Biology subjects

Fan, Q.

Publications and source records attributed to Fan, Q..

At least 19 recordsLinked to original sources

bioRxiv2026

Visibly Transparent, Near-Infrared Absorbing Nanofluids Enable High-Efficiency and Safe Laser Lithotripsy

Laser lithotripsy (LL) is the gold standard for urinary stone management yet maximizing ablation efficiency while maintaining procedural safety remains clinically challenging. Here, we present a visibly transparent, near-infrared (NIR)-absorbing ITO@SiO2 nanofluid irrigation strategy that significantly enhances LL efficiency without compromising endoscopic visibility. By spectrally matching the absorption profile of ITO@SiO2 with the clinical Holmium:YAG laser wavelength, ablation efficiency improved by >200% in the bench-top spot treatments and >100% in the hydrogel kidney model. Mechanistic investigations revealed that the enhanced optical absorption of the nanofluid modifies bubble dynamics and synergistically amplifies photothermal/microexplosion effects and cavitation damage. Importantly, both in-vitro hydrogel and in-vivo porcine kidney models demonstrated a substantial thermal safety margin (maximum temperatures <35 {degrees}C) and excellent acute biocompatibility, with no evidence of thermal tissue injury. Integrating seamlessly into established clinical workflows without requiring stone pretreatment, this strategy offers a highly translatable, safe, and efficient platform for next-generation endoscopic lithotripsy.

bioengineering↗

bioRxiv2026

Selective activation of IRE-1 safeguards restoration of translation and organismal rejuvenation from adult reproductive diapause

In C. elegans, prolonged food deprivation during early larval development results in aging-like phenotypes that can be fully reversed upon refeeding, but it remains unknown whether and how this ability persists into later life stages. Here we subjected C. elegans of the last larval stage to starvation, driving them into adult reproductive diapause (ARD). During starvation, ARD worms exhibited a wide spectrum of aging-like phenotypes, including transcriptomic reprogramming accompanying cellular and functional declines. These phenotypes are largely restored within one day of refeeding, suggesting a rejuvenation effect. Time-series transcriptomics, proteomics, and follow-up analyses of the refeeding/rejuvenation process uncovered an intricate coordination between: (1) activation of the IRE-1 branch of UPRER (unfolded protein response of endoplasmic reticulum) to induce chaperone expression; (2) quiescence of the PEK-1 branch of UPRER to avoid translation suppression; (3) up-regulation of the translation machinery to boost protein synthesis. IRE-1, together with its downstream effector, XBP-1, play an essential role in boosting protein synthesis, which is required for complete rejuvenation from the ARD state. These findings indicate that coordination between a high protein synthesis activity and a high protein folding capacity is key to refeeding-associated rejuvenation. HighlightsO_LIRefeeding rapidly reverses aging-like phenotypes in adult reproductive diapause C_LIO_LIRefeeding selectively activates the IRE-1 branch of UPRER C_LIO_LIRefeeding restores protein synthesis in an IRE-1 dependent manner C_LIO_LIRejuvenation requires enhanced translation activity and protein folding capacity C_LI

cell biology↗

bioRxiv2026

NRF2 pathway activation and SPP1⁺TREM2⁺ macrophages drive chemoradiotherapy resistance in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is among the most aggressive cancers, with low rates of durable response to chemoradiotherapy and limited therapeutic options for relapsed disease. To uncover mechanisms of treatment resistance and relapse, we performed comprehensive multi-omics profiling of >100 pre-treatment and post-relapse ESCC tumors from a prospective clinical trial (NCT04694391), integrating whole-exome/genome sequencing, bulk RNA-sequencing, single-cell RNA sequencing, and spatial transcriptomics. We identify somatic alterations in NFE2L2/KEAP1 in nearly 40% of relapsed patients, which are associated with upregulation of NRF2 signaling targets in resistant tumors and cell line models. At single-cell and spatial resolution, relapsed tumors are enriched for NRF2-activated epithelial cells that physically co-localize with immunosuppressive SPP1TREM2 macrophages. This co-localization suggests a synergistic interaction between NRF2-driven tumor programs and macrophage-mediated immune suppression that promotes relapse after chemoradiotherapy. Our findings nominate NFE2L2/KEAP1 mutations as predictive biomarkers for patient stratification and highlight therapeutic targeting of NRF2 signaling and SPP1TREM2 macrophages as rational strategies to overcome resistance in ESCC.

cancer biology↗

bioRxiv2026

Glycoprotein C Mutations Regulate the Plaque Size of Fusion-Defective Herpes Simplex Virus

Herpes simplex virus 1 (HSV-1) entry and virus-induced cell fusion require the coordinated activity of the essential glycoproteins gD, gH/gL, and gB. Mutations in this core fusion machinery reduce viral entry, fusion, and spread. Previously, we showed that introducing three mutations in gB (gB3A) or replacing HSV-1 gB with saimiriine herpesvirus 1 (SaHV-1) gB resulted in fusion-defective, small-plaque viruses. Serial passage of these viruses selected mutations in gH and gC, and we demonstrated that the gH mutations partially restored fusion function. In this study, we examined whether mutations in gC contribute to plaque formation, fusion, and entry. We generated an additional fusion-defective, small-plaque gD chimeric virus by replacing the profusion domain of HSV-1 gD with the corresponding region from SaHV-1 gD (gDchi). Serial passage of this virus partially restored plaque size and also selected for a mutation in gC. This study demonstrates that the selected gC mutants contributed to the partial restoration of plaque size. Plaque size of all three fusion-defective viruses was enhanced by exogenous expression of the corresponding selected gC mutants, whereas exogenous expression of wild-type gC reduced plaque size of the passaged isolates carrying gC mutations. Although gC mutants did not enhance fusion or entry mediated by the wild-type core fusion machinery, both wild-type and mutant gC enhanced cell-cell fusion when coexpressed with fusion-defective gH mutants. These results indicate that gC functions as a conditional accessory regulator that can partially compensate for defects in the HSV-1 core fusion machinery. IMPORTANCEHerpes simplex virus 1 (HSV-1) entry is mediated by a core fusion machinery comprised of glycoproteins gD, gH/gL, and gB. The contributions of additional viral glycoproteins to this process are not well defined. Glycoprotein C (gC) is known to function in cell attachment to heparan sulfate and immune evasion but is dispensable for viral entry under standard conditions. Here, we show that gC can act as a conditional accessory regulator of HSV-1 entry and fusion. Using serial passage of fusion-defective viruses, we demonstrate that mutations in gC are repeatedly selected and can partially compensate for defects in entry and fusion. These findings indicate that gC contributes to viral fusion under suboptimal conditions and highlight a role for this accessory glycoprotein in the adaptability of herpesvirus entry.

microbiology↗

bioRxiv2025

Normative modeling of brain morphology reveals neuroanatomical heterogeneity and biological subtypes in major depressive disorder

BACKGROUNDMajor Depressive Disorder (MDD) is characterized by high neurobiological heterogeneity, which hinders precise diagnosis and treatment. Traditional group-level neuroimaging analyses fail to capture individual differences, while normative modeling offer a promising approach to quantify individual deviations from healthy brain structure patterns, facilitating the identification of biological subtypes and offering a data-driven framework to dissect this heterogeneity. METHODSUsing 1,190 healthy controls, we constructed normative developmental trajectories of gray matter volume (GMV) across 246 Brainnetome-defined regions using Bayesian linear regression. Deviation maps were derived for 398 MDD patients. k-means clustering was employed to identify GMV-based biotypes. Then, the clinical characteristics and anatomical differences among these subtypes were explored, along with the post-treatment clinical features and treatment responses of participants who completed the 8-week antidepressant treatment within each subtype. RESULTSPatients with MDD exhibited widespread yet individually variable GMV deviations. Clustering analysis revealed two subtypes: Subtype 1 displayed predominantly negative deviations in sensorimotor and occipital cortices, whereas Subtype 2 showed widespread positive deviations in temporal and posterior cingulate regions. Subtype 1 had higher extraversion and symptom-linked deviation patterns; in Subtype 2, deviation burden correlated with generalized anxiety. Longitudinally, Subtype 1s GMV deviation changes predicted symptom improvement, while Subtype 2s deviations correlated with baseline severity. CONCLUSIONSNormative modeling of GMV reveals marked neuroanatomical heterogeneity in MDD and identifies subtypes with distinct clinical and treatment-related characteristics, laying a foundation for precision psychiatry and individualized interventions.

neuroscience↗

bioRxiv2025

Species-Specific gB Ectodomain Interactions and Cytoplasmic Domain Stability Regulate Herpes Simplex Virus Fusion

Entry of herpesviruses into cells requires coordinated action of multiple viral glycoproteins, including gH/gL and gB which comprise the core fusion machinery conserved in herpesviruses. The gH/gL heterodimer activates the gB fusion protein, triggering its refolding from a prefusion to a postfusion form to drive membrane merger. The cytoplasmic tail domain (CTD) of gB is proposed to act as an inhibitory clamp that stabilizes the prefusion state, with interactions between gH and gB CTDs destabilizing this clamp. We previously found that herpes simplex virus 1 (HSV-1) and saimiriine herpesvirus 1 (SaHV-1) gB homologs are functionally interchangeable but mediate reduced fusion when coexpressed with heterotypic gH/gL. To map the regions of gB responsible for species-specific interactions, we generated HSV-1/SaHV-1 gB chimeras by swapping ectodomain, membrane-proximal region (MPR), transmembrane domain (TMD), and CTD segments. Our results show that homotypic CTD interactions alone are insufficient to trigger fusion, suggesting that gH/gL contacts the ectodomain of gB. We show that the HSV-1 gB CTD is hyperfusogenic relative to the SaHV-1 CTD, whereas the HSV-1 MPR is hypofusogenic relative to the SaHV-1 MPR. Together, these findings suggest that functional interaction between gH/gL-gB occur on both sides of the membrane and that gB maintains a balance between promotion and restraint of fusion through coordinated contributions of its domains.

microbiology↗

bioRxiv2025

Six New Species and Two Reinstatements of Viola (Violaceae) from China

We describe six new species and reinstate two species of Viola (Violaceae) from China, based on material collected in Guangxi, Jiangxi, Hubei, and Chongqing. Field surveys, detailed morphological comparisons, and phylogenetic analyses of ITS and GPI gene sequences placed these taxa within section Plagiostigma subsections Diffusae. The GPI data provided higher resolution, revealing complex relationships and suggesting ancient hybridization or incomplete lineage sorting in subsect. Diffusae. Our findings clarify species boundaries and contribute to understanding the diversity and evolution of Viola in China.

plant biology↗

bioRxiv2025

Zyxin Restricts Viral Fusion and Entry across Multiple Virus Families

The entry of enveloped viruses into host cells requires fusion of the viral envelope with a host cell membrane. The composition and dynamics of cellular membranes are impacted by the underlying cytoskeleton. Zyxin, a cytosolic protein that bridges the actin cytoskeleton with adhesion receptor proteins, was recently identified as an antiviral factor that antagonizes HSV-1 entry. To determine if zyxin specifically interferes with membrane fusion, we examined its impact in a quantitative cell-cell fusion assay. HSV-1 entry proteins exhibited enhanced fusion activity with retinal pigment epithelial (RPE) cells when the cells were knocked out (KO) for zyxin. Zyxin-KO cells also showed enhanced fusion activity with pseudorabies virus (PRV), paramyxovirus and rhabdovirus fusion proteins. Additionally, the size of plaques formed following infection with members of each viral family were increased in the absence of zyxin. Bulk RNA sequencing of wild-type (WT) and zyxin-KO RPE cells identified 18 genes that enrich into several ontology groups of interest, including regulation of membrane potential, herpes simplex virus 1 infection (CCL2 and ZNF14), NABA core matrisome (CCL2 and ZNF14), extracellular matrix organization (CTSK, SERPINE1 and TGFB2), cell-cell adhesion (RAC2 and TGFB2), anchoring fibril formation, and regulation of the MAPK cascade (ACKR3 and TGFB2). These results highlight zyxin as a broadly active antiviral factor and suggest potential therapeutic implications for viral infections. IMPORTANCEEnveloped viruses enter host cells by fusing their envelope with a cellular membrane. This process is triggered when a viral glycoprotein(s) engages with a cellular membrane receptor. Less well understood are the cytoplasmic factors that indirectly govern viral fusion and entry. We report that zyxin, a cellular protein that bridges cell-adhesion receptors with the underlying actin cytoskeleton, antagonizes the fusion and entry of several enveloped viruses.

microbiology↗

bioRxiv2025

Procrastination partly reflects an evolutionary byproduct of non-planning impulsivity

Procrastination has immediately visible repercussions on health and survival resilience, yet shows stably heritable and remains increasingly pervasive across human societies. Despite a paradox, this behavior is theoretically explained to represent a byproduct of evolutionary advantages underlying impulsivity, yet not deciphered well by scientific evidences. After adjusting psychometric endogeneity, we demonstrate the unique predictive roles of non-planning impulsivity (NPI) during late adolescence and early adulthood uniquely predicts procrastination in later adulthood in a twin cohort (N = 154). This association was further replicated in two independent cohorts (N = 327, N = 1,543). Using AE models, in conjunction of single-paper meta-analytic synthesis (N = 3,656 twin pairs), we observed significant shared genetic contributions underlying this NPI-procrastination association (rg = 0.51, 95% CI: 0.18 - 0.84). Beyond to the phenotypic heritability, employing a Genome-Wide-Association Study (GWAS), six NPI-procrastination overlapping SNPs are identified, functionally accounting for neural dysregulation. Thus, leveraging neurodevelopmental normative modelling (N = 37,407), online meta-analytic estimations (k = 198, loci = 5,855) and seed-based d mapping estimates (N = 893), cortical deviations in the left dorsolateral prefrontal cortex (DLPFC) - the brain region showing highest probabilistic overlap mapping NPI to procrastination, partly explains their shared genetic variants, but are substantially independent in genetic contribution. Mendelian Randomization analysis finally indicates causal roles of NPI and procrastination both, to DLPFC deviations. Our findings empirically clarified this theory that procrastination partly derives from NPI as an evolutionary byproduct indeed, but is still unique in neurogenetic entities. Brief summaryProcrastination is a puzzling human behavior that compromises survival-relevant outcomes yet remains both widespread and heritable. Although theorized as a byproduct of impulsivitys evolutionary advantages, empirical support for this account has been limited. Here, we provide converging evidence across psychometric, genetic, and neuroimaging modalities to show that non-planning impulsivity during late adolescence and early adulthood uniquely predicts later procrastination, and that the two traits share significant genetic overlap. We further identify specific genetic variants and morphological deviations in the DLPFC that link, but also partially dissociate, their biological pathways. These findings clarify the evolutionary and neurogenetic architecture of procrastination and underscore its partial derivation from impulsivity alongside distinct developmental origins.

neuroscience↗

bioRxiv2025

Mapping neurogenetic characteristics of psychopathological procrastination using normative modeling in a prospective twin cohort

Procrastination, affecting over 70% global population, is pervasively incurring negative outcomes in human society. This has long been studied as a bad daily habit, but it loses in delineating neurogenetic substrates underlying its psychopathological phenotyping. Using a prospective twin adolescent cohort, we demonstrate moderate heritability of this subclinical condition - PPS. Neuroimaging normative modeling analysis, further reveals that neurodevelopmental deviations in nucleus accumbens during adolescence, are predictive of PPS in adulthood, while such deviations-PPS mappings were highly genetically shared. Beyond to regional anomalies, PPS-specific whole-brain deviation patterns, notably in the default mode network, are neurobiologically enriched with changes in cortical manifolds (gradients) and neurotransmitter systems. Integrating these neuroimaging markers with transcriptomic atlas, we capture significant PPS-specific neurogenetic signatures associated with molecular transport system, neuroimmune responses, and neuroinflammation, particularly in serotonergic and dopaminergic pathways. These findings shed light on the multisystem neurogenetic architecture underlying PPS, providing evidence to theoretically conceptualize this psychopathological phenotype as a subclinical "brain disorder". TeaserPsychopathological procrastination is not a bad daily habit solely, but a "brain disorder" associated with multiscale neurodevelopment.

neuroscience↗

bioRxiv2025

β-Glucan Modulates Monocyte Plasticity and Differentiation Capacity to Mitigate DSS-Induced Colitis

Trained immunity involves the reprogramming of innate immune cells after an initial exposure, resulting in heightened inflammatory responses to subsequent stimuli and enhanced bactericidal capacity during infection. However, this proinflammatory state could also exacerbate chronic conditions like inflammatory bowel disease (IBD), which is characterized by persistent inflammation and microbial imbalance. It remains unclear how trained immunity influences IBD pathogenesis and whether it can be harnessed therapeutically. In our study, pretreatment with {beta}-glucan reprogrammed bone marrow hematopoietic progenitors and peripheral monocytes, inducing a profound shift in monocyte plasticity and significantly reducing the severity of dextran sulfate sodium (DSS)-induced colitis. Adoptive transfer of bone marrow or peripheral monocytes from {beta}-glucan-trained mice into naive mice conferred robust protection against colitis, demonstrating that this protective effect is transferable. Trained mice also displayed improved clearance of intestinal bacterial infections. Single-cell RNA sequencing revealed an expansion of reparative Cx3cr1 macrophages derived from Ly6Chi monocytes, correlating with accelerated colonic epithelial regeneration. Collectively, these findings reveal how {beta}-glucan-induced trained immunity modulates monocyte differentiation to ameliorate experimental colitis, highlighting the potential of harnessing trained immunity as a therapeutic strategy to recalibrate innate immune responses and restore gut homeostasis in IBD, shedding light for future clinical applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/653036v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1b969c2org.highwire.dtl.DTLVardef@1ce603dorg.highwire.dtl.DTLVardef@10582forg.highwire.dtl.DTLVardef@10d7de6_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Mediator-29 Limits Caenorhabditis elegans Fecundity

Mediator is an evolutionarily conserved multiprotein complex that acts as a critical coregulator of RNA polymerase II-mediated transcription. While core Mediator components are broadly required for transcription, others govern specific regulatory modules and signalling pathways. Here, we investigated the function of MDT-29/MED29 in the Caenorhabditis elegans germ line. We found that endogenously-tagged MDT-29 is ubiquitously expressed and concentrated in discrete foci within germ cell nuclei. Functionally, depleting MDT-29 in the germ line during larval development boosted fecundity. We determined that the increase in progeny production was likely caused by a combination of an expanded germline stem cell pool and decreased germ cell apoptosis. Thus, MDT-29 may act to optimize specific gene expression programs to control distinct germ cell behaviors, providing flexibility to progeny production in certain environments.

developmental biology↗

bioRxiv2024

DeepSME: De Novo Nanopore Basecalling of Motif-insensitive DNA Methylation and Alignment-free Digital Information Decryptions at Single-Molecule Level

Hidden messages in DNA molecules by employing chemical modifications has been suggested for private data storage and transmission at high information density. However, rapidly decoding these "molecular keys" with corresponding basecallers remains challenging. We present DeepSME, a nanopore sequencing and deep-learning based framework towards single-molecule encryption, demonstrated by using 5-hydroxymethylcytosine (5hmC) substitution for individual nucleotide recognition rather than sequential interactions. This non-natural, motif-insensitive methylation disrupts ion current, resulting in a readout failure of 67.2%-100%, concealing the privacy within the DNAs. We further develop an alignment-free DeepSME basecaller as a key to reconstitute the digital information. Our three-stage training pipeline, expands k-mer size from 46 to 49, achieving over 92% precision and recall from scratch. DeepSME deciphers fully 5hmC concealed text and image within 16x coverage depth with an F1-score of 86.4%, surpassing all the state-of-the-art basecallers. Demonstrated on edge computing devices, DeepSME holds supreme potential for DNA-based private communications and broader bioengineering and medical applications.

bioinformatics↗

bioRxiv2024

Composite Hedges Nanopores: A High INDEL-Correcting Codec System for Rapid and Portable DNA Data Readout

DNA, as the origin for the genetic information flow, has also been a compelling alternative to non-volatile information storage medium. Reading digital information from this highly dense but lightweighted medium nowadays relied on conventional next-generation sequencing (NGS), which involves wash and read cycles for synchronization and the indel (insertion and deletion) errors rarely occur. However, these time-consuming cycles hinder the future of real-time data retrieval. Nanopore sequencing holds the promise to overcome the efficiency problem, but high indel error rates lead to the requirement of large amount of high-quality data for accurate readout using emerging NGS-based codec systems. Here we introduce Composite Hedges Nanopores (CHN), a nanopore-based codec scheme tailored for real-time data retrieval, capable of handling indel rates up to 15.9% and substitution rates up to 7.8%. The overall information density can be doubled from 0.59 to 1.17 by utilizing a degenerated eight-letter alphabet, where one composite strand will be projected into eight normal strands. We demonstrate that sequencing times of 20 and 120 minutes were sufficient for processing representative text and image files (7 and 115 composite strands), respectively. The time-diminishing deviations are mainly originated from the extremely uneven abundance among the composite strands (cross-group variation) as well as the huge inequality among the normal strands (in-group variation). Moreover, to achieve complete data recovery, it is estimated that text and image data require 4x and 8x physical redundancy (coverage) of composite strands, respectively. Our CHN codec system excels on both molecular design and equalized dictionary usage, laying a solid foundation for nucleic acid-based data retrieval and encoding approaching to real-time, applicable in both cloud and edge computing systems.

bioinformatics↗

bioRxiv2024

Enhanced Treatment Efficiency of Holmium:YAG Laser Lithotripsy by Using PEDOT:PSS Nanofluid

Urinary stone disease, characterized by the formation of hard mineral deposits in the urinary tract, has seen a rising prevalence in the U.S. in recent years. This condition often leads to severe pain and typically requires medical intervention. Laser lithotripsy, a minimally invasive treatment, uses laser energy to fragment urinary stones into smaller pieces, facilitating easier removal or natural passage. Among available laser technologies, the holmium:yttrium-aluminum-garnet (Ho:YAG) laser has established itself as the gold standard over the past three decades. Efforts to improve Ho:YAG laser ablation efficiency have largely focused on adjusting laser parameters such as pulse energy and frequency. In this study, we proposed a nanoplasmonic engineering strategy by incorporating nanoparticles (NPs) with strong near-infrared (NIR) absorption into the fluid surrounding the stone, enhancing the light-matter interaction. Using a 0.03 wt.% PEDOT:PSS nanofluid, stone ablation efficiency improved by 38-727% in spot treatment and 26-75% in scanning treatment with a clinical laser lithotripter. The highly absorbing nanofluid accelerates vapor tunnel formation, boosts laser energy transmission to the stone, and permeates stone pores to enhance damage, without increasing thermal tissue injury risk. Cytotoxicity tests also confirmed minimal toxicity at appropriate concentrations. This nanofluid-based approach offers a promising advancement for more efficient and safer laser lithotripsy.

bioengineering↗

bioRxiv2024

Activation of PIEZO1 Inhibits Kidney Cystogenesis

The disruption of calcium signaling associated with polycystin deficiency has been proposed as the primary event underlying the increased abnormally patterned epithelial cell growth characteristic of Polycystic Kidney Disease. Calcium can be regulated through mechanotransduction, and the mechanosensitive cation channel Piezo1 has been implicated in sensing of intrarenal pressure and in urinary osmoregulation. However, a possible role for PIEZO1 in kidney cystogenesis remains undefined. We hypothesized that cystogenesis in ADPKD reflects altered mechanotransduction, suggesting activation of mechanosensitive cation channels as a therapeutic strategy for ADPKD. Here, we show that Yoda-1 activation of PIEZO1 increases intracellular Ca2+ and reduces forskolin-induced cAMP levels in mIMCD3 cells. Yoda-1 reduced forskolin-induced IMCD cyst surface area in vitro and in mouse metanephros ex vivo in a dose-dependent manner. Knockout of polycystin-2 dampened the efficacy of PIEZO1 activation in reducing both cAMP levels and cyst surface area in IMCD3 cells. However, collecting duct-specific Piezo1 knockout neither induced cystogenesis in wild-type mice nor affected cystogenesis in the Pkd1RC/RC model of ADPKD. Our study suggests that polycystin-2 and PIEZO1 play a role in mechanotransduction during cystogenesis in vitro, and ex vivo, but that in vivo cyst expansion may require inactivation or repression of additional suppressors of cystogenesis and/or growth. Our study provides a preliminary proof of concept for PIEZO1 activation as a possible component of combination chemotherapy to retard or halt cystogenesis and/or cyst growth.

cell biology↗

bioRxiv2024

KF4 anti-CELA1 Antibody and Purified α1-Antitrypsin Have Similar but Not Additive Efficacy in Preventing Emphysema in Murine α1-Antitrypsin Deficiency

Alpha-1 antitrypsin (AAT) deficiency is the most common genetic cause of emphysema. Chymotrypsin-like Elastase 1 (CELA1) is a serine protease neutralized by AAT and is important in emphysema progression. Cela1-deficiency is protective in a murine models of AAT-deficient emphysema. KF4 anti-CELA1 antibody prevented emphysema in PPE and cigarette smoke models in wild type mice. We evaluated potential toxicities of KF4 and its ability to prevent emphysema in AAT deficiency. We found Cela1 protein expression in mouse lung, pancreas, small intestine, and spleen. In toxicity studies, mice treated with KF4 25 mg/kg weekly for four weeks showed an elevation in blood urea nitrogen and slower weight gain compared to lower doses or equivalent dose IgG. In histologic grading of tissue injury of the lung, kidney, liver, and heart, there was some evidence of liver injury with KF4 25 mg/kg, but in all tissues, injury was less than in control mice subjected to cecal ligation and puncture. In efficacy studies, KF4 doses as low as 0.5 mg/kg reduced the lung elastase activity of AAT-/-mice treated with 0.2 units of PPE. In this injury model, AAT-/-mice treated with KF4 1 mg/kg weekly, human purified AAT 60 mg/kg weekly, and combined KF4 and AAT treatment had less emphysema than mice treated with IgG 1 mg/kg weekly. However, the efficacy of KF4, AAT, or KF4 & AAT was similar. While KF4 might be an alternative to AAT replacement, combined KF4 and AAT replacement does not confer additional benefit.

pathology↗

bioRxiv2023

Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups identified to have pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model for testing the effect of reticulation on generic circumscription when hybridization and allopolyploidy define a groups evolutionary history. Here, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. The well-inferred phylogenetic backbone revealed an updated generic delimitation of Stranvaesia and a new genus, Weniomeles, characterized by purple-black fruits, trunk and/or branches with thorns, and fruit core with multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Here, we highlight a broadly-applicable workflow for inferring how analyses of reticulate evolution in phylogenomic data can directly shape taxonomic revisions.

evolutionary biology↗