Biology subjects

Nair, R.

Publications and source records attributed to Nair, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Ketogenic diet is protective during endotoxin-induced lung injury through the elevation of BHB

Acute respiratory distress syndrome (ARDS) is marked by severe pulmonary edema and concomitant hypoxia, affecting hundreds of thousands of people a year, especially those in critical care conditions or suffering from septic shock. Previous studies have implicated that the ketogenic diet, a high-fat and low-carbohydrate diet, modulates inflammatory responses. However, the impact of the ketogenic diet on septic ARDS outcomes is unknown. Here, we demonstrated that mice on a ketogenic diet showed strikingly reduced lung injury and inflammation compared to those on a control diet during a murine model of endotoxin-induced lung injury, induced by intratracheal lipopolysaccharide (LPS) injection. Immune mass cytometry studies on lung tissue indicated that the ketogenic diet reduces immune cell infiltration. Treating mice with beta-hydroxybutyrate (BHB), the primary metabolite of ketogenesis, after the onset of ARDS reduced pulmonary edema and lung inflammation, as well as NF-kB activity, suggesting strong therapeutic potential. By multiplex analysis in bronchial alveolar lavage fluid, we observed that the ketogenic diet or BHB administration attenuates the chemotaxis and activation of immune cells. Altogether, our findings reveal that the ketogenic diet provides lung protection during endotoxin-induced lung injury through BHB.

physiology↗

bioRxiv2026

Mapping mouse hippocampal output circuits using direction-selective anterograde transsynaptic transduction

The hippocampus and its projection targets constitute hippocampal output circuits that are essential for memory, navigation, and emotional regulation. Although cortical and subcortical regions receiving hippocampal projections have been well characterized, it remains unclear how hippocampal signals are processed within these projection target regions. To precisely understand information processing in hippocampal output circuits, it is therefore important to gain genetic access to neuronal subpopulations receiving direct hippocampal inputs for structural and functional analyses. Anterograde transsynaptic transduction using adeno-associated virus (AAV) serotype 1 has emerged as a powerful approach for targeting postsynaptic neurons, but its application is limited by unintended retrograde transport, which leads to false-positive labeling in reciprocally connected circuits. Here, we developed a direction-selective anterograde transsynaptic transduction by combining AAV vectors with distinct infection properties and an intersectional gene expression system. Using the hippocampal-entorhinal circuit, we identified an optimal viral combination that enables predominantly anterograde transsynaptic labeling. We further applied this method to map hippocampal projections to reciprocally connected regions, including the amygdala, providing a robust approach for dissecting complex hippocampal output circuits.

neuroscience↗

bioRxiv2026

DEVELOPMENT OF A BIOMIMETIC 3D OVARIAN SCAFFOLD USING DECELLULARIZED EXTRACELLULAR MATRIX AND MECHANICALLY TUNED HYDROGELS

Artificial ovarian scaffolds represent a promising therapeutic strategy for preserving reproductive health in patients. However, current in vitro approaches are limited by inadequate biomimicry of the native tissue microenvironment, leading to poor development of in vitro ovarian models. In this study, we developed region-specific hydrogel scaffolds incorporating solubilized decellularized ovarian extracellular matrix (dECM) with mechanically tuned properties to enhance the functionality of engineered 3D ovarian models. Ovine ovarian dECM was isolated by mechanical and chemical decellularization methods and subsequently solubilized and incorporated in varying concentrations in homogenous alginate (0.5%) and a composite mixture of 1% gelatin with 0.5% alginate (1:1). The synthesized hydrogels were characterized for rheological properties, including Youngs modulus, pore size, and viscosity, and cytocompatibility assays were conducted using Chinese hamster ovary (CHO) cells. The study demonstrated that both 0.5% alginate and the composite gelatin-alginate hydrogels successfully replicated the mechanical properties of native human ovarian cortical and medullary tissue, with Youngs modulus of 0.84 {+/-} 0.16 kPa, pore size (60-150 nm), and toughness of 0.4Pa, respectively. Zonal hydrogel scaffolds incorporating ovarian dECM demonstrated significantly enhanced cell viability compared to hydrogels supplemented with dECM. The study emphasises the critical role of integrating both mechanical and biochemical attributes while developing functional artificial ovarian constructs for transplantation and regenerative medicine applications. This work contributes to advancing strategies for creating physiologically relevant in vitro models of ovarian tissue.

developmental biology↗

bioRxiv2026

Water Stress Induces Diel Patterns of Root Growth

Growth and death of vegetation control both the amount of carbon held in living biomass and much of the flow between the atmosphere and soils, the largest terrestrial carbon reservoir. However, long-term field datasets on belowground growth dynamics are rare. Knowledge is lacking on how root growth patterns relate to the environment, fluctuating carbon and water availability, and internal plant physiological control, at both seasonal and diel scales. We imaged roots using automated minirhizotrons and interpreting root length density (RLD) automatically twice a day for nine months in a temperate grassland. From winter to autumn, we always observed some root growth in individual images, but with decreasing net RLD (indicative of net turnover) becoming predominant later in the season. Roots grew day-round except during a period of about one month in spring when root growth was only in daytime. This was a period without rain, during which soil moisture depleted rapidly, but not at its driest point. We discuss potential causes for both overall and short-term growth patterns, particularly the change in drivers of growth from internal storage to new photosynthates, or limits imposed by water availability - both soil moisture and rainfall - under shifting environmental conditions.

plant biology↗

bioRxiv2025

Guiding treatment response by spatiotemporal control of α-particle deposition in solid tumors: the case for 'affinity cocktails' of antibody-radioconjugates

Antibody-radioconjugates are leading the investigational targeted alpha-particle (-particle) therapies for the treatment of solid tumors that do not respond to approved therapies. Yet, there is still treatment failure in the clinic largely attributed to the heterogenous patterns of tumor irradiation by -particles. Although -particles are essentially impervious to resistance, attributed to the complex double-strand DNA breaks they cause while traversing cells, cells not being directly hit by -particles will likely not be killed. The diffusion-limited poor tumor penetration of high-affinity (strongly-binding) antibody-radioconjugates combined with -particles short-range in tissue (only 40-80m), let tumor regions far from vasculature inadequately irradiated, therefore, possibly escaping treatment. METHODSTo improve penetration of delivered activity within tumors, we engineered separate actinium-225 antibody-radioconjugates of variable affinities ( affinity cocktails) targeting the same marker on cancer cells, that were chosen based on their preferential irradiation of complementary regions of the same tumors. The cocktails comprise: (a) high-affinity antibody-radioconjugates (as the ones on clinical trials), which mostly deliver their cargo in tumor cells close to the vasculature, where the low(er)-affinity antibody-radioconjugates fail to deliver effective doses, due to their fast clearance; and (b) low(er)-affinity antibody-radioconjugates, that penetrate the deeper parts of tumors farther from the vasculature, where the high-affinity antibodies fail to reach. The efficacy of affinity cocktails was assessed in spheroids, that were employed as surrogates of tumor avascular regions, and on mice with subcutaneous xenografts of different cancer origin, expression levels and/or type of the targeted receptor: HER2 highly-expressing BT-474 breast cancer cells, HER2 moderately-expressing HEPG2 hepatoma cells, and/or HER1 low-expressing BxPC-3 pancreatic cancer cells. RESULTSAlthough the high-affinity antibody-radioconjugates were most lethal against cancer cells in monolayers, affinity cocktails were most effective in inhibiting spheroid growth, due to better collective spreading of the antibody-conjugates within the spheroids volume. On all mouse models, and for the same total injected activity, affinity cocktails resulted in the best tumor growth inhibition, even at lower tumor absorbed doses, compared to the high-affinity antibody-radioconjugates alone. CONCLUSIONSThis proof-of-concept study in -particle antibody-delivery to solid tumors demonstrates that separating the two key processes of diffusion and reaction/binding improves treatment efficacy. This generalizable approach may augment antibody-radioconjugates already in clinical trials.

bioengineering↗

bioRxiv2025

Actinium-225 dendrimer-radioconjugates combined with low-dose standard-of-care chemotherapy: site-independent treatment of triple negative breast cancer metastases

PURPOSEMetastatic triple negative breast cancer (mTNBC) is incurable largely due to the development of drug resistance, the lack of selective cell targeting, and/or limitations in tumor drug delivery that vary depending on the different (metastatic) tumor locations. METHODSThe potential of a single type of systemic, targeted alpha-particle therapy (TAT) was investigated for addressing the above challenges of TNBC tumors implanted at different anatomic sites in mice. Actinium-225 dendrimer-radioconjugates alone, and/or after pretreatment with low-dose standard-of-care cisplatin, were assessed in vitro and on immune-competent 4T1-Balb/c mouse models with tumors implanted intracranially, orthotopically or subcutaneously. RESULTSIn vitro, TATs efficacy was enhanced by cisplatin. In vivo, treatment was initiated well after tumors had grown (Vto = 39 {+/-} 14 mm3 in the intracranial model, and Vto=100mm3 in the orthotopic and subcutaneous models). Across all tumor implantation sites, a unified correlation was observed between animal mean survival and the dendrimer-delivered tumor absorbed doses, which were selectively increased by low-dose cisplatin pretreatment. Importantly, in all animal models, the mean survival following systemic treatment with both modalities was significantly longer vs. each modality alone and/or vs. no treatment, at injected doses that did not cause long-term (10-month) toxicities in tumor-free mice. CONCLUSIONSystemically-injected dendrimer-delivered TAT, combined with low-dose cisplatin pretreatment, can safely extend survival independent of mTNBC tumors anatomic site, potentially presenting a single type of therapy to simultaneously treat multi-site mTNBC.

bioengineering↗

bioRxiv2025

Sustained Lysosomal Delivery of Enhanced Cy3-Labeled Acid Nanoparticles Restores Lysosomal pH in Retinal Pigment Epithelial Cells and Astrocytes

Lysosomal pH is frequently elevated in age-dependent neurodegenerations like Age-related Macular Degeneration (AMD), Alzheimers Disease (AD), and Parkinsons Disease (PD). Tools that restore lysosomal pH to an optimal acidic range could enhance enzymatic degradation and reduce waste accumulation. Acidic nanoparticles offer a promising strategy for restoring lysosomal function, but accurate tracking of organelle delivery and long-term retention is needed to optimize dosage. To improve detection and enhance delivery, nanoparticles were synthesized from Poly(D,L-lactide-co-glycolide) (PLGA) polymers covalently linked to the fluorescent Cyanine3 amine (Cy3) probe. Nanoparticle concentration and loading times were optimized to achieve >90% delivery to lysosomes in cultured induced pluripotent stem cell-derived retinal pigment epithelial (iPS-RPE) cells. Uptake was heterogeneous, varying between adjacent cells. Once loaded into lysosomes, the nanoparticles were stably retained, with no detectable changes in concentration, distribution, or size for at least 28 days. iPS-RPE cells internalized more nanoparticles than the ARPE-19 cell line or mouse optic nerve head astrocyte cultures. Functionally, PLGA nanoparticles restored an acidic pH and cathepsin D levels in compromised lysosomes. In summary, Cy3-PLGA nanoparticles enabled improved tracking and long-term delivery to lysosomes, supporting future in vivo applications to restore lysosomal pH in aging and degenerating tissues. Graphical AbstractIncreased lysosomal pH reduces degradative enzyme efficiency and contribute to age-dependent neurodegeneration. This study describes synthesis of nanoparticles to restore an acidic lumen and degradative function. Nanoparticles were optimized for lysosomal delivery to astrocytes and iPS-derived retinal pigmented epithelial (RPE) cells. The fluorescent marker Cy3 was covalently bound to polymers for improved tracking to lysosomes. Particles were stably retained inside the lysosomal lumen for at least 28 days. Nanoparticles restored pH to compromised lysosomes to baseline levels and increased active Cathepsin D. The improved design will aid in vivo tracking and repair in models where lysosomal alkalinization contributes to pathology. Created in BioRender. Mitchell, C. (2025) https://BioRender.com/8hvj96m. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/659991v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@d6fcf1org.highwire.dtl.DTLVardef@7833aborg.highwire.dtl.DTLVardef@188593corg.highwire.dtl.DTLVardef@9aa531_HPS_FORMAT_FIGEXP M_FIG C_FIG New and NoteworthyTools that restore acidic pH in compromised lysosomes can enhance autophagy and waste degradation in degenerative disorders marked by excessive accumulation. Here, we describe the novel synthesis of lysosome-targeted nanoparticles composed of PLGA polymers covalently bound to Cy3 fluorescent dye. These Cy3-PLGA nanoparticles enabled improved tracking of lysosomal delivery and demonstrated sustained long-term retention within lysosomes, supporting their potential for future applications to restore lysosomal pH in aging and degenerating tissues.

cell biology↗

bioRxiv2025

Repurposing statins in combination therapy for effective ablation of metastatic breast cancer

Metastatic breast cancer (mBC) remains an incurable disease with limited treatment options, highlighting the need for novel therapeutic approaches. Combination therapy with chemotherapeutic agents along with targeted therapy are the most common methods of treatment used in the terminal stages of the disease. Eventual development of resistance to these approaches, leading to fatal outcomes suggests the presence or emergence of a heterogenous population of cells intrinsically resistant to commonly used regimens. Previous work identified a heterogeneous population of metastatic tumor cells with distinct molecular characteristics driven by Macc1 (Metastasis Associated in Colon Cancer 1) overexpression, which could be targeted by lovastatin (transcriptional inhibitor of Macc1). Building on this foundation, the efficacy of lovastatin in targeting metastatic cells with high Macc1 expression was evaluated in lung metastasis, and the regulatory pathways governing Macc1 expression and lovastatin treatment in mBC were investigated. The expression of Macc1, in breast cancer biopsies provides insights into the intra and inter tumor heterogeneity of the Macc1 gene and its correlation with disease outcomes. While some studies suggest synergistic effects between statins and chemotherapeutic agents, comprehensive evaluations of various combinations and their therapeutic outcomes are still needed. The therapeutic efficacy of lovastatin combined with chemotherapy to determine the most effective treatment regimen that maximizes tumor cell ablation demonstrated that lovastatin can effectively ablate the chemoresistant tumor cells in mBC. The translational implications of this research will identify patient subgroups that may benefit most from statin-chemotherapy combinations that could support the repurposing of statins as cost-effective adjuvant therapies for mBC.

cancer biology↗

bioRxiv2025

Effects of DNA Origami-Based Nanoagent Design on Apoptosis Induction in a Large 3D Spheroid Model

The extrinsic activation of programmed cell death by FasR/CD95 is a promising minimally invasive strategy for cancer treatment. This can be leveraged using high-precision nanoscale therapeutics: Utilizing DNA origami for precise Fas ligand (FasL) presentation resulted in over 100 times more potent apoptosis induction in single cells. However, treating large, solid tumors poses challenges for DNA origami-based therapeutics, including drug distribution and altered cellular behavior. Here, we addressed these challenges using a 3D spheroid model. First, we assessed DNA origamis ability to penetrate tumor tissue, finding that penetration is influenced by the DNA origami size rather its structural flexibility. Second, we evaluated the apoptosis induction efficacy by DNA origami-FasL nanoagents within the spheroid model. The most potent nanoagents were able to completely eradicate all cells in the spheroid. Results indicated that apoptosis induction depended strongly on FasL attachment strategy rather than DNA origami design. Notably, only a rigid neutravidin linker for FasL attachment, rather than a flexible dsDNA linker, halted spheroid growth and fully eradicated all cancer cells. This study offers critical insights into designing DNA-based therapeutics for complex cellular environments and significantly advances DNA origami nanotherapeutic development, highlighting the impact of nanoagent design on cell fate decisions.

bioengineering↗

bioRxiv2024

Personalized transcriptome signatures in a cardiomyopathy stem cell biobank

BACKGROUNDThere is growing evidence that pathogenic mutations do not fully explain hypertrophic (HCM) or dilated (DCM) cardiomyopathy phenotypes. We hypothesized that if a patients genetic background was influencing cardiomyopathy this should be detectable as signatures in gene expression. We built a cardiomyopathy biobank resource for interrogating personalized genotype phenotype relationships in human cell lines. METHODSWe recruited 308 diseased and control patients for our cardiomyopathy stem cell biobank. We successfully reprogrammed PBMCs (peripheral blood mononuclear cells) into induced pluripotent stem cells (iPSCs) for 300 donors. These iPSCs underwent whole genome sequencing and were differentiated into cardiomyocytes for RNA-seq. In addition to annotating pathogenic variants, mutation burden in a panel of cardiomyopathy genes was assessed for correlation with echocardiogram measurements. Line-specific co-expression networks were inferred to evaluate transcriptomic subtypes. Drug treatment targeted the sarcomere, either by activation with omecamtiv mecarbil or inhibition with mavacamten, to alter contractility. RESULTSWe generated an iPSC biobank from 300 donors, which included 101 individuals with HCM and 88 with DCM. Whole genome sequencing of 299 iPSC lines identified 78 unique pathogenic or likely pathogenic mutations in the diseased lines. Notably, only DCM lines lacking a known pathogenic or likely pathogenic mutation replicated a finding in the literature for greater nonsynonymous SNV mutation burden in 102 cardiomyopathy genes to correlate with lower left ventricular ejection fraction in DCM. We analyzed RNA-sequencing data from iPSC-derived cardiomyocytes for 102 donors. Inferred personalized co-expression networks revealed two transcriptional subtypes of HCM. The first subtype exhibited concerted activation of the co-expression network, with the degree of activation reflective of the disease severity of the donor. In contrast, the second HCM subtype and the entire DCM cohort exhibited partial activation of the respective disease network, with the strength of specific gene by gene relationships dependent on the iPSC-derived cardiomyocyte line. ADCY5 was the largest hubnode in both the HCM and DCM networks and partially corrected in response to drug treatment. CONCLUSIONSWe have a established a stem cell biobank for studying cardiomyopathy. Our analysis supports the hypothesis the genetic background influences pathologic gene expression programs and support a role for ADCY5 in cardiomyopathy.

genomics↗

bioRxiv2023

A Drug-Free Pathogen Capture and Neutralizing Nasal Spray to Prevent Emerging Respiratory Infections

Respiratory infections pose a global health crisis. Vaccines are pathogen specific, and new vaccines are needed for mutants and emerging pathogens. Here, we report a "drug free" prophylactic platform - a "Pathogen Capture and Neutralizing Spray" (PCANS) that acts via a multi-pronged approach to prevent a broad spectrum of respiratory infections. PCANS forms a protective coating in the nasal cavity that enhances the capture of large respiratory droplets. The coating acts as a physical barrier against a broad spectrum of viruses and bacteria, and rapidly neutralizes them, reducing the pathogen load by >99.99%. In mice, PCANS showed nasal retention for at least 8 h and was safe for daily administration. A single prophylactic dose of PCANS protected mice against supra-lethal dosages of a mouse-adapted H1N1 Influenza virus (PR8), reduced lung viral titer by >99.99%, improved survival, and suppressed pathological manifestations. Together, our data suggest PCANS as a promising daily-use prophylactic approach against current and emerging respiratory infections.

bioengineering↗

bioRxiv2023

Androgen blockade primes NLRP3 in macrophages to induce tumor phagocytosis

Immune-based therapies induce durable remissions in subsets of patients across multiple malignancies. However, there is limited efficacy of immunotherapy in metastatic castrate-resistant prostate cancer (mCRPC), manifested by an enrichment of immunosuppressive (M2) tumor- associated macrophages (TAM) in the tumor immune microenvironment (TME). Therefore, therapeutic strategies to overcome TAM-mediated immunosuppression are critically needed in mCRPC. Here we discovered that NLR family pyrin domain containing 3 (NLRP3), an innate immune sensing protein, is highly expressed in TAM from metastatic PC patients treated with standard-of-care androgen deprivation therapy (ADT). Importantly, ex vivo studies revealed that androgen receptor (AR) blockade in TAM upregulates NLRP3 expression, but not inflammasome activity, and concurrent AR blockade/NLRP3 agonist (NLRP3a) treatment promotes cancer cell phagocytosis by immunosuppressive M2 TAM. In contrast, NLRP3a monotherapy was sufficient to enhance phagocytosis of cancer cells in anti-tumor (M1) TAM, which exhibit high de novo NLRP3 expression. Critically, combinatorial treatment with ADT/NLRP3a in a murine model of advanced PC resulted in significant tumor control, with tumor clearance in 55% of mice via TAM phagocytosis. Collectively, our results demonstrate NLRP3 as an AR-regulated "macrophage phagocytic checkpoint", inducibly expressed in TAM by ADT and activated by NLRP3a treatment, the combination resulting in TAM-mediated phagocytosis and tumor control.

cancer biology↗

bioRxiv2023

Combined, yet Separate: cocktails of carriers (not drugs) for α-particle therapy of solid tumors expressing moderate-to-low levels of targetable markers

Alpha-particle radionuclide-antibody conjugates are being clinically evaluated against solid cancers expressing moderate levels of the targeted markers, with promising results. These findings are attributed to the high killing power of alpha-particles in spite of the expected decrease in antibody tumor uptake, that reduces tumor absorbed doses. However, when tumor absorbed doses are reduced, addressing the heterogeneities in delivery of alpha-particles within solid tumors (i.e. enabling uniform irradiation patterns) becomes critical: to maintain efficacy, the fewer alpha-particles delivered within tumors need to traverse/hit as many different cancer cells as possible. This proof-of-concept study describes an approach to complement the antibody- targeted radiotherapy by using a separate carrier to deliver a fraction of the injected radioactivity to tumor regions geographically different than those affected by the antibody; collectively, the two carriers should distribute the alpha-particle emitters, Actinium-225 in particular, more uniformly within tumors maintaining efficacy. MethodsWe monitored the extent(s) of tumor growth inhibition, onset delay of spontaneous metastases and/or survival on orthotopic MDA-MB-213 and MDA-MB-436 triple negative breast cancer mouse models and on an ectopic BxPC3 pancreatic cancer mouse model, treated systemically with the two separate carriers. Tumors were chosen to express different (but low) levels of HER1, utilized as a model antibody-targeted marker. ResultsIndependent of tumor origin and/or resistance to chemotherapy, the two separate carriers: (a) improved the primary tumor growth inhibition, (b) eliminated the formation of spontaneous metastases, and/or (c) prolonged survival, at lower or comparable tumor delivered doses relative to the antibody alone, without noticeable off-target toxicities. ConclusionThis tumor-agnostic strategy is timely and could be used to enhance the efficacy of existing alpha-particle radionuclide-antibody treatments without increasing, possibly even reducing, the total administered radioactivity.

bioengineering↗

bioRxiv2022

GO WIDE TO GO DEEP: AFFORDABLE, REPLICABLE ROBOTIC MINIRHIZOTRON SAMPLING FOR PHENOLOGY STUDIES

Automating dynamic fine root data collection in the field is a longstanding challenge with multiple applications for co-interpretation and synthesis for ecosystem understanding. High frequency root data are only achievable with paired automated sampling and processing. However, automatic minirhizotron (root camera) instruments are still rare and data is often not collected in natural soils nor analysed at high temporal resolution. Instruments must also be affordable for replication and robust under variable natural conditions. Here, we show a system built with off-the-shelf parts which samples at sub-daily resolution. We paired this with a neural network to analyse all images collected. We performed two mesocosm studies and two field trials alongside ancillary data collection (soil CO2 efflux, temperature and moisture content, and PhenoCam-derived above-ground dynamics. We produce robust daily time-series of root dynamics under all conditions. Temporal root changes were a stronger driver than absolute biomass on soil CO2 efflux in mesocosm. Proximal sensed above ground dynamics and belowground from minirhizotron data were not synchronised. Root properties extracted were sensitive to soil moisture and occasionally to time of day (potentially relating to soil moisture). This may only affect high frequency imagery and should be considered in interpreting such data. HIGHLIGHTCompletely automatic root dynamics with method transferrable between field settings.

ecology↗

bioRxiv2021

Clonal hematopoiesis is associated with increased toxicity in large B-cell lymphoma patients treated with chimeric antigen receptor T cell therapy

To explore the role of clonal hematopoiesis (CH) on chimeric antigen receptor (CAR) T-cell therapy outcomes, we performed targeted deep-sequencing on 114 large B-cell lymphoma patients treated with anti-CD19 CAR T-cells. We detected CH in 42 (36.8%) pre-treatment patient samples, most frequently in PPM1D (19/114) and TP53 (13/114) genes. The incidence of grade [≥]3 immune-effector cell-associated neurotoxicity syndrome (ICANS) was higher in CH-positive patients compared to CH-negative patients (45.2% vs. 25.0%, p=0.038). Higher toxicities with CH were primarily driven by three CH genes, DNMT3A, TET2 and ASXL1 (DTA mutations). The incidence of grade [≥]3 ICANS [58.9% vs. 25%, p=0.02] and grade [≥]3 cytokine release syndrome [17.7% vs. 4.2%, p=0.08] were higher in patients with DTA mutations than those without CH. The estimated 24-month cumulative incidence of therapy-related myeloid neoplasms after CAR-T therapy was higher in patients with CH than those without CH (19% [95%CI: 5.5-38.7] vs. 4.2% [95%CI: 0.3-18.4], p=0.028). Statement of SignificanceOur study reveals that clonal hematopoiesis mutations, especially those associated with inflammation (DNMT3A, TET2, ASXL1), are associated with severe grade toxicities in lymphoma patients receiving anti-CD19 chimeric antigen receptor therapy. Further studies to investigate the mechanisms and interventions to improve toxicities in the context of CH are warranted.

genetics↗

bioRxiv2021

Long-term ecosystem nitrogen limitation from foliar δ15N data and a land surface model

The effect of nutrient availability on plant growth and the terrestrial carbon sink under climate change and elevated CO2 remains one of the main uncertainties of the terrestrial carbon cycle. This is partially due to the difficulty of assessing nutrient limitation at large scales over long periods of time. Consistent declines in leaf nitrogen (N) content and leaf {delta}15N have been used to suggest that nitrogen limitation has increased in recent decades, most likely due to the concurrent increase in atmospheric CO2. However, such datasets are often not straightforward to interpret due to the complex factors that contribute to the spatial and temporal variation in leaf N and isotope concentration. We use the land surface model QUINCY, which has the unique capacity to represent N isotopic processes, in conjunction with two large datasets of foliar N and N isotope content. We run the model with different scenarios to test whether foliar {delta}15N isotopic data can be used to infer large scale nitrogen limitation and if the observed trends are caused by increasing atmospheric CO2, changes in climate or changes in sources of anthropogenic N deposition. We show that while the model can capture the observed change in leaf N content and predicts widespread increases in N limitation, it does not capture the pronounced, but very spatially heterogeneous, decrease in foliar {delta}15N observed in the data across the globe. The addition of an observed temporal trend in isotopic composition of N deposition leads to a more pronounced decrease in simulated leaf {delta}15N. Our results show that leaf {delta}15N observations should not, on their own, be used to assess global scale N limitation and that using such a dataset in conjunction with a land surface model can reveal the drivers behind the observed patterns.

ecology↗

bioRxiv2021

Intracranial electrical stimulation alters meso-scale network integration as a function of network topology

Human brain dynamics are organized into a multi-scale network structure that contains multiple tight-knit, meso-scale communities. Recent work has demonstrated that many psychological capacities, as well as impairments in cognitive function secondary to damage, can be mapped onto organizing principles at this mesoscopic scale. However, we still dont know the rules that govern the dynamic interactions between regions that are constrained by the topology of the broader network. In this preregistered study, we utilized a unique human dataset in which whole brain BOLD-fMRI activity was recorded simultaneously with intracranial electrical stimulation, to characterize the effects of direct neural stimulation on the dynamic reconfiguration of the broader network. Direct neural stimulation increased the extent to which the stimulation sites own mesoscale community integrated with the rest of the brain. Further, we found that these network changes depended on the topological role of the stimulation site itself: stimulating regions with high participation coefficients led to global integration, whereas stimulating sites with low participation coefficients integrated that regions own community with the rest of the brain. These findings provide direct causal evidence for how network topology shapes and constrains inter-regional coordination, and suggest applications for targeted therapeutic interventions in patients with deep-brain stimulation.

neuroscience↗

bioRxiv2020

An evolutionarily acquired microRNA shapes development of mammalian cortical projections

The corticospinal tract is unique to mammals and the corpus callosum is unique to placental mammals (eutherians). The emergence of these structures is thought to underpin the evolutionary acquisition of complex motor and cognitive skills. Corticospinal motor neurons (CSMN) and callosal projection neurons (CPN) are the archetypal projection neurons of the corticospinal tract and corpus callosum, respectively. Although a number of conserved transcriptional regulators of CSMN and CPN development have been identified in vertebrates, none are unique to mammals and most are co-expressed across multiple projection neuron subtypes. Here, we discover seventeen CSMN-enriched microRNAs (miRNAs), fifteen of which map to a single genomic cluster that is exclusive to eutherians. One of these, miR-409-3p, promotes CSMN subtype identity in part via repression of LMO4, a key transcriptional regulator of CPN development. In vivo, miR-409-3p is sufficient to convert deep-layer CPN into CSMN. This is the first demonstration of an evolutionarily acquired miRNA in eutherians that refines cortical projection neuron subtype development. Our findings implicate miRNAs in the eutherians increase in neuronal subtype and projection diversity, the anatomic underpinnings of their complex behavior. Significance StatementThe mammalian central nervous system contains unique projections from the cerebral cortex thought to underpin complex motor and cognitive skills, including the corticospinal tract and corpus callosum. The neurons giving rise to these projections - corticospinal and callosal projection neurons - develop from the same progenitors, but acquire strikingly different fates. The broad evolutionary conservation of known genes controlling cortical projection neuron fates raises the question of how the more narrowly conserved corticospinal and callosal projections evolved. We identify a microRNA cluster selectively expressed by corticospinal projection neurons and exclusive to placental mammals. One of these microRNAs promotes corticospinal fate via regulation of the callosal gene LMO4, suggesting a mechanism whereby microRNA regulation during development promotes evolution of neuronal diversity.

neuroscience↗