Biology subjects

Metzger, E.

Publications and source records attributed to Metzger, E..

7 recordsLinked to original sources

bioRxiv2026

Spatial/molecular heterogeneity and treatment response in HER2+ early breast cancer: Translational analyses from the DAPHNe trial

Given the heterogeneity of HER2-positive breast cancer, reliable biomarkers to guide treatment are needed. We conducted multi-platform biomarker analyses of baseline tumor tissue from the DAPHNe trial of neoadjuvant paclitaxel/trastuzumab/pertuzumab (THP) for HER2-positive early breast cancer to characterize inter- and intra-tumor heterogeneity and to identify molecular predictors of response. A total of 98 patients with stage II-III HER2-positive breast cancer received neoadjuvant THP followed by surgery. Gene expression profiling, spatial protein profiling, and single-cell imaging (cyclic immunofluorescence) were performed on pre-treatment biopsies and a subset of residual disease specimens. Pathologic response was assessed using the residual cancer burden (RCB) score. Among HER2-positive patients included in the biomarker analysis, 34% of patients had node-positive breast cancer, and 66% had hormone receptor (HR)-positive tumors. HR-positive and HR-negative tumors differed significantly across gene expression, protein expression, and single-cell profiling. High ERBB2 gene signature, p53 gene signature, and HER2 protein expression predicted favorable response (RCB 0/1), while ESR1/PGR gene, estrogen receptor (ER) signaling gene signature, and ER alpha protein expression were associated with unfavorable response (RCB 2/3). Single-cell spatial analysis revealed that cancer cells clustered by shared HER2, ER, and PR expression, suggesting local expansion of phenotypically distinct subpopulations. ER-positive cancer cells were associated with lower HLA-A and PD-L1 expression, suggesting a less immunologically active tumor cell state. Baseline HER2 and ER expression are key predictors of response to neoadjuvant HER2-targeted therapy. Single-cell spatial profiling highlights intra-tumoral heterogeneity and suggests ER-driven immune exclusion as a potential mechanism of resistance.

cancer biology↗

bioRxiv2026

Androgen Receptor mediates beige adipocyte homeostasis and plasticity

Male adipose tissue undergoes profound post-pubertal remodeling characterized by the progressive transition of beige adipocytes toward a white adipocyte phenotype. Although androgen signaling has been implicated in adipose tissue biology, its role in beige adipocyte remodeling and metabolic plasticity remains poorly understood. Here we show that androgen receptor (AR) signaling is dynamically activated in inguinal white adipose tissue during the post-pubertal beige-to-white transition in male mice. Inducible deletion of AR in beige adipocytes impaired this remodeling process, resulting in the persistence of multilocular beige-like adipocytes despite reduced thermogenic competence and marked mitochondrial abnormalities. Transcriptomic and cistromic analyses identified AR as a direct regulator of adipocyte metabolic and differentiation programs, whereas immune-related transcriptional signatures in AR-deficient adipose tissue primarily reflected macrophage infiltration and inflammatory remodeling. Loss of AR promoted mitochondrial dysfunction, mitophagy, and altered glucose handling, while cell-autonomous AR silencing in beige adipocytes recapitulated key defects in mitochondrial organization and adipocyte identity. Longitudinal and metabolic challenge studies further demonstrated that AR signaling is required for age-associated adipose remodeling and adaptive beige adipocyte plasticity during high-fat diet feeding and cold exposure. Together, these findings identify AR as a central regulator of beige adipocyte remodeling, mitochondrial homeostasis, and adaptive metabolic function in male adipose tissue.

physiology↗

bioRxiv2025

Tracking Sleep-Linked Brain Fluid Dynamics Using Modified fNIRS: A Novel Noninvasive Window into Glymphatic Function

BackgroundThe glymphatic system, a brain-wide perivascular and interstitial waste and signal transport pathway for cerebrospinal fluid (CSF) to exchange with interstitial fluid (ISF), has pronounced activity during non-rapid eye movement (NREM) sleep and has been implicated in the pathophysiology of traumatic brain injury, Alzheimers disease, and mood disorders. However, direct measurement in humans is limited because current imaging methods rely on intrathecal contrast-enhanced magnetic resonance imaging (MRI), which is unsuitable for routine or naturalistic sleep studies. The absence of real-time, noninvasive monitoring methods that allow for natural sleep poses a major barrier to advancing glymphatic research in clinical settings. MethodsTo address this barrier, we developed a non-invasive functional near-infrared spectroscopy (fNIRS) forehead array in a wearable headband using non-standard wavelengths to allow for better sensitivity for water measurement. We monitored cortical blood and water dynamics during overnight sleep, quantifying oscillatory patterns of oxyhemoglobin (HbO) and water across sleep stages within the outer layers of the frontal cortex, subarachnoid space, and scalp. A component of the extracted water metrics is hypothesized to serve as a proxy for glymphatic transport without the need for contrast agents or surgical intervention. ResultsOur results demonstrate water concentrations were highest in SWS (d = 1.93, p=0.0002), while HbO concentrations also showed a modest elevation (d = 1.06, ns). Additionally, low-frequency oscillations (LFOs) of both water and HbO signals exhibited distinct dynamics of suprathreshold envelope peak (SEP) frequencies during NREM stages (N2 and N3) as compared to REM and wake, with effect size (d= 1.31, p = 0.003) for water. Interestingly, these water-derived metrics correlate with EEG slow-wave activity, linking fluid-sensitive oscillations to established electrophysiological markers of sleep depth. These findings indicate that water-sensitive oscillatory processes are selectively amplified during deep sleep and scale with EEG-defined sleep depth, consistent with a role for glymphatic-related fluid transport in human sleep. ConclusionWe report novel cortical water shift parameters that are robustly sensitive to sleep stage transitions via a wearable, non-invasive, scalable headband, consistent with predicted glymphatic activity. Future work will cross-validate this method with MRI and other techniques. DisclaimerThe views, information or content, and conclusions presented do not represent the official position or policy of, nor should any official endorsement be inferred on the part of, the Uniformed Services University, the Department of War, the U.S. Government, or Walter Reed National Military Medical Center.

neuroscience↗

bioRxiv2025

Tracing colorectal malignancy transformation from cell to tissue scale

The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remains poorly resolved. Here, we survey colorectal tumorigenesis by combining whole-transcriptome spatial molecular imaging (WTx CosMx SMI) with single-nucleus RNA-sequencing (snPATHO-seq) and digital histopathology on colon samples containing reference mucosa, adenomas and carcinomas, as well as a metastatic lymph node. Leveraging (discrete) histological annotations and (continuous) data-driven trajectories, we quantify the dynamics of cellular density, heterogeneity, function and signaling along the reference-adenoma-carcinoma axis, which is concordant in its spatial and molecular definition. This combination of analytical approaches across different data views let us chart tissue transformation across dimensions (physical/transcriptional) and scales (cell/tissue). We resolve [~]3.5 million cells into 43 epithelial, immune, and stromal subpopulations that exhibit a bi-furcating tumor evolution: On the one hand, LGR5+ stem-like epithelial cells are enriched in highly homogeneous proliferative tumor cores. On the other hand, MMP7+ fetal-like states are restricted to immunosuppressive invasive fronts, rich in cancer-associated fibroblasts (CAFs) and tumor-associated macrophages. These subpopulations form concentric spatial layers that organize transformed regions, and their compound aligns with histological malignancy. We further define transition crypts - single colonic crypts with divided histological and transcriptional makeup - that arise from rare crypt fusion or abrupt transformation events. Finally, we trace MMP7+ fetal-like tumor cell states and concomitant myofibroblast-like FAP+ CAFs to lymphovascular invasion sites and matched lymph node metastases, thereby recapitulating invasive programs at single-cell resolution and across sites. In all, we present single cell- and WTx-resolved spatial data that are among the first of their kind. These open up spatial-centric, out-of-the-box analytical avenues to resolve the molecular, cellular and architectural dynamics that attend tissue transformation during CRC onset, progression and dissemination.

cancer biology↗

bioRxiv2025

The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs

The Spatial Atlas of Human Anatomy (SAHA) represents the first multimodal, subcellular- resolution reference of healthy adult human tissues across multiple organ systems. Integrating spatial transcriptomics, proteomics, and histological features across over 15 million cells from more than 100 donors, SAHA maps conserved and organ-specific cellular niches in gastrointestinal and immune tissues. High-resolution profiling using CosMx SMI, 10x Xenium, RNAscope, GeoMx DSP, and single-nucleus RNA-seq reveals spatially organized cell states, rare adaptive immune populations, and tissue-specific cell-cell interactions and ligand-receptor pairs. Comparative analyses with colorectal cancer and inflammatory bowel disease demonstrate the power of SAHA to detect disease-associated spatial disruptions, including crypt dedifferentiation, perineural invasion, and therapy-resistant immune remodeling. All data are openly accessible through a FAIR-compliant interactive portal to support exploration, benchmarking, and machine learning model training. Through SAHA, we provide a foundational framework for spatial diagnostics and next-generation precision medicine grounded in a comprehensive human tissue atlas, enabling the development of context-aware models that simulate tissue behavior, decode complex pathologies, and accelerate therapeutic innovation at unprecedented scale.

systems biology↗

bioRxiv2024

Sub-cellular Imaging of the Entire Protein-Coding Human Transcriptome (18933-plex) on FFPE Tissue Using Spatial Molecular Imaging

Single-cell RNA-seq revolutionized single-cell biology, by providing a complete whole transcriptome view of individual cells. Regrettably, this was accomplished only for individual, tissue-dissociated cells. High-plex spatial biology has begun to recover the x, y, and z-coordinates of single-cells, but typically at the expense of far less than whole transcriptome coverage. To solve this problem, Bruker Spatial Biology has accomplished a commercial-grade panel (CosMx(R) Spatial Molecular Imager Whole Transcriptome Panel (WTx)), using 37,872 imaging barcodes, capable of sub-cellular imaging of the entire human protein-coding transcriptome. The imaging barcodes are encoded with 156 bits of information (4 on-cycles and 35 dark-cycles per code), at a Hamming Distance of 4 from each other to achieve a very low false-code detection. Key to achieving this high-plex capability was the ability to manufacture imaging barcodes that require no in-tissue amplification (every barcode is manufactured under GMP to contain exactly 30 fluorescent dyes) and uniform, size-exclusion purified, extremely small imaging barcodes ([~] 20 nm). A detailed study of six different human FFPE tissue types was performed (Colon, Pancreas, Hippocampus, Skin, Breast, Kidney), yielding over 5.4 billion transcripts from 2.7 million cells. We counted over 1,550 transcripts-per-cell on average and observed 900 unique genes per cell (measured as the median). Single fixed-cells containing well over 10,000 subcellularly imaged transcripts were accomplished. Advancing single-cell imaging to the whole transcriptome level opens a single unified approach to accomplish essentially all single-cell experiments, both imaging and non-imaging. Depending upon the sample type (e.g. fixed-cells, organoids, tissue sections, etc.), the transcripts per cell and genes per cell measured using the whole transcriptome panel often exceeds that obtained by the highest-resolution single-cell RNA-seq, can be performed on a single 5 {micro}m FFPE tissue section, with no dissociation bias (every cell is counted). Pathway analysis within the tumor bed of a colon adenocarcinoma sample found evidence of enrichment in pathways suggestive of an aggressive tumor type, and localized ligand-receptor analysis showed spatially restricted patterns related to adhesion, migration, and proliferation. The high-dimensional whole transcriptome data is streamed directly to a cloud-based Spatial Informatics Platform, allowing for the scalable processing of millions-of-single-cells and billions-of-transcripts per operation. The WTx data are combined with high-resolution antibody-based cell-morphology imaging and data-driven machine-learning cell segmentation algorithms, to generate the most complete view of single cell and sub-cellular spatial biology that has ever been obtained.

genomics↗

bioRxiv2022

KDM4A promotes NEPC progression through regulation of MYC expression

Neuroendocrine prostate cancer (NEPC) represents one of the most lethal forms of prostate cancer (PCa) and lacks life-prolonging treatment. The incidence of NEPC is increased due to the widespread use of AR pathway inhibitors (ARPIs) in the treatment of non-metastatic CRPC and hormone-sensitive metastatic tumors. Here, we identified histone lysine demethylase KDM4A as a key player in NEPC progression and an effective therapeutic target. We found that KDM4A mRNA and protein are overexpressed in human and mouse NEPC compared to prostate adenocarcinoma. Knockdown (KD) or knockout (KO) of KDM4A in NEPC cell lines suppressed cancer cell growth in vitro and in vivo. Mechanistically, we found that KDM4A promotes NEPC progression, in part, through direct transcriptional regulation of MYC. We showed that MYC is hyper-activated in human and mouse NEPC. KDM4A KD led to suppression of MYC signaling. MYC KD or inhibition profoundly suppressed NEPC cell proliferation. Furthermore, a potent pan-KDM4 inhibitor QC6352 significantly reduced NEPC cell growth in vitro and in vivo. Taken together, we demonstrated that KDM4A is an important regulator of NEPC progression and targeting KDM4A may potentially be an effective therapeutic strategy for NEPC. SignificanceNeuroendocrine prostate cancer (NEPC) is a highly aggressive prostate cancer subtype that is resistant to potent androgen receptor pathway inhibitors (ARPIs) and currently lacks effective therapeutic options. Histone lysine demethylase KDM4A is an important epigenetic regulator of gene expression in development and cancer. In this study, we show that KDM4A is highly expressed in NEPC and is required for NEPC proliferation, anchorage-independent growth, and in vivo growth, which is in part mediated through the regulation of MYC expression. Importantly, we demonstrate that inhibition of KDM4A significantly impairs NEPC growth in preclinical models. Thus, our findings provide valuable insights into the molecular mechanisms underlying NEPC progression and offer a rationale for clinical trials with KDM4 inhibitor in NEPC patients.

cancer biology↗