Biology subjects

Knox, K.

Publications and source records attributed to Knox, K..

7 recordsLinked to original sources

bioRxiv2026

Proteome-wide discovery of novel diagnostic antigens for coccidioidomycosis

Coccidioidomycosis, commonly called Valley Fever (VF), caused by Coccidioides spp., is an understudied fungal disease that accounts for a substantial fraction of pneumonias in endemic areas. Diagnosis remains challenging because the mainstay of diagnosis is serology, and current assays have modest sensitivity in early infection. Discovery of new antigens could improve serologic detection early in disease. Here, we use PepSeq, a DNA-programmable serology platform, to represent the complete proteome of Coccidioides within a library of 244,000 DNA-barcoded peptides. By profiling antibody reactivity at the protein and epitope levels in VF patients, naturally infected pigtail macaques, and healthy controls, we identify numerous previously-unrecognized antigens and epitopes, including some shared between humans and macaque responses. When translated into a pooled peptide ELISA, we show that a subset of identified antigens can discriminate VF cases from controls in an independent cohort with high accuracy (AUC = 0.91). These findings establish high-dimensional peptide serology as a scalable approach for fungal antigen discovery and identify new targets for improved VF diagnosis.

immunology↗

bioRxiv2026

A Humanized Mouse Model of DRPLA Recapitulates Epilepsy and Demonstrates Antisense Oligonucleotide-Mediated Disease Modification

Dentatorubral-pallidoluysian atrophy (DRPLA) is an ultra-rare progressive myoclonus epilepsy caused by a glutamine-coding CAG repeat expansion in atrophin-1 (ATN1). Mutant ATN1 (mATN1) expression results in symptoms that inversely correlate to CAG-expansion size: young-onset cases have the most CAG repeats and developmental delay, high-frequency treatment-resistant seizures, and early mortality. We sought to characterize the seizure susceptibility of a fully humanized ATN1 mouse expressing human mATN1 with 112 CAG repeats to then assess therapeutic antisense oligonucleotide (ASO) intervention on seizure-related outcomes. Atn1Q112/+ or wild-type (WT) mice were treated with investigational ASO targeting human, CAG-expanded, ATN1 or saline (P2 and then again at 4 weeks-old) before acute seizure testing, ataxia profiling, and chronic in vivo video-EEG recording for spontaneous seizures up to 8 weeks-old. Saline-treated Atn1Q112/+ mice were more seizure prone with early death. However, ASO administration to Atn1Q112/+ mice normalized seizure threshold, decreased ataxia, and protected against early death. Atn1Q112/+ mice exhibited spontaneous behavioral seizures recorded over 2 weeks, which were absent in ASO-treated Atn1Q112/+ and WT mice, with a specific mATN1 expression-driven decrease in delta and theta EEG frequencies. Atn1Q112/+ mice are highly seizure prone, validating this model for DRPLA epilepsy. ATN1 represents a novel epilepsy-related risk factor for therapeutic investigation.

neuroscience↗

bioRxiv2024

Alzheimer's disease-associated genotypes differentially influence chronic evoked seizure outcomes and antiseizure medicine activity in aged mice

Structured AbstractO_ST_ABSINTRODUCTIONC_ST_ABSAlzheimers disease (AD) patients are at greater risk of focal seizures than similarly aged adults; these seizures, left untreated, may worsen functional decline. Older people with epilepsy generally respond well to antiseizure medications (ASMs). However, whether specific ASMs can differentially control seizures in AD is unknown. The corneal kindled mouse model of acquired chronic secondarily generalized focal seizures allows for precisely timed drug administration studies to quantify the efficacy and tolerability of ASMs in an AD-associated genetic model. We hypothesized that mechanistically distinct ASMs would exert differential anticonvulsant activity and tolerability in aged AD mice (8-15 months) to define whether rational ASM selection may benefit specific AD genotypes. METHODSAged male and female PSEN2-N141I versus age-matched non-transgenic control (PSEN2 control) C57Bl/6J mice, and APPswe/PS1dE9 versus transgene negative (APP control) littermates underwent corneal kindling to quantify latency to fully kindled criterion. Dose-related ASM efficacy was then compared in each AD model versus matched control over 1-2 months using ASMs commonly prescribed in older adults with epilepsy: valproic acid, levetiracetam, lamotrigine, phenobarbital, and gabapentin. RESULTSSex and AD genotype differentially impacted seizure susceptibility. Male PSEN2-N141I mice required more stimulations to attain kindling criterion (X2=5.521; p<0.05). Male APP/PS1 mice did not differ in kindling rate versus APP control mice, but they did have more severe seizures. There were significant ASM class-specific differences in acute seizure control and dose-related tolerability. APP/PS1 mice were more sensitive than APP controls to valproic acid, levetiracetam, and gabapentin. PSEN2-N141I mice were more sensitive than PSEN2 controls to valproic acid and lamotrigine. DISCUSSIONAD genotypes may differentially impact ASMs activity and tolerability in vivo with advanced biological age. These findings highlight the heterogeneity of seizure risk in AD and suggest that precisely selected ASMs may beneficially control seizures in AD, thus reducing functional decline.

neuroscience↗

bioRxiv2023

E2F1 Mediates SOX17 Deficiency-Induced Pulmonary Hypertension

RationaleRare genetic variants and genetic variation at loci in an enhancer in SRY-Box Transcription Factor 17 (SOX17) are identified in patients with idiopathic pulmonary arterial hypertension (PAH) and PAH with congenital heart disease. However, the exact role of genetic variants or mutation in SOX17 in PAH pathogenesis has not been reported. ObjectivesTo investigate the role of SOX17 deficiency in pulmonary hypertension (PH) development. MethodsHuman lung tissue and endothelial cells (ECs) from IPAH patients were used to determine the expression of SOX17. Tie2Cre-mediated and EC-specific deletion of Sox17 mice were assessed for PH development. Single-cell RNA sequencing analysis, human lung ECs, and smooth muscle cell culture were performed to determine the role and mechanisms of SOX17 deficiency. A pharmacological approach was used in Sox17 deficiency mice for therapeutic implication. Measurement and Main ResultsSOX17 expression was downregulated in the lungs and pulmonary ECs of IPAH patients. Mice with Tie2Cre mediated Sox17 knockdown and EC-specific Sox17 deletion developed spontaneously mild PH. Loss of endothelial Sox17 in EC exacerbated hypoxia-induced PH in mice. Loss of SOX17 in lung ECs induced endothelial dysfunctions including upregulation of cell cycle programming, proliferative and anti-apoptotic phenotypes, augmentation of paracrine effect on pulmonary arterial smooth muscle cells, impaired cellular junction, and BMP signaling. E2F Transcription Factor 1 (E2F1) signaling was shown to mediate the SOX17 deficiency-induced EC dysfunction and PH development. ConclusionsOur study demonstrated that endothelial SOX17 deficiency induces PH through E2F1 and targeting E2F1 signaling represents a promising approach in PAH patients.

physiology↗

bioRxiv2022

T-cell cellular stress and reticulocyte signatures, but not loss of naive T lymphocytes, characterize severe COVID-19 in older adults

In children and younger adults up to 39 years of age, SARS-CoV-2 usually elicits mild symptoms that resemble the common cold. Disease severity increases with age starting at 30 and reaches astounding mortality rates that are ~330 fold higher in persons above 85 years of age compared to those 18-39 years old. To understand age-specific immune pathobiology of COVID-19 we have analyzed soluble mediators, cellular phenotypes, and transcriptome from over 80 COVID-19 patients of varying ages and disease severity, carefully controlling for age as a variable. We found that reticulocyte numbers and peripheral blood transcriptional signatures robustly correlated with disease severity. By contrast, decreased numbers and proportion of naive T-cells, reported previously as a COVID-19 severity risk factor, were found to be general features of aging and not of COVID-19 severity, as they readily occurred in older participants experiencing only mild or no disease at all. Single-cell transcriptional signatures across age and severity groups showed that severe but not moderate/mild COVID-19 causes cell stress response in different T-cell populations, and some of that stress was unique to old severe participants, suggesting that in severe disease of older adults, these defenders of the organism may be disabled from performing immune protection. These findings shed new light on interactions between age and disease severity in COVID-19.

immunology↗

bioRxiv2020

Intranasal Administration of ACIS KEPTIDE™ Prevents SARS-CoV2-Induced Acute Toxicity in K18-hACE2 Humanized Mouse Model of COVID-19: A Mechanistic Insight for the Prophylactic Role of KEPTIDE™ in COVID-19

Previously, we have demonstrated that ACIS KEPTIDE, a chemically modified peptide, selectively binds to ACE-2 receptor and prevents the entry of SARS-CoV2 virions in vitro in primate kidney Cells. However, it is not known if ACIS KEPTIDE attenuates the entry of SARS-CoV2 virus in vivo in lung and kidney tissues, protects health, and prevent death once applied through intranasal route. In our current manuscript, we demonstrated that the intranasal administration of SARS-CoV2 (1*106) strongly induced the expression of ACE-2, promoted the entry of virions into the lung and kidney cells, caused acute histopathological toxicities, and mortality (28%). Interestingly, thirty-minutes of pre-treatment with 50 g/Kg Body weight ACIS normalized the expression of ACE-2 via receptor internalization, strongly mitigated that viral entry, and prevented mortality suggesting its prospect as a prophylactic therapy in the treatment of COVID-19. On the contrary, the peptide backbone of ACIS was unable to normalize the expression of ACE-2, failed to improve the health vital signs and histopathological abnormalities. In summary, our results suggest that ACIS is a potential vaccine-alternative, prophylactic agent that prevents entry of SARS-CoV2 in vivo, significantly improves respiratory health and also dramatically prevents acute mortality in K18-hACE2 humanized mice. HighlightsO_LIACIS KEPTIDE stimulates the internalization of ACE-2 receptor (Fig. 2) and buffers the membrane localization of ACE-2 receptors (Fig. 2, 6 & 8). Intranasal inoculation of SARS-CoV2 upregulates the expression of ACE-2 in lung epithelium (Fig.6) and kidney tubular cells (Fig.8). ACIS KEPTIDE normalizes the expression of ACE-2 in the kidney tubular cells of virus-treated K18-hACE2mice (Fig. 8). C_LIO_LIACIS KEPTIDE completely prevents the entry of SARS-CoV2 in Bronchiolar epithelium (Fig.6), alveolar parenchyma (Fig. 6), and kidney tubular cells (Fig.8). C_LIO_LIACIS KEPTIDE improves the pulmonary (Fig. 5) and renal pathological changes (Fig. 7) caused by the SARS-CoV2 virus insult. C_LIO_LIIntranasal administration of 0.05% Beta-propiolactone ({beta}PL)-inactivated SARS-CoV2 (1 *106) causes significant death (28%) in K18-hACE2 humanized mice after 24 hrs of intranasal inoculation (Supplemental videos) suggesting that SARS-CoV2 does not require its infective properties and genetic mechanism to be functional to cause mortality. C_LIO_LIThe peptide backbone of ACIS KEPTIDE provides much less and insignificant protection in the prevention of pathological changes in Lungs (Fig.5 & 6) and Kidney (Fig.7 & 8). Peptide failed to normalize the upscaled expression of ACE-2 in kidney tubular cells (Fig.8) of SARS-CoV2-treated K18-hACE2 mice. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/378257v1_fig2.gif" ALT="Figure 2"> View larger version (51K): org.highwire.dtl.DTLVardef@15c9911org.highwire.dtl.DTLVardef@453819org.highwire.dtl.DTLVardef@65f8a0org.highwire.dtl.DTLVardef@a602d8_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2.C_FLOATNO Effect of KEPTIDE on the Expression of ACE-2 Receptor on the Membrane of CALU-3 Human Lung Cells. Human lung epithelial cells. CALU-3 cells were grown in complete DMEM cells for 2 days until it reached 70% confluency followed by starving with serum for 2 hrs. After that, 25 M of ACIS KEPTIDE were treated for 30 mins, 1 hr, 2 hrs and 6 hrs. After each time point cells were fixed and stained for ACE-2 (Green; Rabbit anti-ACE-2 antibody; Abcam; 1:250 dilution) and KEPTIDE (blue). Thirty minutes of KEPTIDE treatment significantly stimulated the internalization of ACE-2 along with KEPTIDE. Subsequent incubation periods displayed significant down-regulation of ACE-2 receptors. Experiments were confirmed after three different experiments. C_FIG O_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC="FIGDIR/small/378257v1_fig6.gif" ALT="Figure 6"> View larger version (98K): org.highwire.dtl.DTLVardef@104bd7forg.highwire.dtl.DTLVardef@34ecc1org.highwire.dtl.DTLVardef@a3ac74org.highwire.dtl.DTLVardef@18f0570_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 6.C_FLOATNO Protective effect of ACIS KEPTIDE on the expression of ACE-2 and the entry of SARS-CoV2 virions in lung of SARS-CoV2-insulted K18-hACE2 mice. (A-D) Dual IHC staining of ACE-2 (red) and SARS-CoV2 (brown) in bronchiolar epithelium in (A) vehicle-treated (0.05% PL-inactivated VEROE6 sup, (B)virus, (C) virus + KEPTIDE, and (D) virus + peptide-treated K18-hACE2 mice (n= 7-8). (a-h) Magnified views of outer layers and inner layers of bronchiolar epithelia of respective images enclosed in a dotted squares. Arrows were justified in the bottom of each image. Results are confirmed after three independent experiments. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/378257v1_fig8.gif" ALT="Figure 8"> View larger version (87K): org.highwire.dtl.DTLVardef@ae105aorg.highwire.dtl.DTLVardef@1b39472org.highwire.dtl.DTLVardef@d6e3e9org.highwire.dtl.DTLVardef@ce6d6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 8.C_FLOATNO Protective effect of ACIS KEPTIDE on the expression of ACE-2 and prevention of SARS-CoV2 entry in kidney of K18-hACE2 mice twenty-four hours post SARS-CoV2 inoculation. Eight to ten weeks old K18-hACE2 mice (n=7-8 per group) were intranasally administered with 50 g/kg Bwt KEPTIDE or 50 g/kg Bwt peptide for 30 mins followed by inoculation with PL-inactivated 1*106 virus. In group1 mice (n=8) were inoculated with vehicle only (0.05% PL-treated VEROE6 sup); in group 2, mice (n=7) were treated with virus only (0.05% PL-inactivated; in group 3, mice (n=8) were treated with virus +KEPTIDE; and, in group 4 mice (n=8) were treated with virus + PEPTIDE. (Results are confirmed after three independent experiments. (A-D) Dual IHC of ACE-2 (red) and SARS-CoV2 (brown) in tubular epithelium in (A) vehicle, (B) Virus, (C) Virus + KEPTIDE-, and (D) Virus + peptide-treated groups. (a) showed magnified view of kidney cortex vehicle-treated mouse with basal expression of ACE-2 (red), (b) magnified view of kidney of virus-tread animal. Upscaled expression of ACE-2(red) with degenerated Bowmans capsule and invasion of SARS CoV2 (Brown arrow). (c) Magnified view of Glomerulus of Virus + KEPTIDE-treated group. Significantly less ACE-2 expression (red arrow) and no virus-infiltration were noted. (d) Elevated expression of ACE-2 in virus +Peptide-treated group. Results were confirmed after three different experiments in 7-8 animals. C_FIG O_FIG O_LINKSMALLFIG WIDTH=190 HEIGHT=200 SRC="FIGDIR/small/378257v1_fig5.gif" ALT="Figure 5"> View larger version (123K): org.highwire.dtl.DTLVardef@1072b3aorg.highwire.dtl.DTLVardef@1a70702org.highwire.dtl.DTLVardef@bd227corg.highwire.dtl.DTLVardef@12335bd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 5.C_FLOATNO ACIS KEPTIDE protects acute histopathological changes in Lungs of K18-hACE2 mice twenty-four hours post SARS-CoV2 inoculation. Eight to ten weeks old K18-hACE2 mice (n=7-8 per group) were intranasally administered with 50 g/kg Bwt KEPTIDE or 50 g /kg Bwt peptide for 30 mins followed by inoculation with PL-inactivated 1*106 virus. In group1 mice (n=8) were inoculated with vehicle only (0.05% PL-treated media); in group 2, mice (n=7 were treated with virus only (0.05% PL-inactivated; in group 3, mice (n=8) were treated with virus +KEPTIDE; and, in group 4 mice (n=8) were treated with virus + PEPTIDE. (A-D) Hematoxylin Background staining of small airway alveolar parenchyma. (E-H) H & E staining of Bronchiolar epithelium, surrounding cartilaginous and alveolar parenchyma. Magnified views of bronchiolar epithelia of (Ei) Control (orange arrow indicates intact epithelial lining: orange star demonstrates preserved connective tissue), (Fii) Virus only (thin red arrow indicates the degenerated bronchiolar epithelium), (Giii) Virus + KEPTIDE (thin blue arrow indicates protected epithelium), and (Hiv) Virus + Peptide-treated (thin green arrow indicates degenerated epithelium). Results are confirmed after three different experiments in 7-8 animals. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/378257v1_fig7.gif" ALT="Figure 7"> View larger version (150K): org.highwire.dtl.DTLVardef@9d3c17org.highwire.dtl.DTLVardef@d40a51org.highwire.dtl.DTLVardef@f17652org.highwire.dtl.DTLVardef@8f3230_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 7.C_FLOATNO Effect of ACIS KEPTIDE on the protection of acute histopathological changes in Kidney of K18-hACE2 mice twenty-four hours post SARS-CoV2 inoculation. Eight to ten weeks old K18-hACE2 mice (n=7-8 per group) were intranasally administered with 50 g/kg Bwt KEPTIDE or 50 g/kg Bwt peptide for 30 mins followed by inoculation with PL-inactivated 1*106 virus. In group1 mice (n=8) were inoculated with vehicle only (0.05% PL-treated VEROE6 sup); in group 2, mice (n=7) were treated with virus only (0.05% PL-inactivated; in group 3, mice (n=8) were treated with virus +KEPTIDE; and, in group 4 mice (n=8) were treated with virus + PEPTIDE. (A-D) H & E staining of kidney cortex with detailed structures of glomeruli, tubular epithelium, and Bowmans capsule in all 4 groups. Results are confirmed after three independent experiments. C_FIG

animal behavior and cognition↗

bioRxiv2020

ACIS, A Novel KepTide™, Binds to ACE-2 Receptor and Inhibits the Infection of SARS-CoV2 Virus in vitro in Primate Kidney Cells: Therapeutic Implications for COVID-19

Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome (SARS) caused by a virus known as SARS-Coronavirus 2 (SARS-CoV2). Without a targeted-medicine, this disease has been causing a massive humanitarian crisis not only in terms of mortality, but also imposing a lasting damage to social life and economic progress of humankind. Therefore, an immediate therapeutic strategy needs to be intervened to mitigate this global crisis. Here, we report a novel KepTide (Knock-End Peptide) therapy that nullifies SARS-CoV2 infection. SARS-CoV2 employs its surface glycoprotein "spike" (S-glycoprotein) to interact with angiotensin converting enzyme-2 (ACE-2) receptor for its infection in host cells. Based on our in-silico-based homology modeling study validated with a recent X-ray crystallographic structure (PDB ID:6M0J), we have identified that a conserved motif of S-glycoprotein that intimately engages multiple hydrogen-bond (H-bond) interactions with ACE-2 enzyme. Accordingly, we designed a peptide, termed as ACIS (ACE-2 Inhibitory motif of Spike), that displayed significant affinity towards ACE-2 enzyme as confirmed by biochemical assays such as BLItz and fluorescence polarization assays. Interestingly, more than one biochemical modifications were adopted in ACIS in order to enhance the inhibitory action of ACIS and hence called as KEpTide. Consequently, a monolayer invasion assay, plaque assay and dual immunofluorescence analysis further revealed that KEpTide efficiently mitigated the infection of SARS-CoV2 in vitro in VERO E6 cells. Finally, evaluating the relative abundance of ACIS in lungs and the potential side-effects in vivo in mice, our current study discovers a novel KepTide therapy that is safe, stable, and robust to attenuate the infection of SARS-CoV2 virus if administered intranasally.

biochemistry↗