Biology subjects

Harris, D. R.

Publications and source records attributed to Harris, D. R..

6 recordsLinked to original sources

bioRxiv2025

Skeletal Muscle Regeneration is Accelerated Following Injection of Time Release Ion Matrix in Injured Mice

IntroductionSkeletal muscle injury remains a significant cause of disability with limited treatment options. Here we report accelerated skeletal muscle regeneration following injection of an inorganic biomaterial alone, cobalt oxide time-release ion matrix (CoO-TRIM). MethodsThe tibialis anterior (TA) muscle of adult C57BL/6J mice was injured with 70 {micro}L of barium chloride, with uninjured limbs serving as contralateral controls. Following the acute inflammatory phase (3 days post injury, dpi), mice were randomly separated into three groups: untreated controls, 70 {micro}l sterile saline injection alone (vehicle control) or 70 {micro}l CoO-TRIM (5 {micro}g/{micro}l) and evaluated at 8- and 14 dpi. Results14 dpi, injured TA muscles receiving a single injection of CoO-TRIM exhibited greater recovery of maximal force production (means {+/-} SEM: Healthy; TRIM, 31.8 {+/-} 0.6 N/cm3; Untreated, 31.7 {+/-} 0.8 N/cm3; Saline, 31.6 {+/-} 0.8 N/cm3, Injured; TRIM, 31.8 {+/-} 0.8 N/cm3; Untreated, 26.1 {+/-} 1.1 N/cm3, P= <0.01 vs. TRIM Injured; Saline, 26.0 {+/-} 1.3 N/cm3, P= <0.01 vs. TRIM Injured), increased fiber size (Healthy; TRIM, 2466 {+/-} 128 {micro}m2 vs. Untreated, 2351 {+/-} 131 {micro}m2; vs. Saline, 2460 {+/-} 129 {micro}m2, Injured; TRIM, 2179 {+/-} 63 {micro}m2 vs. Untreated, 1525 {+/-} 52 {micro}m2, P= <0.01; vs. Saline, 1470 {+/-} 99 {micro}m2, P= <0.01), and accelerated muscle regeneration (TRIM, 32.7 {+/-} 6.8 eMyHC+ fibers/mm2 vs. Untreated, 91.8 {+/-} 11.8 eMyHC+ fibers/mm2, P= <0.01; vs. Saline, 94.0 {+/-} 9.6 eMyHC+ fibers/mm2, P= <0.01). Vascular endothelial growth factor was elevated 14 dpi (TRIM, 17.3 {+/-} 2.9 pg/mg vs. Untreated, 10.3 {+/-} 1.1 pg/mg, P= 0.04; Saline, 5.5 {+/-} 1.2 pg/mg, P= <0.01), with increased muscle microvascular area (TRIM, 119.9 {+/-} 4.2 {micro}m2/fiber vs. Untreated, 94.9 {+/-} 4.2 {micro}m2/fiber, P= <0.01; Saline, 91.3 {+/-} 4.0 {micro}m2/fiber, P= <0.01) following CoO-TRIM treatment. There were early increases in inflammatory responses 8 dpi in injured TA muscles receiving CoO-TRIM (IL-6; TRIM, 29.1 {+/-} 8.2 pg/ml vs. Untreated, 12.4 {+/-} 1.5 pg/ml, P= 0.02; Saline, 11.7 {+/-} 0.8 pg/mg, P= 0.01), with early resolution of degenerative inflammatory cytokines and elevated regenerative cytokines 14 dpi (IL-10; SEM: TRIM, 2.4 {+/-} 0.1 pg/ml vs. Untreated, 2.1 {+/-} 0.1 pg/ml, P= 0.25; Saline, 2.0 {+/-} 0.1 pg/ml, P= 0.04). No differences were observed in healthy contralateral limbs following treatment with CoO-TRIM compared to healthy control mice at 8- and 14 dpi. DiscussionThis work suggests CoO-TRIM enhances muscle regeneration following injury, possibly through an immune cell-mediated mechanism. Statement of Clinical RelevanceThis is the first report of an injected, inorganic biomaterial alone to accelerate regeneration of injured skeletal muscle with no observed effects on healthy muscle. These findings suggest enhancements to skeletal muscle regeneration following CoO-TRIM treatment may be immune cell mediated with an increased local inflammatory response and subsequent improvements to muscle microvasculature and myogenic regulatory factors.

physiology↗

bioRxiv2024

Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide

Broadly neutralizing antibodies have been proposed as templates for HIV-vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To provide insight, here we compare the recognition of naturally elicited and vaccine-elicited antibodies targeting the HIV-1-fusion peptide, which comprises envelope (Env) residues 512-526, with the most common sequence being AVGIGAVFLGFLGAA. Naturally elicited antibodies bound peptides with negative-charge substitutions around residues 517-520 substantially better than the most common sequence, despite these substitutions rarely appearing in HIV; by contrast, vaccine-elicited antibodies were less tolerant of sequence variation, with no substitution of residues 512-516 showing increased binding. Molecular dynamics analysis and cryo-EM structure of the naturally elicited ACS202 antibody in complex with HIV-Env trimer with A517E suggested enhanced binding to result from electrostatic interactions with positively charged antibody residues. Overall, vaccine-elicited antibodies appeared to be more fully optimized to bind the most common fusion peptide sequence. HIGHLIGHTSPeptide substitution scan reveals naturally elicited antibodies against fusion peptide (FP) can bind select non-canonical FP sequences with high affinity. Peptide substitution scan data for FP antibodies correlates significantly with their differential selection indicating variation in binding relates to neutralization tolerance. Structure and energetic analysis of naturally elicited ACS202 with HIV-Env trimer reveals basis for improved recognition of A517E mutant. Atomic level interactions from MD simulation analysis corroborate trends observed with peptide substitutions. verall, peptide substitution scans reveal vaccine-elicited antibodies against FP to be less permissive to FP-sequence variability than naturally elicited antibodies.

immunology↗

bioRxiv2024

HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene

Broadly neutralizing antibodies targeting the V2 apex of the HIV-1 envelope trimer are among the most common specificities elicited in HIV-1-infected humans and simian-human immunodeficiency virus (SHIV)-infected macaques. To gain insight into the prevalent induction of these antibodies, we isolated and characterized 11 V2 apex-directed neutralizing antibody lineages from SHIV-infected rhesus macaques. Remarkably, all SHIV-induced V2 apex lineages were derived from reading frame two of the rhesus DH3-15*01 gene. Cryo-EM structures of envelope trimers in complex with antibodies from nine rhesus lineages revealed modes of recognition that mimicked three canonical human V2 apex-recognition modes. Notably, amino acids encoded by DH3-15*01 played divergent structural roles, inserting into a hole at the trimer apex, H-bonding to an exposed strand, or forming part of a loop scaffold. Overall, we identify a DH3-15*01-signature for rhesus V2 apex broadly neutralizing antibodies and show that highly selected genetic elements can play multiple roles in antigen recognition. HighlightsO_LIIsolated 11 V2 apex-targeted HIV-neutralizing lineages from 10 SHIV-infected Indian-origin rhesus macaques C_LIO_LICryo-EM structures of Fab-Env complexes for nine rhesus lineages reveal modes of recognition that mimic three modes of human V2 apex antibody recognition C_LIO_LIAll SHIV-elicited V2 apex lineages, including two others previously published, derive from the same DH3-15*01 gene utilizing reading frame two C_LIO_LIThe DH3-15*01 gene in reading frame two provides a necessary, but not sufficient, signature for V2 apex-directed broadly neutralizing antibodies C_LIO_LIStructural roles played by DH3-15*01-encoded amino acids differed substantially in different lineages, even for those with the same recognition mode C_LIO_LIPropose that the anionic, aromatic, and extended character of DH3-15*01 in reading frame two provides a selective advantage for V2 apex recognition compared to B cells derived from other D genes in the naive rhesus repertoire C_LIO_LIDemonstrate that highly selected genetic elements can play multiple roles in antigen recognition, providing a structural means to enhance recognition diversity C_LI

immunology↗

bioRxiv2022

A multispecific antibody confers pan-reactive SARS-CoV-2 neutralization and prevents immune escape

Summary ParagraphDespite effective countermeasures, SARS-CoV-2 persists worldwide due to its ability to diversify and evade human immunity1. This evasion stems from amino-acid substitutions, particularly in the receptor-binding domain of the spike, that confer resistance to vaccines and antibodies 2-16. To constrain viral escape through resistance mutations, we combined antibody variable regions that recognize different receptor binding domain (RBD) sites17,18 into multispecific antibodies. Here, we describe multispecific antibodies, including a trispecific that prevented virus escape >3000-fold more potently than the most effective clinical antibody or mixtures of the parental antibodies. Despite being generated before the evolution of Omicron, this trispecific antibody potently neutralized all previous variants of concern and major Omicron variants, including the most recent BA.4/BA.5 strains at nanomolar concentrations. Negative stain electron microscopy revealed that synergistic neutralization was achieved by engaging different epitopes in specific orientations that facilitated inter-spike binding. An optimized trispecific antibody also protected Syrian hamsters against Omicron variants BA.1, BA.2 and BA.5, each of which uses different amino acid substitutions to mediate escape from therapeutic antibodies. Such multispecific antibodies decrease the likelihood of SARS-CoV-2 escape, simplify treatment, and maximize coverage, providing a strategy for universal antibody therapies that could help eliminate pandemic spread for this and other pathogens.

immunology↗

bioRxiv2022

Potent and pan-neutralization of SARS-CoV-2 variants of concern by DARPins

We report the engineering and selection of two synthetic proteins - FSR16m and FSR22 - for possible treatment of SARS-CoV-2 infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon and exhibit broad spectrum neutralization of SARS-Cov-2 strains. The IC50 values of FSR16m against authentic B.1.351, B.1.617.2 and BA.1.1 variants are 3.4 ng/mL, 2.2 ng/mL and 7.4 ng/mL, respectively, comparable to currently used therapeutic antibodies. Despite the use of the spike protein from a now historical wild-type virus for design, FSR16m and FSR22 both exhibit increased neutralization against newly-emerged variants of concern (39- to 296-fold) in pseudovirus assays. Cryo-EM structures revealed that these DARPins recognize a region of the receptor binding domain (RBD, residues 455-456, 486-489) overlapping a critical portion of the ACE2-binding surface. K18-hACE2 transgenic mice inoculated with a B.1.617.2 variant and receiving intranasally-administered FSR16m were protected as judged by less weight loss and 10-100-fold reductions in viral burden in the upper and lower respiratory tracts. The strong and broad neutralization potency make FSR16m and FSR22 promising candidates for prevention and treatment of infection by current and potential future strains of SARS-CoV-2.

bioengineering↗

bioRxiv2021

Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529

With B.1.1.529 SARS-CoV-2 variants rapid spread and substantially increased resistance to neutralization by vaccinee and convalescent sera, monoclonal antibodies with potent neutralization are eagerly sought. To provide insight into effective neutralization, we determined cryo-EM structures and evaluated potent receptor-binding domain (RBD) antibodies for their ability to bind and neutralize this new variant. B.1.1.529 RBD mutations altered 16% of the RBD surface, clustering on a ridge of this domain proximal to the ACE2-binding surface and reducing binding of most antibodies. Significant inhibitory activity was retained, however, by select monoclonal antibodies including A19-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309 and LY-CoV1404, which accommodated these changes and neutralized B.1.1.529 with IC50s between 5.1-281 ng/ml, and we identified combinations of antibodies with potent synergistic neutralization. Structure-function analyses delineated the impact of resistance mutations and revealed structural mechanisms for maintenance of potent neutralization against emerging variants. Summary SentenceWe show potent B.1.1.529 neutralization by select antibodies and use EM structures to reveal how potency can be retained.

immunology↗