Luminous Clusters Research Articles

Closing classification gaps in luminal breast cancer with single-cell RNA-seq insights from normal breast lineages.

e13168 Background: Almost two decades ago, invasive breast cancer was classified into five subgroups based on expression patterns, each with distinct biological and prognostic characteristics. Advances in single-cell RNA sequencing offers insights into the expression profiles of normal luminal epithelial cells. Here, we investigate the connection between breast cancer (BC) classification and luminal expression profiles. Methods: We applied single-cell data from recent studies (Table) to compile gene signatures corresponding to expression profiles of luminal epithelial cell clusters in normal breast tissue. Normalized enrichment scores (ESs) of these signatures were calculated for bulk RNA-seq gene expression data from open source cohorts (TCGA-BRCA, SCAN-B, METABRIC). The BC molecular subtype of each tumor sample was predicted based on a modified PAM50 classification using gene expression profiling (1); LumA and LumB subtypes were combined into Luminal. ESs of signatures were compared between the BC subtypes (Table). Results: The ESs of all signatures differed significantly across BC subtypes (p < 0.001, Kruskal-Wallis test, Table 1). The ESs of signatures for LumSec-major and Luminal progenitor clusters are the highest in subtypes HER2-low and Basal-like (p < 0.001, Dwass-Steel-Critchlow-Fligner test [DSCF]). Basal-like also had the highest enrichment of the ductal signature (p < 0.001, DSCF). Luminal subtype showed the highest ESs of signatures corresponding to HR+ clusters of mature luminal cells and of the TDLU signature (p < 0.001, DSCF). HER2-low subtype showed the highest ES of the LumSec-lac signature (p < 0.001, DSCF). Conclusions: Our analyses challenge traditional classifications by showing that luminal breast cancers are less similar to most luminal epithelial clusters in normal breast tissue than other breast cancer subtypes. These findings suggest traditional expression classification may not fully capture the complexity of this largest subset of luminal-type breast cancers. 1. Turova et al., SABCS, 2023. [Table: see text]

Molecular Characterization and Subtyping of Breast Cancer Cell Lines Provide Novel Insights into Cancer Relevant Genes.

Continuous cell lines are important and commonly used in vitro models in breast cancer (BC) research. Selection of the appropriate model cell line is crucial and requires consideration of their molecular characteristics. To characterize BC cell line models in depth, we profiled a panel of 29 authenticated and publicly available BC cell lines by mRNA-sequencing, mutation analysis, and immunoblotting. Gene expression profiles separated BC cell lines in two major clusters that represent basal-like (mainly triple-negative BC) and luminal BC subtypes, respectively. HER2-positive cell lines were located within the luminal cluster. Mutation calling highlighted the frequent aberration of TP53 and BRCA2 in BC cell lines, which, therefore, share relevant characteristics with primary BC. Furthermore, we showed that the data can be used to find novel, potential oncogenic fusion transcripts, e.g., FGFR2::CRYBG1 and RTN4IP1::CRYBG1 in cell line MFM-223, and to elucidate the regulatory circuit of IRX genes and KLF15 as novel candidate tumor suppressor genes in BC. Our data indicated that KLF15 was activated by IRX1 and inhibited by IRX3. Moreover, KLF15 inhibited IRX1 in cell line HCC-1599. Each BC cell line carries unique molecular features. Therefore, the molecular characteristics of BC cell lines described here might serve as a valuable resource to improve the selection of appropriate models for BC research.

Precision MARS Mass Reconstruction of A2744: Synergizing the Largest Strong-lensing and Densest Weak-lensing Data Sets from JWST

We present a new high-resolution free-form mass model of A2744 that combines both weak-lensing (WL) and strong-lensing (SL) data sets from JWST. The SL data set comprises 286 multiple images, presenting the most extensive SL constraint to date for a single cluster. The WL data set, employing photo-z selection, yields a source density of ∼350arcmin−2 , marking the densest WL constraint ever. The combined mass reconstruction enables the highest-resolution mass map of A2744 within the ∼1.8 Mpc × 1.8 Mpc reconstruction region to date, revealing an isosceles triangular structure with two legs of ∼1 Mpc and a base of ∼0.6 Mpc. Although our algorithm, which is called MAximum-entropy ReconStruction (MARS), is entirely blind to the cluster galaxy distribution, the resulting mass reconstruction traces the brightest cluster galaxies remarkably well. The five strongest mass peaks coincide with the five most luminous cluster galaxies within ≲2″. We do not detect any unusual mass peaks that are not traced by the cluster galaxies, unlike the findings in previous studies. Our mass model shows the smallest scatter of SL multiple images in both source (∼0.″05) and image (∼0.″1) planes, which is lower than in previous studies by a factor of ∼4. Although MARS represents the mass field with an extremely large number of free parameters (∼300,000), it converges to a solution within a few hours because we use a deep-learning technique. We make our mass and magnification maps publicly available.

Redox signalling regulates breast cancer metastasis via phenotypic and metabolic reprogramming due to p63 activation by HIF1α.

Redox signaling caused by knockdown (KD) of Glutathione Peroxidase 2 (GPx2) in the PyMT mammary tumour model promotes metastasis via phenotypic and metabolic reprogramming. However, the tumour cell subpopulations and transcriptional regulators governing these processes remained unknown. We used single-cell transcriptomics to decipher the tumour cell subpopulations stimulated by GPx2 KD in the PyMT mammary tumour and paired pulmonary metastases. We analyzed the EMT spectrum across the various tumour cell clusters using pseudotime trajectory analysis and elucidated the transcriptional and metabolic regulation of the hybrid EMT state. Integration of single-cell transcriptomics between the PyMT/GPx2 KD primary tumour and paired lung metastases unraveled a basal/mesenchymal-like cluster and several luminal-like clusters spanning an EMT spectrum. Interestingly, the luminal clusters at the primary tumour gained mesenchymal gene expression, resulting in epithelial/mesenchymal subpopulations fueled by oxidative phosphorylation (OXPHOS) and glycolysis. By contrast, at distant metastasis, the basal/mesenchymal-like cluster gained luminal and mesenchymal gene expression, resulting in a hybrid subpopulation using OXPHOS, supporting adaptive plasticity. Furthermore, p63 was dramatically upregulated in all hybrid clusters, implying a role in regulating partial EMT and MET at primary and distant sites, respectively. Importantly, these effects were reversed by HIF1α loss or GPx2 gain of function, resulting in metastasis suppression. Collectively, these results underscored a dramatic effect of redox signaling on p63 activation by HIF1α, underlying phenotypic and metabolic plasticity leading to mammary tumour metastasis.

Global survey of star clusters in the Milky Way

Aims. We built Galactic open star cluster mass functions (CMFs) for different age sub-samples and spatial locations in the wider solar neighbourhood. Here, we present a simple cluster formation and evolution model to reproduce the main features of the CMFs. Methods. We used an unbiased working sample of 2227 clusters of the Milky Way Star Cluster (MWSC) catalogue, which occupy the heliocentric cylinders with magnitude-dependent completeness radii of 1–5 kpc. The MWSC survey provides an extended set of open star cluster parameters, including tidal radii, distances, and ages. From an analytic three-component Galaxy model, we derived tidal masses of clusters with a typical accuracy of about 70%. Our simple model includes a two-section cluster initial mass function, constant cluster formation rate, supervirial phase after a sudden expulsion of the remaining gas, and cluster mass loss due to stellar evolution and the clusters’ gradual destruction in the Galactic tidal field. The dynamical evolution model is based on previous N-body simulations. Results. The obtained tidal masses have been added to the MWSC catalogue. A general CMF (GCMF), built for all cluster ages around the Sun, has a bell-like shape and extends over four decades in mass. The high-mass slope found for tidal mass log mt/M⊙ ≥ 2.3 is equal to 1.14 ± 0.07. The CMFs for different age groups show the same high-mass slopes, while the low-mass slope is nearly flat for the youngest sub-sample (clusters younger than 20 Myr) and about −0.7 for the others. The inner and outer sub-samples covering Galactocentric radii R = 4.2–8.1 kpc and 8.9–13.5 kpc, respectively, are consistent with the GCMF, once the exponential decline of the Galactic disc density is taken into account. The model suggests star formation with low efficiency of 15–20%, where only 10% of stars remain bound in a cluster after gas expulsion and subsequent violent relaxation. The cluster formation rate required to reproduce the observed distributions in age and mass is about 0.4 M⊙ pc−2 Gyr−1. Conclusions. The obtained high-mass slope of the GCMF for the wide neighbourhood of the Sun is similar to slopes determined earlier in nearby galaxies for more luminous clusters with log m/M⊙ > 3.8. The MWSC catalogue supports models with a low star-formation efficiency, where 90% of stars are lost quickly after gas expulsion. The obtained cluster formation rate corresponds to open clusters’ contribution to the stellar content of the thin disc at the level of 30%.

Scaling relations of X-ray luminous clusters in the Hyper Suprime-Cam Subaru Strategic Program field

ABSTRACT We present the XMM–Newton X-ray analysis of 19 X-ray luminous galaxy clusters of low- to mid-redshift (<0.4) selected from the MCXC (Meta-Catalog of X-Ray Detected Clusters of Galaxies) cluster catalogue in the Hyper Suprime-Cam Subaru Strategic Programme field. We derive the hydrostatic equilibrium mass and study scaling relations using (i) the whole sample, (ii) only relaxed clusters, and (iii) only disturbed clusters. When considering the whole sample, the YX–Mtot and Mgas–Mtot relations agree with self-similarity. In terms of morphology, relaxed clusters show a flatter relation in LX,ce–Mtot, LX,bol–Mtot, LX,ce–T, Lbol,ce–T, Mgas–Mtot, and YX–Mtot. The Lbol,ce–Mtot, LX,ce–Mtot Lbol,ce–T, and LX,ce–T relations show a slope ∼3σ steeper. The residuals in the Mgas–Mtot and T–Mtot relations and the intrinsic covariance between Mgas and T show hints of positive correlation, casting doubt on whether the YX parameter is a truly low-scatter mass proxy. The Mgas–Mtot and T–Mtot plots colour coded with the offset of the LX,ce–Mtot relation show these two relations to be brightness dependent but not the LX,ce–T relation, suggesting that relations involving Mtot are biased due to sample selection based on luminosity. Following the work that studied an optical sample and combining our result with literature studies, we find that Mtot derived not using mass proxies deviates from LX ∝ $M_{\rm gas}^{2}M_{\rm tot}^{-1}$ and Mtot based on hydrostatic equilibrium is more massive than what is expected by their relation using caustic masses. This indicates that mass bias plays an important role in scaling relations.

Transcriptomic Signature and Growth Factor Regulation of Castration-Tolerant Prostate Luminal Progenitor Cells.

Background: The molecular and cellular mechanisms that drive castration-resistant prostate cancer (CRPC) remain poorly understood. LSCmed cells defines an FACS-enriched population of castration-tolerant luminal progenitor cells that has been proposed to promote tumorigenesis and CRPC in Pten-deficient mice. The goals of this study were to assess the relevance of LSCmed cells through the analysis of their molecular proximity with luminal progenitor-like cell clusters identified by single-cell (sc)RNA-seq analyses of mouse and human prostates, and to investigate their regulation by in silico-predicted growth factors present in the prostatic microenvironment. Methods: Several bioinformatic pipelines were used for pan-transcriptomic analyses. LSCmed cells isolated by cell sorting from healthy and malignant mouse prostates were characterized using RT-qPCR, immunofluorescence and organoid assays. Results: LSCmed cells match (i) mouse luminal progenitor cell clusters identified in scRNA-seq analyses for which we provide a common 15-gene signature including the previously identified LSCmed marker Krt4, and (ii) Club/Hillock cells of the human prostate. This transcriptional overlap was maintained in cancer contexts. EGFR/ERBB4, IGF-1R and MET pathways were identified as autocrine/paracrine regulators of progenitor, proliferation and differentiation properties of LSCmed cells. The functional redundancy of these signaling pathways allows them to bypass the effect of receptor-targeted pharmacological inhibitors. Conclusions: Based on transcriptomic profile and pharmacological resistance to monotherapies that failed in CRPC patients, this study supports LSCmed cells as a relevant model to investigate the role of castration-tolerant progenitor cells in human prostate cancer progression.

Tidal Distortions in NGC1052-DF2 and NGC1052-DF4: Independent Evidence for a Lack of Dark Matter

Two ultra-diffuse galaxies in the same group, NGC1052-DF2 and NGC1052-DF4, have been found to have little or no dark matter and to host unusually luminous globular cluster populations. Such low-mass diffuse objects in a group environment are easily disrupted and are expected to show evidence of tidal distortions. In this work, we present deep new imaging of the NGC1052 group, obtained with the Dragonfly Telephoto Array, to test this hypothesis. We find that both galaxies show strong position-angle twists and are significantly more elongated at their outskirts than in their interiors. The group’s central massive elliptical NGC1052 is the most likely source of these tidal disturbances. The observed distortions imply that the galaxies have a low total mass or are very close to NGC1052. Considering constraints on the galaxies’ relative distances, we infer that the dark matter halo masses of these galaxies cannot be much greater than their stellar masses. Calculating pericenters from the distortions, we find that the galaxies are on highly elliptical orbits, with a ratio of pericenter to present-day radius R peri/R 0 ∼ 0.1 if the galaxies are dark matter–free and R peri/R 0 ∼ 0.01 if they have a normal dark halo. Our findings provide strong evidence, independent of kinematic constraints, that both galaxies are dark matter–deficient. Furthermore, the similarity of the tidal features in NGC1052-DF2 and NGC1052-DF4 strongly suggests that they arose at comparable distances from NGC1052. In Appendix A, we describe sbcontrast, a robust method for determining the surface brightness limits of images.

XMM-Newton study of six massive, X-ray luminous galaxy cluster systems in the redshift range z = 0.25–0.5

Massive galaxy clusters are interesting astrophysical and cosmological objects to study, but they are relatively rare. In the redshift range z = 0.25–0.5 which is, for example, a favourable region for gravitational lensing studies, about 100 such systems are known. Most of them have been studied in X-rays. In this paper we study the six remaining massive clusters in this redshift interval in the highly complete CLASSIX (Cosmic Large-Scale Structure in X-rays) survey which have so far not been observed with sufficiently deep exposures in X-rays. With data from our new XMM-Newton observations we characterise their structures, derive X-ray properties such as the X-ray luminosity and intracluster medium temperature, and estimate their gas and total masses. We find that one cluster, RXCJ1230.7+3439, is dynamically young with three distinct substructures in the cluster outskirts and RXCJ1310.9+2157/RXCJ1310.4+2151 is a double cluster system. Mass determination is difficult in the systems with substructure. We therefore discuss several methods of mass estimation including scaling relations. In summary, we find that five of the six targets of study are indeed massive clusters as expected, while the last cluster RXCJ2116.2−0309 is a close projection of a distant and a nearby cluster which has led to a previous overestimation of its mass. In the XMM-Newton observation fields, we also find three low redshift clusters close to the targets which are also analysed and described here. In the field of RXCJ2116.2−0309, we discover serendipitously a highly variable X-ray source which has decreased its flux within a year by more than a factor of eight. This source is most probably an active galactic nucleus (AGN).

LoVoCCS. I. Survey Introduction, Data Processing Pipeline, and Early Science Results

We present the Local Volume Complete Cluster Survey (LoVoCCS; we pronounce it as “low-vox” or “law-vox,” with stress on the second syllable), an NSF’s National Optical-Infrared Astronomy Research Laboratory survey program that uses the Dark Energy Camera to map the dark matter distribution and galaxy population in 107 nearby (0.03 < z < 0.12) X-ray luminous ([0.1–2.4 keV] L X500 > 1044 erg s−1) galaxy clusters that are not obscured by the Milky Way. The survey will reach Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) Year 1–2 depth (for galaxies r = 24.5, i = 24.0, signal-to-noise ratio (S/N) > 20; u = 24.7, g = 25.3, z = 23.8, S/N > 10) and conclude in ∼2023 (coincident with the beginning of LSST science operations), and will serve as a zeroth-year template for LSST transient studies. We process the data using the LSST Science Pipelines that include state-of-the-art algorithms and analyze the results using our own pipelines, and therefore the catalogs and analysis tools will be compatible with the LSST. We demonstrate the use and performance of our pipeline using three X-ray luminous and observation-time complete LoVoCCS clusters: A3911, A3921, and A85. A3911 and A3921 have not been well studied previously by weak lensing, and we obtain similar lensing analysis results for A85 to previous studies. (We mainly use A3911 to show our pipeline and give more examples in the Appendix.)

Abstract 3922: Proteomic profiling of muscle invasive bladder cancer

Abstract Background: Only one quarter of patients with muscle invasive urothelial bladder cancer (MIBC) gain approximately 5% improvement in 5-year overall survival from cisplatin-based neoadjuvant chemotherapy (NAC). For patients with residual invasive cancer post radical cystectomy there is no standard of care and high mortality. Previous TCGA projects focused on pre-NAC MIBC genomic and transcriptomic alterations and identified 5 molecular subtypes with differential risk and response. For this study we hypothesized that comprehensive proteomic and phosphoproteomic profiling of MIBC prior to NAC will further define mechanisms responsible for chemotherapy resistance, and identify specific and actionable targeted therapies for patients with NAC-resistant tumors. Methods: OCT-embedded and flash frozen tissue samples from 143 eligible patients were processed and tested for proteomics quality control (QC). Samples containing &amp;gt;45% tumor content, less than 10% muscle content and &amp;gt;2,000 protein identifications in a single-shot quality control assay were selected for deep-scale proteomic and phosphoproteomic profiling. A final cohort of 60 samples (52 pre-treatment and 8 patient-matched post-treatment tumors) were multiplexed using tandem mass tags (TMT-11), fractionated by basic reverse phase chromatography and analyzed by liquid chromatography and mass spectrometry (LC-MS). Results: Over 12,000 proteins were identified in total, and 8,353 proteins identified in all samples, including 425 kinases and 77 targets of FDA approved cancer therapies. Principal component analysis identified two distinct resistant clusters and one sensitive cluster. The samples were clustered based on the 5 TCGA subtypes which resulted in the sub stratification of the resistant clusters into two resistance-enriched basal-squamous clusters (BS1 and BS2 respectively), one infiltrated-luminal cluster (L1), one sensitive luminal cluster (L2) and one intermediary cluster (L3) (with 86% samples resistant). UV response, Epithelial to Mesenchymal transition and Myogenesis were significantly elevated in both L1 and L3 (resistant) relative to L2 (sensitive). Similar, these pathways are significantly altered in L1 relative to L3. EGFR, CDK6, ITPKC and CSNK1 were elevated in the B4 subtype, all of which are potentially druggable targets. Matched samples and phosphoproteomics data will be presented. Conclusion: Surrounding non-tumor tissue can obfuscate true tumor signatures in MIBC, cohort selection through stringent pathologic QC allows proteomic profiling to identify tumor features that correlate with NAC resistance. This dataset provides proof of principle that actionable targets and subtype distinctions can be identified through discovery proteomics and further analysis in NAC treated cohorts are justified. Citation Format: Matthew V. Holt, Meggie N. Young, Karoline Kremers, Alexander Saltzman, Antrix Jain, Mei Leng, Hugo Villanueva, Lacey E. Dobrolecki, Beom-Jun Kim, Meenakshi Anurag, Matthew J. Ellis, Anna Malovannaya, Seth P. Lerner. Proteomic profiling of muscle invasive bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3922.

A Population of Luminous Globular Clusters and Stripped Nuclei with Elevated Mass to Light Ratios around NGC 5128* * This paper includes data gathered with the 6.5 m Magellan Telescope at Las Campanas Observatory, Chile.

The dense central regions of tidally disrupted galaxies can survive as ultracompact dwarfs (UCDs) that hide among the luminous globular clusters (GCs) in the halo of massive galaxies. An exciting confirmation of this model is the detection of overmassive black holes in the centers of some UCDs, which also lead to elevated dynamical mass-to-light ratios (M/L dyn). Here we present new high-resolution spectroscopic observations of 321 luminous GC candidates in the massive galaxy NGC 5128/Centaurus A. Using these data we confirm 27 new luminous GCs, and measure velocity dispersions for 57 luminous GCs (with g-band luminosities between 2.5 × 105 and 2.5 × 107 L ⊙), of which 48 are new measurements. Combining these data with size measurements from Gaia, we determine the M/L dyn for all 57 luminous GCs. We see a clear bimodality in the M/L dyn distribution, with a population of normal GCs with mean M/L dyn = 1.51 ± 0.31, and a second population of ∼20 GCs with elevated mean M/L dyn = 2.68 ± 0.22. We show that black holes with masses ∼4%–18% of the luminous GCs can explain the elevated mass-to-light ratios. Hence, it is plausible that the NGC 5128 sources with elevated M/L dyn are mostly stripped galaxy nuclei that contain massive central black holes, though future high spatial resolution observations are necessary to confirm this hypothesis for individual sources. We also present a detailed discussion of an extreme outlier, VHH81-01, one of the largest and most massive GC in NGC 5128, making it an exceptionally strong candidate to be a tidally stripped nucleus.

Abstract P1-05-04: Novel breast cancer proteomic subtyping with connection to cell of origin

Abstract Introduction: In clinical practice, immunohistochemistry (IHC) is combined with clinicopathologic information to stratify patients into subtypes and guide treatment decisions. In our mass spectrometry study of 116 breast cancers (BrCAs), we identified 34 significant proteins which provide additional prognostic information. This novel proteomic subtyping, combining IHC with proteomics, separates HER2 negative (Her2-) BrCA patients into Luminal-like and TN-like subtypes. A novel subtype, luminal by IHC and TN-like by proteomics (L/T), is associated with unfavorable outcome compared with the luminal subtype (L/L) by both IHC and proteomics. These IHC-based Her2- subtypes are described as L/L, L/T, T/L and T/T subtypes. We investigated the cell-of-origin of our enhanced subtypes using gene set enrichment analysis with gene sets consisting of breast cancer cell-of-origin signatures. We further identified genes representing our 34 proteins in the significant gene sets and investigated their association with survival outcomes across The Cancer Genome Atlas (TCGA) pan-cancers. Method: The single-cell RNA-sequencing data analyses of health breast samples identified 23 breast cell-of-origin signatures (Bhat-Nakshatri et al., 2021) with 46 up and down-regulated gene sets based on the provided fold changes. Using our cohort, we performed differential analysis for each enhanced subtype (L/L, L/T, T/T) versus the other subtypes separately. Pre-ranked gene set enrichment analyses were used to identify significantly enriched gene sets. The significance of enriched gene sets was reported at FDR&amp;lt;0.05. We further identified genes of 34 biomarkers that overlapped in the identified significant gene sets and investigated the impact of the genes on survival across TCGA pan-cancers. Univariate overall survival (OS) and progression-free interval (PFI) analyses were performed on each cancer cohort and the significance of the association with survival outcome was reported by log-rank p-value &amp;lt;0.05. Results: Our signature was compared to the clusters from healthy tissues. We found up-regulated genes in L/L subtype were enriched in gene sets elevated in mature luminal annotated clusters (N8 and N12). Down-regulated genes in L/L subtype were enriched in the elevated genes in the N3 (luminal progenitor) and N9 (luminal progenitor/basal) clusters. Up-regulated genes in L/T subtype were enriched in the elevated genes in the N19 (luminal progenitor) and N11 (basal) clusters. Down-regulated genes in L/T were enriched in the elevated genes in the N8 (mature luminal) cluster and down-regulated genes in the N9 (luminal progenitor/basal) cluster. Up-regulated genes in T/T subtype were enriched in genes highly expressed in the luminal progenitor (N3) and luminal progenitor/basal (N9) clusters. Down-regulated genes in T/T subtype were enriched in the elevated genes in the mature luminal annotated clusters (N8, N12). One gene, KPNA2, was up-regulated in both the N9 (luminal progenitor/basal) cluster and the Basal-like (TN-like) subtype. The higher expression of this gene had significant association with worse OS outcomes in most of the cancers. Conclusions: T/T and L/T subtypes likely arise from progenitor and basal cells. The L/L subtype may arise from mature luminal cells. The novel L/T subtype appears to have characteristics that result in poorer survival. Disclaimers The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of USUHS, HJF, the DOD or the Departments of the Army, Navy, or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Guisong Wang, Punit Shah, Rick Searfoss, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Brenda Deyarmin, Rebecca N. Zingmark, Stella Somiari, Jianfang Liu, Leonid Kvecher, Lori A. Sturtz, Praveen-Kumar Raj-Kumar, Elder Granger, Linda Vahdat, Niven R. Narain, Mary L. Cutler, Rangaprasad Sarangarajan, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Craig D. Shriver. Novel breast cancer proteomic subtyping with connection to cell of origin [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-05-04.

Abstract PD6-07: Whole genome sequencing-based circulating tumor DNA profiling of metastatic breast cancer patients for molecular characterization and therapy response prediction

Abstract Background Previous studies proposed low-pass whole genome sequencing (LP-WGS)-based circulating tumor DNA (ctDNA) analysis as a versatile tool for genomic profiling and therapeutic monitoring of cancer patients. Here we demonstrate LP-WGS ctDNA genomic profiles and its clinical significance in metastatic breast cancer patients. Patients and methods This prospective exploratory study enrolled 207 treatment-naïve metastatic breast cancer patients from Feb 2017 to September 2020 in Yonsei Cancer Center. The median follow-up duration of patients was 35 months. The baseline (n=207) and post-progression (n=48) plasma samples were prospectively collected on first-line systemic therapy, and LP-WGS was employed for ctDNA somatic copy number alteration (CNA) analysis. The CNA burden of ctDNA was scored by “I-score” method, which was developed to measure genome-wide chromosomal instabilities, to be matched with therapy response. The unsupervised molecular clustering and homologous recombination deficiency (HRD) estimation by shallowHRD algorithm were performed using locus-level CNA profiles with 1 mega base pair resolution. Results The baseline I-score ctDNA CNA burden was highest in triple-negative breast cancer (TNBC) patients among subtypes, and the patients were dichotomized by median I-score level 5.54 (range 2.55 to 12.98). The high baseline ctDNA I-score was independently associated with poor overall survival (hazard ratio [HR] = 3.98, p &amp;lt; 0.001) with adjustment of tumor subtype, visceral metastasis, and disease status (de novo stage IV versus recurrent). The progression-free survival (PFS) on endocrine plus CDK4/6 inhibitors (HR = 2.75, p = 0.005), anti-HER2 therapy (HR = 2.52, p = 0.032), and cytotoxic chemotherapy (HR = 2.33, p = 0.012) was also shorter in high baseline I-score patients than in low I-score patients. The locus-level CNA profile was analyzed in high I-score patients (n=103), and the patients were classified into five molecular clusters with distinct overall survival by unsupervised k-means clustering of CNA profile: basal-like, EGFR-high basal-like, CCND1-high, luminal, and HER2-enriched clusters. Patients with BCL6 (p = 0.009) and PIK3CA amplification (p &amp;lt; 0.001) on baseline ctDNA showed significantly shorter PFS on CDK4/6 inhibitor treatment. The matched baseline and post-progression ctDNA analysis found emergence of FGFR1 amplification and MYC amplification after CDK4/6 inhibitor treatment (n=1, each). The ctDNA shallowHRD score was highest in TNBC patients among subtypes, and TNBC patients with high shallowHRD score (≥10) showed high response rate on (58.3% versus 28.6%) on platinum-based chemotherapy. Conclusion LP WGS-based ctDNA analysis provides a robust tool for non-invasive genomic clustering, therapy response prediction, and HRD estimation in metastatic breast cancer patients. All patients (n=207)Low I-score (n=104)High I-score (n=103)N (%)N (%)N (%)Age, Median (Interquartile range)54 (46-62)53 (47-60)54(44-62)GenderFemale205 (99)102 (98.1)103Male2 (1)2 (1.9)0SubtypeHR+ HER2-106 (51.2)61 (58.7)45 (43.7)HR- HER2+33 (15.9)14 (13.5)19 (18.4)HR+ HER2+22 (10.6)11 (10.6)11 (10.7)HR- HER2- (TNBC)46 (22.2)18 (17.3)28 (27.2)Disease statusDe novo stage IV74 (35.7)31 (29.8)43 (41.7)Recurrent133 (64.3)73 (70.2)60 (58.3)Primary therapyEndocrine + CDK 4/6 inhibitor97 (46.9)55 (52.9)42 (40.8)Anti-HER2 based therapy54 (26.1)24 (23.1)30 (29.1)Chemotherapy45 (21.7)16 (15.4)29 (28.2)Others11 (5.3)9 (8.7)2 (1.9)Visceral metastasisYes142 (68.6)60 (57.7)82 (79.6)No65 (31.4)44 (42.3)21 (20.4)Metastasis SitesLung89 (43)43 (41.3)46 (44.7)Brain19 (9.2)4 (3.8)15 (14.6)Liver59 (28.5)13 (12.5)46 (44.7)Bone120 (58)47 (45.2)73 (70.9)Lymph node90 (43.7)32 (30.8)58 (56.9)Pleura33 (15.9)17 (16.3)16 (15.5) Citation Format: Joohyuk Sohn, Min Hwan Kim, Jin Mo Ahn, Won-Ji Ryu, Seul-Gi Kim, Jee Hung Kim, Tae Yeong Kim, Hyun Ju Han, Jee Ye Kim, Hyung Seok Park, Seho Park, Byeong Woo Park, Seung Il Kim, Eun Hae Cho, Gun Min Kim. Whole genome sequencing-based circulating tumor DNA profiling of metastatic breast cancer patients for molecular characterization and therapy response prediction [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD6-07.

HST Observations of the Globular Cluster NGC 6402 (M14) and Its Peculiar Multiple Populations

Abstract We present Hubble Space Telescope (HST) photometric results for NGC 6402, a highly reddened, very luminous Galactic globular cluster (GC). Recent spectroscopic observations of its red giant stars have shown a quite peculiar behavior in the chemistry of its multiple populations. These results have prompted UV and optical HST observations aimed at obtaining the cluster’s “chromosome map” (ChM), an efficient tool for classifying GCs and characterizing their multiple populations. We find that the discontinuity in the abundance distributions of O, Mg, Al, and Na inferred from spectroscopy is more nuanced in the ChM, which is mostly sensitive to nitrogen. Nevertheless, photometry in optical bands reveals a double main sequence, indicating a discontinuity in the helium content of the populations. The population with the largest chemical anomalies (extreme) peaks at a helium mass fraction Y ∼ 0.31. This helium content is consistent with results from the analysis of the distribution of horizontal branch stars and the spectrophotometry of the red giants. The ChM and the color–magnitude diagrams are compared with those of NGC 2808, a prototype GC with helium abundances up to Y ≳ 0.35, and both confirm that NGC 6402 does not host stellar populations with such extreme helium content. Further, the ChM reveals the presence of a group of stars with higher metallicity, thus indicating that NGC 6402 is a Type II cluster. The modalities of formation of the multiple populations in NGC 6402 are briefly surveyed, with main attention on the asymptotic giant branch and supermassive star models, and on possible cluster merging.

Coordinate control of basal epithelial cell fate and stem cell maintenance by core EMT transcription factor Zeb1.

Maintenance of undifferentiated, long-lived, and often quiescent stem cells in the basal compartment is important for homeostasis and regeneration of multiple epithelial tissues, but the molecular mechanisms that coordinately control basal cell fate and stem cell quiescence are elusive. Here, we report an epithelium-intrinsic requirement for Zeb1, a core transcriptional inducer of epithelial-to-mesenchymal transition, for mammary epithelial ductal side branching and for basal cell regenerative capacity. Our findings uncover an evolutionarily conserved role of Zeb1 in promoting basal cell fate over luminal differentiation. We show that Zeb1 loss results in increased basal cell proliferation at the expense of quiescence and self-renewal. Moreover, Zeb1 cooperates with YAP to activate Axin2 expression, and inhibition of Wnt signaling partially restores stem cell function to Zeb1-deficient basal cells. Thus, Zeb1 is a transcriptional regulator that maintains both basal cell fate and stem cell quiescence, and it functions in part through suppressing Wnt signaling.

The Cosmic Large-Scale Structure in X-rays (CLASSIX) Cluster Survey

It is important to map the large-scale matter distribution in the local Universe for cosmological studies, such as the tracing of the large-scale peculiar velocity flow, the characterisation of the environment for different astronomical objects, and for precision measurements of cosmological parameters. We used X-ray luminous clusters to map this matter distribution and find that about 51% of the groups and clusters are members of superclusters which occupy only a few percent of the volume. In this paper we provide a detailed description of these large-scale structures. With a friends-to-friends algorithm, we find eight superclusters with a cluster overdensity ratio of at least two with five or more galaxy group and cluster members in the cosmic volume out to z = 0.03. The four most prominent ones are the Perseus-Pisces, the Centaurus, the Coma, and the Hercules supercluster, with lengths from about 40 to over 100 Mpc and estimated masses of 0.6 − 2.2 × 1016 M⊙. The largest of these structures is the Perseus-Pisces supercluster. The four smaller superclusters include the Local and the Abell 400 supercluster and two superclusters in the constellations Sagittarius and Lacerta. We provide detailed maps, member catalogues, and physical descriptions of the eight superclusters. By constructing superclusters with a range of cluster sub-samples with different lower X-ray luminosity limits, we show that the main structures are always reliably recovered.

Dark Matter Deficient Galaxies and Their Member Star Clusters Form Simultaneously during High-velocity Galaxy Collisions in 1.25 pc Resolution Simulations

Abstract How diffuse dwarf galaxies that are deficient in dark matter—such as NGC1052-DF2 and NGC1052-DF4—formed remains a mystery. Along with their luminous member globular clusters (GCs), the so-called dark matter deficient galaxies (DMDGs) have challenged observers and theorists alike. Here we report a suite of galaxy collision simulations using the adaptive mesh refinement code Enzo with 1.25 pc resolution, which demonstrates that high-velocity galaxy collisions induce the formation of DMDGs and their star clusters (SCs) simultaneously. With a numerical resolution that is significantly better than our previous study, we resolve the dynamical structure of the produced DMDGs and the detailed formation history of their SCs, which are possible progenitors of the DMDG’s member GCs. In particular, we show that a galaxy collision with a high relative velocity of ∼300 km s−1, invoking severe shock compression, spawns multiple massive SCs M ⋆ ≳ 10 6 M ⊙ in &lt;150 Myr after the collision. At the end of the ∼800 Myr evolution in our fiducial run, the resulting DMDG of M ⋆ ≃ 3.5 × 108 M ⊙ hosts 10 luminous M V ≲ −8.5 mag, gravitationally bound SCs with a line-of-sight velocity dispersion 11.2 km s−1. Our study suggests that DMDGs and their luminous member SCs could form simultaneously in high-velocity galaxy collisions while being in line with the key observed properties of NGC1052-DF2 and NGC1052-DF4.

The Cosmic Large-Scale Structure in X-rays (CLASSIX) Cluster Survey

Previous studies of the galaxy and galaxy cluster distribution in the local Universe found indications for a large extension of the Local Supercluster up to a radius of 190 h70−1 Mpc. We are using our large and highly complete CLASSIX survey of X-ray luminous galaxy clusters detected in the ROSAT All Sky Survey to trace the matter distribution in the local Universe and to explore the size of the flattened local density structure associated with the Local Supercluster. The Local Supercluster is oriented almost perpendicular to the Galactic plane. Since Galactic extinction increases towards the Galactic plane, objects are on average more easily visible perpendicular to the plane than close to it, also producing an apparent concentration of objects along the Local Supercluster. We can correct for this bias by a careful treatment of the survey selection function. We find a significant overdensity of clusters in a flattened structure along the Supergalactic plane with a thickness of about 50 Mpc and an extent of about 100 Mpc radius. Structures at a distance larger than 100 Mpc are not correlated to the Local Supercluster any more. The matter density contrast of the local superstructure to the surroundings is about a factor of 1.3−2.3. Within the Supergalactic plane the matter is concentrated mostly in two superclusters, the Perseus-Pices Chain and Hydra-Centaurus supercluster. We have shown in our earlier work that the local Universe in a region with a radius of 100−170 Mpc has a lower density than the cosmic mean. For this reason, the Local Supercluster is not overdense with respect to the cosmic mean density. Therefore this local superstructure will not collapse as a whole in the future, but rather fragment.

The Cosmic Large-Scale Structure in X-rays (CLASSIX) Cluster Survey

The Perseus-Pisces supercluster is known as one of the largest structures in the nearby Universe that has been charted by the galaxy and galaxy cluster distributions. For the latter mostly clusters from the Abell catalogue have been used. Here we take a new approach to a quantitative characterisation of the Perseus-Pisces supercluster using a statistically complete sample of X-ray luminous galaxy groups and clusters from our CLASSIX galaxy cluster redshift survey. We used a friends-of-friends technique to construct the supercluster membership. We also studied the structure of the Southern Great Wall, which merges with the Perseus-Pisces supercluster with a slightly increased friends-of-friends linking length. In this work we discuss the geometric structure of the superclusters, compare the X-ray luminosity distribution of the members with that of the surroundings, and provide an estimate of the supercluster mass. These results establish Perseus-Pisces as the largest superstructure in the Universe at redshifts z ≤ 0.03. With the new data this supercluster extends through the zone of avoidance, which has also been indicated by some studies of the galaxy distribution by means of HI observations. We investigated whether the shapes of the member groups and clusters in X-rays are aligned with the major axis of the supercluster. We find no evidence for a pronounced alignment, except for the ellipticities of Perseus and AWM7, which are aligned with the separation vector of the two systems and weakly with the supercluster.