Biology subjects

Lee, H.

Publications and source records attributed to Lee, H..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Enhanced mRNA delivery using ultrasound-delivered click reactive anchors

Therapeutic nucleic acid delivery has many potential applications, but it remains challenging to target extrahepatic tissues in a flexible and image-guided manner. To address this issue, we report a bioorthogonal pre-targeting strategy that uses focused ultrasound to promote the delivery of mRNA-loaded lipid nanoparticles (mRNA-LNP). We synthesized amphiphilic click reactive anchors (ACRAs) consisting of a phospholipid PEG-conjugate functionalized with transcyclooctene (TCO) or its companion reactive partner methyltetrazine (mTz), yielding ACRA-TCO and ACRA-mTz. ACRA derivatives were screened for cellular activity, yielding functionalized DOPE-PEG (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N- (polyethylene glycol)) derivatives outperforming those containing saturated lipid or branched PEG. Nanobubbles encapsulating ultrasound-responsive gas precursor delivered ACRA-TCO to targeted cells and tissues using focused ultrasound, and this pre-targeting promoted the subsequent delivery of mRNA- LNP functionalized with companion ACRA-mTz. In cell cultures and in mice, ultrasound pre-targeting enhanced the accumulation of mTz-functionalized small molecule and nanoparticle compounds by 75% and 3.6-fold, respectively, and increased gene expression using mRNA-LNP in vivo. Taken together, this report presents a modular, ultrasound-enabled strategy for enhancing nucleic acid delivery in targeted tissues.

bioengineering↗

bioRxiv2025

Investigation of All Disease-Relevant Lysine Acetylation Sites in α-Synuclein Enabled by Non-canonical Amino Acid Mutagenesis

Aggregates of -synuclein (S) are hallmarks of synucleinopathies, including Parkinsons Disease (PD) and Multiple System Atrophy (MSA). We have recently shown that S lysine acetylation in the soluble monomer pool varies between healthy controls, PD, and MSA patients. We used non-canonical amino acid (ncAA) mutagenesis to express and purify all 12 currently known disease-relevant variants of S and studied their binding to membranes as well as their aggregation propensities. We found that acetylation of lysine 12, 43, and 80 had particularly strong effects. To understand the implications for acetylation of monomeric S found in healthy cells, we performed NMR experiments to study protein conformation and fluorescence correlation spectroscopy experiments to quantify lipid binding. We also investigated the effects of acetylation at lysine 12, 43, and 80 on fibril seeding in neurons. Collectively, our biochemical and cell biological investigations indicated that acetylation of K80 could inhibit aggregation without conferring negative effects on monomer function in healthy cells. Therefore, we studied the structures of fibrils with K80 acetylation through cryo-electron microscopy to uncover the structural basis for these effects. Finally, we identified inhibition of HDAC8 as a way of potentially increasing acetylation at K80 and other inhibitory sites for therapeutic benefit.

biochemistry↗

bioRxiv2025

TCR signaling via NFATc1 constrains IL-15-induced NK-like activation of human memory CD8+ T cells

Here we investigated the regulatory mechanisms of TCR-independent bystander activation and NK-like cytotoxicity of human memory CD8+ T cells. We found that TCR signals suppressed characteristic features of IL-15-induced CD8+ T-cell activation, including increased NKG2D expression and upregulation of genes related to NK cytotoxicity and IFN response. Moreover, ionomycin suppressed IL-15-induced bystander activation and NK-like cytotoxicity, indicating that Ca2+-calcineurin signaling is responsible for TCR-mediated suppression of IL-15-induced bystander activation. In detail, NFATc1 suppressed IL-15-induced bystander activation via binding to AP-1 that is necessary for the IL-15-induced upregulation of NK cytotoxicity-related genes. Consistent with these results, calcineurin inhibitors enhanced IL-15-induced NKG2D expression in the presence of TCR signals. Additionally, we defined genes upregulated by IL-15 and downregulated by concurrent TCR signals as an IL-15-induced bystander activation gene set, and found that this gene signature was upregulated in bystander CD8+ T cells from patients with hepatitis A virus infection. This study paves the way for further investigation of bystander CD8+ T-cell activation in various pathological conditions, and its regulation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/632884v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1e6c320org.highwire.dtl.DTLVardef@114a23eorg.highwire.dtl.DTLVardef@1a7b9edorg.highwire.dtl.DTLVardef@9faccc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITCR signaling downregulates IL-15-induced transcriptomic features related to NK-like bystander activation of human memory CD8+ T cells via the Ca2+-calcineurin pathway. C_LIO_LINFATc1 suppresses IL-15-induced bystander activation via binding to AP-1, which is responsible for IL-15-induced NK-like cytotoxic activity. C_LIO_LICalcineurin inhibitors cannot suppress IL-15-induced bystander CD8+ T-cell activation, and paradoxically increase IL-15-induced NKG2D expression in the presence of TCR signals. C_LIO_LIGenes upregulated by IL-15 and downregulated by concurrent TCR signals define the gene set of bystander CD8+ T-cell activation, which was validated in disease contexts. C_LI

immunology↗

bioRxiv2025

Unique transcriptional profiles of adult human immature neurons in healthy aging, Alzheimer's disease, and cognitive resilience

The existence and functional significance of immature neurons in the adult human brain, particularly in the context of neurodegenerative disorders, remain controversial. While rodent studies have highlighted active roles for adult-born immature neurons in the hippocampus under both healthy conditions and in Alzheimers disease (AD), evidence from the human brain is limited and lacks detailed molecular characterization. To address this gap, we performed single-nucleus RNA sequencing in aged healthy, AD and dementia-resilient human hippocampus to probe immature neuronal signatures and gene expression alterations associated with AD pathology and resilience. Employing a novel experimental and computational pipeline, we identified persistent populations of immature neurons across all donor groups, with transcriptional profiles distinct from both fetal counterparts and adult mature hippocampal neurons. These profiles were associated with juvenile cellular functions, suggesting that the presence of these immature neuronal populations per se may actively contribute to maintaining homeostasis within the aged human hippocampus, a role that may be disrupted in AD. In the resilient brain, immature neurons were involved in transcriptional programs and intercellular interactions associated with anti-inflammatory, neurotrophic, neuroprotective, myelinating, anti-apoptotic and anti-amyloidogenic signaling pathways, suggesting active roles for the immature cells in enhancing cognitive resilience in the presence of AD pathology. Our findings reveal novel, putative physiological roles for immature neurons in the healthy and resilient adult human brain, and offer a resource for probing new strategies with potential functional relevance in AD.

neuroscience↗

bioRxiv2024

dGAMLSS: An exact, distributed algorithm to fit Generalized Additive Models for Location, Scale, and Shape for privacy-preserving population reference charts

There is growing interest in estimating population reference ranges across age and sex to better identify atypical clinically-relevant measurements throughout the lifespan. For this task, the World Health Organization recommends using Generalized Additive Models for Location, Scale, and Shape (GAMLSS) which can model non-linear growth trajectories under complex distributions that address the heterogeneity in human populations. Fitting GAMLSS models requires large, generalizable sample sizes, especially for accurate estimation of extreme quantiles, but obtaining such multi-site data can be challenging due to privacy concerns and practical considerations. In settings where patient data cannot be shared, privacy-preserving distributed algorithms for federated learning can be used, but no such algorithm exists for GAMLSS. We propose distributed GAMLSS (dGAMLSS), a distributed algorithm which can fit GAMLSS models across multiple sites without sharing patient-level data. We demonstrate the effectiveness of dGAMLSS in constructing population reference charts across clinical, genomics, and neuroimaging settings.

bioinformatics↗

bioRxiv2024

Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

Trichomonas vaginalis is the causative agent of the venereal disease trichomoniasis which infects men and women globally and is associated with serious outcomes during pregnancy and cancers of the human reproductive tract. Trichomonads parasitize a range of hosts in addition to humans including birds, livestock, and domesticated animals. Recent genetic analysis of trichomonads recovered from columbid birds has provided evidence that these parasite species undergo frequent host-switching, and that a current epoch spillover event from columbids likely gave rise to T. vaginalis in humans. We undertook a comparative evolutionary genomics study of seven trichomonad species, generating chromosome-scale reference genomes for T. vaginalis and its avian sister species Trichomonas stableri, and assemblies of five other species that infect birds and mammals. Human-infecting trichomonad lineages have undergone recent and convergent genome size expansions compared to their avian sister species, and the major contributor to their increased genome size is increased repeat expansions, especially multicopy gene families and transposable elements, with genetic drift likely a driver due to relaxed selection. Trichomonads have independently host-switched twice from birds to humans, and genes implicated in the transition to the human host include those associated with host tissue adherence and phagocytosis, extracellular vesicles, and CAZyme virulence factors.

microbiology↗

bioRxiv2024

Spatially ordered zygotic genome activation fulfills embryo quality control

Early embryo development features autonomous, maternally-driven cell divisions that self- organize the multicellular blastula or blastocyst tissue. Maternal control cedes to the zygote starting with the onset of widespread zygotic genome activation (ZGA), which is essential for subsequent cell fate determination and morphogenesis. Intriguingly, although the onset of ZGA is highly regulated at the level of an embryo, it can be non-homogenous and precisely patterned at the single-cell level. We previously demonstrated a stereotyped spatial and temporal ordering of ZGA in a model vertebrate embryo. Unknown, however, was whether this precise ZGA patterning was required for development. To address this fundamental question, we devised a strategy to spatially control cell divisions in the embryo that perturb blastula embryo organization. We demonstrate the feasibility of spatially inverting the cell size pattern of embryos and find that these inverted embryos undergo a flipped pattern of ZGA. Mispatterned ZGA along the animal-vegetal axis causes embryo apoptosis, revealing that gastrula embryos have a built-in quality control system to sense inappropriate ZGA patterning, including regional defects in transcriptional onset. The quality control response is non-autonomous which may depend on anti-apoptotic signals that repress cell death outside of the animal hemisphere. These results reveal the requirement of properly patterned ZGA for normal development and the existence of an embryo quality control response exquisitely tuned to the spatial and temporal ordering of genome activation and zygotic gene expression.

developmental biology↗

bioRxiv2024

Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing

Oxford Nanopore Technologies (ONT) long-read sequencing (LRS) has emerged as a promising tool for genomic analysis, but comprehensive comparisons with established platforms across diverse datasets remain limited. We present a multi-platform benchmark using 14 human genomes sequenced with ONT LRS, Illumina short-read sequencing (SRS), and Illumina microarrays. Our study evaluates LRS performance for various genetic variants across genomic contexts, while also examining the impact of experimental factors such as multiplexing, depth, and read length. In high-complexity regions, LRS demonstrated competitive yet slightly lower accuracy than SRS for SNV detection (F-measure: 0.954 vs. 0.968), with performance gaps narrowing in low-complexity regions. For indel detection, LRS showed robust performance for small indels (1-5bp) in high-complexity regions (F-measure: 0.869), but accuracy decreased significantly in low-complexity regions and for larger indels. LRS identified 2.86 times more structural variants than SRS, with superior detection of large-scale variations. Sequencing depth strongly influenced variant calling performance across all variant types, while multiplexing effects were minimal after controlling for depth. Our findings provide valuable insights for optimising ONT LRS applications in genomic research and clinical diagnostics.

bioinformatics↗

bioRxiv2024

CD38 biallelic loss is a recurrent mechanism of resistance to anti-CD38 antibodies in multiple myeloma.

Monoclonal antibodies targeting CD38 are a therapeutic mainstay in multiple myeloma (MM). While they have contributed to improved outcomes, most patients still experience disease relapse, and little is known about tumor-intrinsic mechanisms of resistance to these drugs. Antigen escape has been implicated as a mechanism of tumor cell evasion in immunotherapy. Yet, it is unknown whether MM cells can develop permanent resistance to anti-CD38 antibodies by acquiring genomic events leading to biallelic disruption of the CD38 gene locus. Here, by using whole genome and whole exome sequencing data from 701 newly diagnosed patients, 67 patients at relapse with naivety to anti-CD38 antibodies, and 50 patients collected at relapse following anti-CD38 antibodies. We report a loss of CD38 in 20% (10/50) of patients post-CD38 therapy, three of which exhibited a loss of both copies. Two of these cases showed convergent evolution where distinct subclones independently acquired similar advantageous variants. Functional studies on missense mutations involved in biallelic CD38 events revealed that two variants, L153H and C275Y, decreased binding affinity and antibody-dependent cellular cytotoxicity of the commercial antibodies Daratumumab and Isatuximab. However, a third mutation, R140G, conferred selective resistance to Daratumumab, while retaining sensitivity to Isatuximab. Clinically, patients with MM are often rechallenged with CD38 antibodies following disease progression and these data support a role for next generation sequencing to guide treatment selection.

cancer biology↗

bioRxiv2024

In vivo human neurite exchange imaging (NEXI) at 500 mT/m diffusion gradients

Evaluating tissue microstructure and membrane integrity in the living human brain through diffusion-water exchange imaging is challenging due to requirements for a high signal-to-noise ratio and short diffusion times dictated by relatively fast exchange processes. The goal of this work was to demonstrate the feasibility of in vivo imaging of tissue micro-geometries and water exchange within the brain gray matter using the state-of-the-art Connectome 2.0 scanner equipped with an ultra-high-performance gradient system (maximum gradient strength=500 mT/m, maximum slew rate=600 T/m/s). We performed diffusion MRI measurements in 15 healthy volunteers at multiple diffusion times (13-30 ms) and b-values up to 17.5 ms/m2. The anisotropic Karger model was applied to estimate the exchange time between intra-neurite and extracellular water in gray matter. The estimated exchange time across the cortical ribbon was around (median{+/-}interquartile range) 13{+/-}8 ms on Connectome 2.0, substantially faster than that measured using an imaging protocol compatible with Connectome 1.0-alike systems on the same cohort. Our investigation suggested that the NEXI exchange time estimation using a Connectome 1.0 compatible protocol was more prone to residual noise floor biases due to the small time-dependent signal contrasts across diffusion times when the exchange is fast ([≤]20 ms). Furthermore, spatial variation of exchange time was observed across the cortex, where the motor cortex, somatosensory cortex and visual cortex exhibit longer exchange times compared to other cortical regions. Non-linear fitting for the anisotropic Karger model was accelerated 100 times using a GPU-based pipeline compared to the conventional CPU-based approach. This study highlighted the importance of the chosen diffusion times and measures to address Rician noise in dMRI data, which can have a substantial impact on the estimated NEXI exchange time and require extra attention when comparing NEXI results between various hardware setups. Highlights- The Connectome 2.0 scanner equipped with 500 mT/m gradients enables high-sensitivity diffusion MRI for imaging exchange times in vivo - The global exchange time across the living human cortex was estimated to be about 13 ms on Connectome 2.0, faster than measured using a protocol compatible to Connectome 1.0 - Spatially varying exchange times were observed across the cortex - A GPU-accelerated tool was developed to speed up parameter estimation by 100 times - The narrow pulse approximation used in neurite exchange imaging does not affect estimation performance in high gradient performance MRI systems

neuroscience↗

bioRxiv2024

Periaqueductal gray passes over disappointment and signals continuity of remaining reward expectancy

Disappointment is a vital factor in the learning and adjustment of strategies in reward-seeking behaviors. It helps them conserve energy in environments where rewards are scarce, while also increasing their chances of maximizing rewards by prompting them to escape to environments where richer rewards are anticipated (e.g., migration). However, another key factor in obtaining the reward is the ability to monitor the remaining possibilities of obtaining the outcome and to tolerate the disappointment in order to continue with subsequent actions. The periaqueductal gray (PAG) has been reported as one of the key brain regions in regulating negative emotions and escape behaviors in animals. The present study suggests that the PAG could also play a critical role in inhibiting escape behaviors and facilitating ongoing motivated behaviors to overcome disappointing events. We found that PAG activity is tonically suppressed by reward expectancy as animals engage in a task to acquire a reward outcome. This tonic suppression of PAG activity was sustained during a series of sequential task procedures as long as the expectancy of reward outcomes persisted. Notably, the tonic suppression of PAG activity showed a significant correlation with the persistence of animals reward-seeking behavior while overcoming intermittent disappointing events. This finding highlights that the balance between distinct tonic signaling in the PAG, which signals remaining reward expectancy, and phasic signaling in the LHb, which signals disappointment, could play a crucial role in determining whether animals continue or discontinue reward-seeking behaviors when they encounter an unexpected negative event. This mechanism would be essential for animals to efficiently navigate complex environments with various reward volatilities and ultimately contributes to maximizing their reward acquisition.

neuroscience↗

bioRxiv2024

A core set of neural states underlying memory reactivation of naturalistic events in the posterior medial cortex

In the posterior midline default mode network, spatial activity patterns similar to those during the initial experience are reactivated during the successful recall of past events. Prior studies have shown that these event-specific activity patterns are consistent across individuals recalling a shared experience, suggesting that common functional responses underlying episodic recall do exist. However, the spatial organization of function during episodic encoding and subsequent recall, especially in the absence of external stimuli, remains poorly understood. To address this, we leverage fMRI data collected during the encoding and recall of naturalistic movies to identify a core set of neural states in the posterior medial cortex. These states are stimulus-locked, reactivated during recall, and have a shared spatial organization across brains (i.e., individuals). We show that a surprisingly small number of these states (16 states across hemispheres) is sufficient to achieve the same levels of reactivation in the posterior medial cortex as when using the standard methods of the field. Additionally, these states are linked to actions and social-affective features of events in the movies. Our findings elucidate the properties of a common, spatially organized code within the posterior default mode network which appears during natural recollection of memories.

neuroscience↗

bioRxiv2024

Naturally ornate RNA-only complexes revealed by cryo-EM

Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryogenic electron microscopy at resolutions of 2.9-3.1 [A]. Without precedent among previously characterized natural RNA molecules, Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD), Rumen-Originating, Ornate, Large (ROOL), and Ornate Large Extremophilic (OLE) RNAs form homo-oligomeric complexes whose stoichiometries are retained at concentrations lower than expected in the cell. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome. Extensive intra- and intermolecular A-minor interactions, kissing loops, an unusual A-A helix, and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.

biophysics↗

bioRxiv2024

OST Catalytic Subunit Redundancy Enables Therapeutic Targeting of N-Glycosylation

Protein asparagine (N)-glycosylation, which promotes folding and trafficking of cell surface receptors such as the EGFR, has not been considered a viable target in oncology due to the essential and non-redundant enzymatic activities required for glycan synthesis and transfer. In mammals an exception to this rule is the presence of the oligosaccharyltransferase (OST) catalytic subunit paralogs, STT3A and STT3B. Here we delineate the chemical biology of OST inhibitors and develop an approach for limited inhibition of N-glycosylation optimized for downstream effects on EGFR. Small molecules with enhanced pharmacokinetic properties and preferences for STT3A or STT3B were synthesized, characterized in vitro, and advanced to in vivo testing. The lead from this series, NGI-189, causes tumor regression or growth delay of patient derived and TKI resistant EGFR-mutant lung cancer xenografts without toxicity. Together these results suggest that bioavailable OST inhibitors can be developed as therapeutic agents for oncology. SUMMARYA mechanistic approach for partial inhibition of N-glycosylation delivers small molecules with anti-tumor activity in EGFR mutant NSCLC.

cancer biology↗

bioRxiv2024

C. elegans huntingtin, htt-1, promotes robust autophagy induction and survival under stress conditions

Huntingtin (HTT) is the gene responsible for Huntingtons disease (HD), a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion mutation. While HD pathogenesis has traditionally been attributed to the toxic gain-of-function effects of mutant huntingtin (mHTT), increasing evidence underscores the critical role of wild-type HTT loss-of-function. Understanding the physiological roles of HTT is essential for elucidating HD mechanisms and developing effective therapeutic strategies. The C. elegans htt-1 gene, an ortholog of human HTT, remains largely uncharacterized. Here, we demonstrate that htt-1 promotes survival under stress conditions that requires autophagy as a defense mechanism. Specifically, we identify intestinal htt-1 as a key regulator of C. elegans survival during Pseudomonas aeruginosa PA14 infection. Our findings reveal that htt-1 functions downstream of the MPK-1/ERK pathway to induce systemic autophagy and enhance host defense during immune challenges. Moreover, expression of wild-type human HTT in htt-1 mutant worms rescues the survival defect during PA14 infection. Expression of mutant human HTT, on the other hand, exacerbates survival deficits, underscoring the conserved function of HTT across species. Additionally, we found that htt-1 affects survival and autophagy under heat shock stress conditions. These results establish htt-1 as a critical regulator of survival and autophagy in response to both pathogenic bacterial infection and thermal stress. Author summaryHuntingtin plays essential roles in selective autophagy across various organisms, including Drosophila, mice, and humans. Notably, the C. elegans huntingtin ortholog, htt-1, remains largely uncharacterized. Here, we describe a novel pro-survival role htt-1 in stress resistance. We show that htt-1 mutants exhibit significantly reduced survival during Pseudomonas aeruginosa infection. Expression of wild-type human HTT rescues the reduced survival of htt-1 mutants, whereas mutant HTT further exacerbates the phenotype. These findings establish C. elegans htt-1 as a valuable model for studying huntingtin biology and its roles in stress resistance. Downregulation of ERK in htt-1 mutants had no additional effect on survival, suggesting that htt-1 functions downstream of ERK. Interestingly, htt-1 mutants display reduced autophagy, indicating that htt-1 functions in the ERK-autophagy signaling cascade during infection. Mechanistically, we propose that htt-1 regulates autophagy at the protein level. HTT-1 remains cytoplasmic, and autophagy-related gene transcripts remain stable, without downregulation, in htt-1 mutants following infection. Additionally, htt-1 mutants exhibit reduced survival and impaired autophagy under heat stress. These results suggest that htt-1 may have a broader role in stress resilience extending beyond immune defense.

cell biology↗

bioRxiv2024

Adherent-suspension plasticity promotes the dissemination and colonization of circulating tumor cells

Cell competition within the primary tumor drives tumor growth by promoting the uncontrolled proliferation of winner cells and eliminating loser cells by sensing cell fitness. However, the mechanism of how cell competition confers the loser cells with the metastatic potential of circulating tumor cells (CTCs) to transit between dissemination and colonization remains elusive. Here we found cell competition gives rise to less fit but viable cells that transformed into CTCs via adherent-to-suspension transition (AST) mechanisms. The induction of hematopoietic transcription factors hijacked by solid tumor cells rendered CTCs competent to reprogram their anchorage dependency and disseminate into the bloodstream, while subsequent suppression of these factors was critical to regain adhesion and colonize metastatic lesions. Disrupting the oscillatory dynamics of AST factors blocked the adherent-suspension plasticity (ASP) of breast cancer CTCs and suppressed lung metastasis. Furthermore, multiregional single-cell transcriptomic analyses of matched primary tumors, CTCs, and metastatic lesions from de novo metastatic breast cancer patients demonstrate the critical role of ASP in metastasis. SignificanceWe demonstrate cell competition-mediated displacement of loser cells manifests dynamic oscillation of AST factors that confer anchorage plasticity to circulating tumor cells critical for their dissemination and colonization in metastasis. These findings highlight the potential of targeting AST factors to develop effective anti-metastatic therapies.

cancer biology↗

bioRxiv2024

The single-cell spatial landscape of stage III colorectal cancers

We conducted a spatial analysis using imaging mass cytometry applied to stage III colorectal adenocarcinomas. This study used multiplexed markers to distinguish individual cells and their spatial organization from 52 colorectal cancers. We determined the landscape features of cellular spatial features in the CRC tumor microenvironment. This spatial single-cell analysis identified 10 unique cell phenotypes in the tumor microenvironment that included stromal and immune cells with a subset which had a proliferative phenotype. These special features included spatial neighborhood interactions between single cells as well as different tissue niches, especially the tumor infiltrating lymphocyte regions. We applied a robust statistical analysis to identify significant correlations of cell features with phenotypes such as microsatellite instability or recurrence. We determined that microsatellite stable (MSS) colorectal cancers had an increased risk of recurrence if they had the following features: 1) a low level of stromal tumor-infiltrating lymphocytes, and 2) low interactions between CD4+ T cells and stromal cells. Our results point to the utility of spatial single-cell interaction analysis in defining novel features of the tumor immune microenvironments and providing useful clinical cell-related spatial biomarkers.

cancer biology↗

bioRxiv2024

Bone marrow microenvironment signatures associate with patient survival after guadecitabine and atezolizumab therapy in HMA-resistant MDS

Almost 50% of patients with myelodysplastic syndrome (MDS) are refractory to first-line hypomethylating agents (HMAs), which presents a significant clinical challenge considering the lack of options for salvage. Past work revealed that immune checkpoint molecules on peripheral myeloblasts and immune cells are up-regulated after HMA treatment. Therefore, we conducted a Phase I/II clinical trial combining guadecitabine (an HMA) and atezolizumab (an immune checkpoint inhibitor) to treat HMA-relapsed or refractory (HMA-R/R) MDS patients. This combination therapy showed median overall survival of 15.1 months relative to historical controls (4-6 months). Here, we profiled the cell composition and gene expression signatures of cells from bone marrow aspirates from trial participants with short-term (<15 months) or long-term (>15 months) survival at single-cell resolution. Long-term survivors showed a significant reduction of immunosuppressive monocytes, and an expansion of effector lymphocytes after combination therapy. Further immune profiling suggests that gamma delta T cell activation through primed dendritic cells was associated with global interferon activation in the bone marrow microenvironment of long-term survivors. Short-term survivors exhibited elevated inflammation and senescence-like gene signatures that were not resolved by combination therapy. We propose that distinct bone marrow microenvironment features, such as senescence-associated inflammation or immunosuppressive monocyte presence, could improve patient stratification for HMA and immunotherapy combinations in HMA-R/R MDS patients.

cancer biology↗