Biology subjects

Hecht, F.

Publications and source records attributed to Hecht, F..

9 recordsLinked to original sources

bioRxiv2026

Enabling high-plex spectral imaging via DNA-barcoded signal tuning and panel optimization

High-plex spectral imaging has the potential to transform the analysis of spatial organization in cells and tissues, yet its practical implementation remains limited by challenges in panel design, sample preparation, signal balancing, and experimental validation. While cyclic imaging approaches are widely used in spatial omics, spectral imaging across the full fluorescence spectrum and computational unmixing remain underutilized due to these challenges. Here, we present a generalizable framework for high-plex spectral imaging that leverages DNA-barcoded labeling and programmable signal amplification to provide precise control over fluorescence signal composition. Orthogonal DNA barcodes decouple target labeling from fluorophore detection, enabling reversible fluorophore application and systematic panel optimization directly on the same sample. Programmable DNA-based amplification further enables independent and quantitative tuning of fluorescence intensities across targets, overcoming a key limitation of spectral unmixing, namely imbalanced signal contributions in overlapping channels, and thereby improving accuracy and robustness. The framework also supports the generation of experiment-specific ground truth datasets and systematic evaluation of unmixing algorithms, providing a quantitative basis for panel validation and performance assessment. We demonstrate the practical implementation of this framework by developing a panel for simultaneous imaging of 15 subcellular structures without fluidic cycling and using the optimized panel to profile the effects of chemical perturbations on subcellular organization. We quantitatively evaluate panel compilation and provide a rigorous assessment unmixing performance using both linear and reference-free unmixing methods. Importantly, we leverage foundation models trained on standard fluorescence data, for segmentation-free, high-dimensional analysis of spectrally unmixed images without needing large datasets or model retraining. Together, we establish a practical and tunable framework for high-plex spectral imaging that lowers experimental barriers and enables broader adoption of spectral unmixing for biological and biomedical applications.

bioengineering↗

bioRxiv2025

Multi-step implementation of meiotic crossover patterning

Crossover formation during meiosis is a tightly controlled process in which genetic information is exchanged between homologous chromosomes to increase the diversity of the progeny. In this process, an excess of double-strand breaks is introduced, but only a limited subset is ultimately processed into crossovers. Imbalances in the distribution of crossovers can lead to errors in chromosome segregation, with devastating consequences on the health of the progeny. However, the selection of which breaks are designated to become crossovers is still poorly understood, as both its timing and the ultimate molecular mechanisms are under debate. Here, we used 3D dual-color single-molecule localization microscopy and real-time confocal imaging, combined with advanced image analysis, to investigate the timing and mechanism of crossover designation in C. elegans. We show that meiotic crossover patterning is not established by a single decision point but depends on a dynamic, multi-layered regulation process. An initial, early selection process restricts potential crossovers to a small subset of double-strand break sites that already exhibit basic patterning features, including assurance and interference. A second, later step fine-tunes this pattern to ultimately ensure genome integrity and promote accurate chromosome segregation. Real-time imaging reveals that although the full process takes more than seven hours, key molecular events occur within minutes, high-lighting how rapid local dynamic changes can give rise to an overall slow but extremely robust crossover regulation program.

cell biology↗

bioRxiv2025

MYC and Epithelial to Mesenchymal Transition (EMT) Independently Predict Circadian Rhythm Disruption in Lung Adenocarcinoma

The molecular circadian clock is known to be disrupted in lung adenocarcinoma, and its disruption is pro-tumorigenic in mouse models of this disease. However, the determinants of disruption of the molecular clock in human cancer are not clear. We hypothesized that derangement in expression of specific circadian clock genes or elevated MYC expression could correlate with circadian disruption in human tumors, and used Clock Correlation Distance (CCD) to compare clock order and strength in tumors based on the expression of these genes. While the expression of individual circadian genes did not consistently correlate with disruption, tumors with the highest expression of MYC or high MYC pathway activation had significantly disrupted rhythms compared to those with lower MYC. Unexpectedly, a subset of tumors with very low levels of MYC, below that found in normal lung, also showed disruption of circadian rhythms, prompting us to explore novel determinants of disruption in these tumors. We found that expression of programs associated with epithelial to mesenchymal Transition (EMT) and TGF-{beta} signaling were enriched in tumors with the lowest MYC expression, and that, surprisingly, those tumors with a mesenchymal expression pattern had more ordered (stronger) rhythms. To directly test this correlation between cell state and rhythms, we exposed lung adenocarcinoma cells to TGF-{beta} to induce EMT. TGF-{beta} induced a quasi-mesenchymal phenotype and caused a significant increase in the amplitude of oscillations in these cells. Together, our data show that MYC expression, pathway activation, and a mesenchymal cell state are both independent determinants of circadian status in lung adenocarcinoma.

cancer biology↗

bioRxiv2025

NF-κB dependent gene expression and plasma IL-1β, TNFα and GCSF drive transcriptomic diversity and CD4:CD8 ratio in people with HIV on ART.

Despite antiretroviral therapy (ART), people with HIV (PWH) on ART experience higher rates of morbidity and mortality vs. age-matched HIV negative controls, which may be driven by chronic inflammation due to persistent virus. We performed bulk RNA sequencing (RNA-seq) on peripheral CD4+ T cells, as well as quantified plasma immune marker levels from 154 PWH on ART to identify host immune signatures associated with immune recovery (CD4:CD8) and HIV persistence (cell-associated HIV DNA and RNA). Using a novel dimension reduction tool - Pairwise Controlled Manifold Approximation (PaCMAP), we defined three distinct participant transcriptomic clusters. We found that these three clusters were largely defined by differential expression of genes regulated by the transcription factor NF-{kappa}B. While clustering was not associated with HIV reservoir size, we observed an association with CD4:CD8 ratio, a marker of immune recovery and prognostic factor for mortality in PWH on ART. Furthermore, distinct patterns of plasma IL-1{beta}, TNF- and GCSF were also strongly associated with the clusters, suggesting that these immune markers play a key role in CD4+ T cell transcriptomic diversity and immune recovery in PWH on ART. These findings reveal novel subgroups of PWH on ART with distinct immunological characteristics, and define a transcriptional signature associated with clinically significant immune parameters for PWH. A deeper understanding of these subgroups could advance clinical strategies to treat HIV-associated immune dysfunction.

microbiology↗

bioRxiv2024

Catabolism of extracellular glutathione supplies amino acids to support tumor growth

Restricting amino acids from tumors is an emerging therapeutic strategy with significant promise. While typically considered an intracellular antioxidant with tumor-promoting capabilities, glutathione (GSH) is a tripeptide of cysteine, glutamate, and glycine that can be catabolized, yielding amino acids. The extent to which GSH-derived amino acids are essential to cancers is unclear. Here, we find that GSH catabolism promotes tumor growth. We show that depletion of intracellular GSH does not perturb tumor growth, and extracellular GSH is highly abundant in the tumor microenvironment, highlighting the potential importance of GSH outside of tumors. We find supplementation with GSH can rescue cancer cell survival and growth in cystine-deficient conditions, and this rescue is dependent on the catabolic activity of {gamma}-glutamyltransferases (GGTs). Finally, pharmacologic targeting of GGTs activity prevents the breakdown of circulating GSH, lowers tumor cysteine levels, and slows tumor growth. Our findings indicate a non-canonical role for GSH in supporting tumors by acting as a reservoir of amino acids. Depriving tumors of extracellular GSH or inhibiting its breakdown is potentially a therapeutically tractable approach for patients with cancer. Further, these findings change our view of GSH and how amino acids, including cysteine, are supplied to cells.

cancer biology↗

bioRxiv2023

Glutathione supports lipid abundance in vivo

Cells rely on antioxidants to survive. The most abundant antioxidant is glutathione (GSH). The synthesis of GSH is non-redundantly controlled by the glutamate-cysteine ligase catalytic subunit (GCLC). GSH imbalance is implicated in many diseases, but the requirement for GSH in adult tissues is unclear. To interrogate this, we developed a series of in vivo models to induce Gclc deletion in adult animals. We find that GSH is essential to lipid abundance in vivo. GSH levels are reported to be highest in liver tissue, which is also a hub for lipid production. While the loss of GSH did not cause liver failure, it decreased lipogenic enzyme expression, circulating triglyceride levels, and fat stores. Mechanistically, we found that GSH promotes lipid abundance by repressing NRF2, a transcription factor induced by oxidative stress. These studies identify GSH as a fulcrum in the livers balance of redox buffering and triglyceride production.

biochemistry↗

bioRxiv2023

Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection

The major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective antiretroviral therapy (ART). Most prior host genetic HIV studies have focused on identifying DNA polymorphisms (e.g., CCR5{Delta}32, MHC class I alleles) associated with viral load among untreated "elite controllers" (~1% of HIV+ individuals who are able to control virus without ART). However, there have been few studies evaluating host genetic predictors of viral control for the majority of people living with HIV (PLWH) on ART. We performed host RNA sequencing and HIV reservoir quantification (total DNA, unspliced RNA, intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. Multivariate models included covariates for timing of ART initiation, nadir CD4+ count, age, sex, and ancestry. Lower HIV total DNA (an estimate of the total reservoir) was associated with upregulation of tumor suppressor genes NBL1 (q=0.012) and P3H3 (q=0.012). Higher HIV unspliced RNA (an estimate of residual HIV transcription) was associated with downregulation of several host genes involving inflammasome (IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10) and innate immune (TLR7) signaling, as well as novel associations with potassium (KCNJ2) and gap junction (GJB2) channels, all q<0.05. Gene set enrichment analyses identified significant associations with TLR4/microbial translocation (q=0.006), IL-1{beta}/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. HIV intact DNA (an estimate of the "replication-competent" reservoir) demonstrated trends with thrombin degradation (PLGLB1) and glucose metabolism (AGL) genes, but data were (HIV intact DNA detected in only 42% of participants). Our findings demonstrate that among treated PLWH, that inflammation, innate immune responses, bacterial translocation, and tumor suppression/cell proliferation host signaling play a key role in the maintenance of the HIV reservoir during ART. Further data are needed to validate these findings, including functional genomic studies, and expanded epidemiologic studies in female, non-European cohorts. Author SummaryAlthough lifelong HIV antiretroviral therapy (ART) suppresses virus, the major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective ART, "the HIV reservoir." HIV eradication strategies have focused on eliminating residual virus to allow for HIV remission, but HIV cure trials to date have thus far failed to show a clinically meaningful reduction in the HIV reservoir. There is an urgent need for a better understanding of the host-viral dynamics during ART suppression to identify potential novel therapeutic targets for HIV cure. This is the first epidemiologic host gene expression study to demonstrate a significant link between HIV reservoir size and several well-known immunologic pathways (e.g., IL-1{beta}, TLR7, TNF- signaling pathways), as well as novel associations with potassium and gap junction channels (Kir2.1, connexin 26). Further data are needed to validate these findings, including functional genomic studies and expanded epidemiologic studies in female, non-European cohorts.

genetics↗

bioRxiv2021

Host Variation in Interferon, MHC Class I, Glycosylation, and Viral Transcription Genes Predict HIV Persistence

ObjectivePrior genomewide association studies have identified variation in MHC Class I alleles and CCR5{Delta}32 as genetic predictors of viral control, especially in "elite" controllers, individuals who remain virally suppressed in the absence of therapy. DesignCross-sectional genomewide association study. MethodsWe analyzed custom whole exome sequencing and direct HLA typing from 202 ART-suppressed HIV+ non-controllers in relation to four measures of the peripheral CD4+ T cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T cell count, pre-ART HIV RNA, timing of ART initiation, and duration of ART suppression. ResultsPreviously reported "protective" host genetic mutations related to viral setpoint (e.g., among elite controllers) were found to predict smaller HIV reservoir size. The HLA "protective" B*57:01 was associated with significantly lower HIV usRNA (q=3.3x10-3), and among the largest subgroup, European ancestry individuals, the CCR5{Delta}32 deletion was associated with smaller HIV tDNA (p=4.3x10-3) and usRNA (p=8.7x10-3). In addition, genomewide analysis identified several SNPs in MX1 (an interferon stimulated gene) that were significantly associated with HIV tDNA (q=0.02), and the direction of these associations paralleled MX1 gene eQTL expression. ConclusionsWe observed a significant association between previously reported "protective" MHC class I alleles and CCR5{Delta}32 with the HIV reservoir size in non-controllers. We also found a novel association between MX1 and HIV total DNA (in addition to other interferon signaling relevant genes, PPP1CB, DDX3X). These findings warrant further investigation in future validation studies.

genomics↗

bioRxiv2019

High photon count rate super-resolution fluorescence fluctuation spectroscopy

Probing the diffusion of molecules has become a routine measurement across the life sciences, chemistry and physics. It provides valuable insights into reaction dynamics, oligomerisation, molecular (re-)organisation or cellular heterogeneities. Fluorescence correlation spectroscopy (FCS) is one of the widely applied techniques to determine diffusion dynamics in two and three dimensions. This technique relies on the temporal autocorrelation of intensity fluctuations but recording these fluctuations has thus far been limited by the detection electronics, which could not efficiently and accurately time-tag photons at high count rates. This has until now restricted the range of measurable dye concentrations, as well as the data quality of the FCS recordings, especially in combination with super-resolution stimulated emission depletion (STED) nanoscopy. Here, we investigate the applicability and reliability of (STED-)FCS at high photon count rates (average intensities of up to 40 MHz) using novel detection equipment, namely hybrid detectors and real-time gigahertz sampling of the photon streams implemented on a commercial microscope. By measuring the diffusion of fluorophores in solution and cytoplasm of live cells, as well as in model and cellular membranes, we show that accurate diffusion and concentration measurements are possible in these previously inaccessible high photon count regimes. Specifically, it offers much greater flexibility of experiments with biological samples with highly variable intensity, e.g. due to a wide range of expression levels of fluorescent proteins. In this context, we highlight the independence of diffusion properties of cytosolic GFP in a concentration range of approx. 0.01-1 M. We further show that higher photon count rates also allow for much shorter acquisition times, and improved data quality. Finally, this approach also pronouncedly increases the robustness of challenging live cell STED-FCS measurements of nanoscale diffusion dynamics, which we testify by confirming a free diffusion pattern for a fluorescent lipid analogue on the apical membrane of adherent cells.

biophysics↗