GeV CEBAF accelerator. Furthermore, this document outlines the significant physics outcomes and unique aspects of these programs that distinguish them from other existing or planned facilities. In summary, this document provides an exciting rationale for the energy upgrade of CEBAF to 22 GeV, outlining the transformative scientific potential that lies within reach, and the remarkable opportunities it offers for advancing our understanding of hadron physics and related fundamental phenomena.Comment: Updates to the list of authors; Preprint number changed from theory to experiment; Updates to sections 4 and 6, including additional figure

Cell-cycle inhibition and immune microenvironment in breast cancer treated with ribociclib and letrozole or chemotherapy

Abstract In this study, we performed genomic analyses of cell cycle and tumor microenvironment changes during and after ribociclib and letrozole or chemotherapy in the CORALLEEN trial. 106 women with untreated PAM50-defined Luminal B early breast cancers were randomly assigned to receive neoadjuvant ribociclib and letrozole or standard-of-care chemotherapy. Ki67 immunohistochemistry, tumor-infiltrating lymphocytes quantification, and RNA sequencing were obtained from tissue biopsies pre-treatment, on day 14 of treatment, and tumor specimens from surgical resection. Results showed that at surgery, Ki67 and the PAM50 proliferation scores were lower after ribociclib compared to chemotherapy. However, consistent reactivation of tumor cell proliferation from day 14 to surgery was only observed in the ribociclib arm. In tumors with complete cell cycle arrest (CCCA) at surgery, PAM50 proliferation scores were lower in the ribociclib arm compared to chemotherapy (p < 0.001), whereas the opposite was observed with tumor cellularity (p = 0.002). Gene expression signatures (GES) associated with antigen-presenting cells (APCs) and innate immune system activity showed increased expression post-chemotherapy but decreased expression post-ribociclib. Interferon-associated GES had decreased expression with CCCA and increased expression with non-CCCA. Our findings suggest that while both treatment strategies decreased proliferation, the depth and the patterns over time differed by treatment arm. Immunologically, ribociclib was associated with downregulated GES associated with APCs and the innate immune system in Luminal B tumors, contrary to existing preclinical data. Further studies are needed to understand the effect of CDK4/6 inhibition on the tumor cells and microenvironment, an effect which may vary according to tumor subtypes

Toll-like receptor 3 increases antigen-presenting cell responses to a pro-apoptotic stimulus, yet does not contribute to systemic lupus erythematosus genetic susceptibility

Objectives: TLR3 mediates skin solar injury by binding nuclear material released from apoptotic keratinocytes, resulting in the production of pro-inflammatory cytokines. Because the TLR3 gene is located in 4q35, a known systemic lupus erythematosus (SLE) susceptibility locus, we wondered whether TLR3 single nucleotide polymorphisms (SNPs) were associated with inflammatory mechanisms relevant to the development of SLE, and disease susceptibility. Methods: Functional assays were carried out in TLR3-transfected HEK293 cells and in monocyte-derived dendritic cells (moDCs). TLR3 and IFNβ immunofluorescence studies were performed in skin samples from 7 SLE patients and 3 controls. We performed a SNP association study in a discovery cohort of 153 patients and 105 controls, followed by a confirmation study in an independent cohort of 1,380 patients and 2,104 controls. Results: TLR3 and IFNβ are overexpressed in SLE skin lesions. TLR3 overexpression in HEK293 cells amplifies their sensitivity to a pro-apoptotic stimulus. Taking advantage of a naturally occurring polymorphic TLR3 variant (rs3775291) that weakly versus strongly responds to poly I:C stimulation, we found that TLR3 is associated with amplified apoptotic responses, production of the Ro/SSA autoantigen and increased maturation of myeloid-derived dendritic cells (moDC) after exposure to UV irradiation. However, TLR3 SNPs are not associated with susceptibility to SLE in a large population of patients and controls. Conclusions: TLR3 is overexpressed in SLE skin lesions and amplifies apoptotic and inflammatory responses to UV-irradiation in antigen-presenting cells in vitro. However, TLR3 SNPs do not impact susceptibility to the development of the disease

The prognostic potential of alternative transcript isoforms across human tumors

Background: Phenotypic changes during cancer progression are associated with alterations in gene expression, which can be exploited to build molecular signatures for tumor stage identification and prognosis. However, it is not yet known whether the relative abundance of transcript isoforms may be informative for clinical stage and survival. Methods: Using information theory and machine learning methods, we integrated RNA sequencing and clinical data from The Cancer Genome Atlas project to perform the first systematic analysis of the prognostic potential of transcript isoforms in 12 solid tumors to build new signatures for stage and prognosis. This study was also performed in breast tumors according to estrogen receptor (ER) status and melanoma tumors with proliferative and invasive phenotypes. Results: Transcript isoform signatures accurately separate early from late-stage groups and metastatic from non-metastatic tumors, and are predictive of the survival of patients with undetermined lymph node invasion or metastatic status. These signatures show similar, and sometimes better, accuracies compared with known gene expression signatures in retrospective data and are largely independent of gene expression changes. Furthermore, we show frequent transcript isoform changes in breast tumors according to ER status, and in melanoma tumors according to the invasive or proliferative phenotype, and derive accurate predictive models of stage and survival within each patient subgroup. Conclusions: Our analyses reveal new signatures based on transcript isoform abundances that characterize tumor phenotypes and their progression independently of gene expression. Transcript isoform signatures appear especially relevant to determine lymph node invasion and metastasis and may potentially contribute towards current strategies of precision cancer medicine.This work was supported by grants BIO2014-52566-R and Consolider RNAREG (CSD2009-00080) from the MINECO (Spanish Government) and FEDER, by AGAUR (2014-SGR1121) and by the Sandra Ibarra Foundation for Cancer (FSI2013)

Life cycle assessment in green chemistry: overview of key parameters and methodological concerns

Several articles within the area of green chemistry often promote new techniques or products as 'green' or 'more environmentally benign' than their conventional counterpart although these articles often do not quantitatively assess the environmental performance. In order to do this, life cycle assessment (LCA) is a valuable methodology. However, on the planning stage, a full-scale LCA is considered to be too time consuming and complicated. Two reasons for this have been recognised, the method is too comprehensive and it is hard to find inventory data. In this review, key parameters are presented with the purpose to reduce the time-consuming steps in LCA. In this review, several LCAs of so-called 'green chemicals' are analysed and key parameters and methodological concerns are identified. Further, some conclusions on the environmental performance of chemicals were drawn. For fossil-based platform chemicals several LCAs exists but for chemicals produced with industrial biotechnology or from renewable resources the number of LCAs is limited, with the exception of biofuels, for which a large number of studies are made. In the review, a significant difference in the environmental performance of bulk and fine chemicals was identified. The environmental performance of bulk chemicals are closely connected to the production of the raw material and thereby different land use aspects. Here, a lot can be learnt from biofuel LCAs. In many of the reviewed articles focusing on bulk chemicals a comparison regarding fossil and renewable raw material was done. In most of the comparisons the renewable alternative turned out to be more environmentally preferable, especially for the impact on GWP and energy use. However, some environmental concerns were identified as important to include to assess overall environmental concern, for example eutrophication and the use of land. To assess the environmental performance of green chemicals, quantitative methods are needed. For this purpose, both simple metrics and more comprehensive methods have been developed, one recognised method being LCA. However, this method is often too time consuming to be valuable in the process planning stage. This is partly due to a lack of available inventory data, but also because the method itself is too comprehensive. Here, key parameters for the environmental performance and methodological concerns were described to facilitate a faster and simpler use of LCA of green chemicals in the future

Treatment and long-term clinical outcomes of incidental pulmonary embolism in patients with cancer: An international prospective cohort study

PURPOSE Pulmonary embolism is incidentally diagnosed in up to 5% of patients with cancer on routine imaging scans. The clinical relevance and optimal therapy for incidental pulmonary embolism, particularly distal clots, is unclear. The aim of the current study was to assess current treatment strategies and the long-term clinical outcomes of incidentally detected pulmonary embolism in patients with cancer. PATIENTS AND METHODS We conducted an international, prospective, observational cohort study between October 22, 2012, and December 31, 2017. Unselected adults with active cancer and a recent diagnosis of incidental pulmonary embolism were eligible. Outcomes were recurrent venous thromboembolism, major bleeding, and all-cause mortality during 12 months of follow-up. Outcome events were centrally adjudicated. RESULTS A total of 695 patients were included. Mean age was 66 years and 58% of patients were male. Most frequent cancer types were colorectal (21%) and lung cancer (15%). Anticoagulant therapy was initiated in 675 patients (97%), of whom 600 (89%) were treated with low-molecular-weight heparin. Recurrent venous thromboembolism occurred in 41 patients (12-month cumulative incidence, 6.0%; 95% CI, 4.4% to 8.1%), major bleeding in 39 patients (12-month cumulative incidence, 5.7%; 95% CI, 4.1% to 7.7%), and 283 patients died (12-month cumulative incidence, 43%; 95% CI, 39% to 46%). The 12-month incidence of recurrent venous thromboembolism was 6.4% in those with subsegmental pulmonary embolism compared with 6.0% in those with more proximal pulmonary embolism (subdistribution hazard ratio, 1.1; 95% CI, 0.37 to 2.9; P = .93). CONCLUSION In patients with cancer with incidental pulmonary embolism, risk of recurrent venous thromboembolism is significant despite anticoagulant treatment. Patients with subsegmental pulmonary embolism seemed to have a risk of recurrent venous thromboembolism comparable to that of patients with more proximal clots