Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes.

Development of vaccines and therapeutics that are broadly effective against known and emergent coronaviruses is an urgent priority. Current strategies for developing pan-coronavirus countermeasures have largely focused on the receptor binding domain (RBD) and S2 regions of the coronavirus Spike protein; it has been unclear whether the N-terminal domain (NTD) is a viable target for universal vaccines and broadly neutralizing antibodies (Abs). Additionally, many RBD-targeting Abs have proven susceptible to viral escape. We screened the circulating B cell repertoires of COVID-19 survivors and vaccinees using multiplexed panels of uniquely barcoded antigens in a high-throughput single cell workflow to isolate over 9,000 SARS-CoV-2-specific monoclonal Abs (mAbs), providing an expansive view of the SARS-CoV-2-specific Ab repertoire. We observed many instances of clonal coalescence between individuals, suggesting that Ab responses frequently converge independently on similar genetic solutions. Among the recovered antibodies was TXG-0078, a public neutralizing mAb that binds the NTD supersite region of the coronavirus Spike protein and recognizes a diverse collection of alpha- and beta-coronaviruses. TXG-0078 achieves its exceptional binding breadth while utilizing the same VH1-24 variable gene signature and heavy chain-dominant binding pattern seen in other NTD supersite-specific neutralizing Abs with much narrower specificity. We also report the discovery of CC24.2, a pan-sarbecovirus neutralizing mAb that targets a novel RBD epitope and shows similar neutralization potency against all tested SARS-CoV-2 variants, including BQ.1.1 and XBB.1.5. A cocktail of TXG-0078 and CC24.2 provides protection against in vivo challenge with SARS-CoV-2, suggesting potential future use in variant-resistant therapeutic Ab cocktails and as templates for pan-coronavirus vaccine design.

Functional antibodies exhibit light chain coherence.

The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1-CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2-22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.

Computational and ¹³C investigations of the diazadienes and oxazadienes formed via the rearrangement of methylenecyclopropyl hydrazones and oximes.

Computational and further experimental investigations of the previously reported diazadienes, obtained via the rearrangement of methylenecyclopropyl hydrazone 1 are reported. Calculations at the CCSD(T)/cc-pVTZ//B3LYP/6-31G(d) level of theory indicate that the initially reported product 3 would, if formed, undergo rapid electrocyclic ring opening and, hence, would be unstable under the reaction conditions. Based on this computational prediction, further analysis of the (13)C NMR spectrum, previously attributed to 3, led to the revision of structure 3 to that of its N-tosylaminopyrrole constitutional isomer 11. Similarly, structure 8, formed in the rearrangement of oxime 6, was revised to that of N-hydroxypyrrole 12.

Adenosine signaling promotes regeneration of pancreatic ß cells in vivo.

Diabetes can be controlled with insulin injections, but a curative approach that restores the number of insulin-producing ß cells is still needed. Using a zebrafish model of diabetes, we screened ~7,000 small molecules to identify enhancers of ß cell regeneration. The compounds we identified converge on the adenosine signaling pathway and include exogenous agonists and compounds that inhibit degradation of endogenously produced adenosine. The most potent enhancer of ß cell regeneration was the adenosine agonist 5'-N-ethylcarboxamidoadenosine (NECA), which, acting through the adenosine receptor A2aa, increased ß cell proliferation and accelerated restoration of normoglycemia in zebrafish. Despite markedly stimulating ß cell proliferation during regeneration, NECA had only a modest effect during development. The proliferative and glucose-lowering effect of NECA was confirmed in diabetic mice, suggesting an evolutionarily conserved role for adenosine in ß cell regeneration. With this whole-organism screen, we identified components of the adenosine pathway that could be therapeutically targeted for the treatment of diabetes.

Dachshund homologues play a conserved role in islet cell development.

All metazoans use insulin to control energy metabolism, but they secrete it from different cells: neurons in the central nervous system in invertebrates and endocrine cells in the gut or pancreas in vertebrates. Despite their origins in different germ layers, all of these insulin-producing cells share common functional features and gene expression patterns. In this study, we tested the role in insulin-producing cells of the vertebrate homologues of Dachshund, a transcriptional regulator that marks the earliest committed progenitors of the neural insulin-producing cells in Drosophila. Both zebrafish and mice expressed a single dominant Dachshund homologue in the pancreatic endocrine lineage, and in both species loss of this homologue reduced the numbers of all islet cell types including the insulin-producing ß-cells. In mice, Dach1 gene deletion left the pancreatic progenitor cells unaltered, but blocked the perinatal burst of proliferation of differentiated ß-cells that normally generates most of the ß-cell mass. In ß-cells, Dach1 bound to the promoter of the cell cycle inhibitor p27Kip1, which constrains ß-cell proliferation. Taken together, these data demonstrate a conserved role for Dachshund homologues in the production of insulin-producing cells.

Feeding and metabolism in mice lacking pituitary adenylate cyclase-activating polypeptide.

Disruption of the pituitary adenylate cyclase-activating polypeptide (PACAP) gene in mice has demonstrated a role for this highly conserved neuropeptide in the regulation of metabolism and temperature control. Localization of PACAP neurons within hypothalamic nuclei that regulate appetite suggest PACAP may affect feeding and thus energy balance. We used PACAP-null mice to address this question, examining both food intake and energy expenditure. PACAP-null mice were leaner than wild-type littermates due to decreased adiposity and displayed increased insulin sensitivity. The lean phenotype in the PACAP-null mice was completely eliminated if animals were fed a high-fat diet or housed near thermoneutrality (28 C). Further metabolic analyses of PACAP-null mice housed at 21 C indicated that the reduced body weight could not be explained by decreased food intake, increased metabolic rate, or increased locomotor activity. The thyroid hormone axis of PACAP-null mice was affected, because mRNA levels of hypothalamic TRH and brown adipose tissue type 2 deiodinase were reduced in PACAP-null mice housed at room temperature, and brain deiodinase activity was lower in PACAP-null mice after an acute cold challenge compared with wild-type controls. These results demonstrate that PACAP is not required for the regulation of food intake yet is necessary to maintain normal energy homeostasis, likely playing a role in central cold-sensing mechanisms.

Knocked down and out: PACAP in development, reproduction and feeding.

One approach to understanding the role of PACAP in vivo is to knockdown the translation of PACAP mRNA to protein or to knock out the PACAP gene by targeted disruption. In this paper, we review the effect of PACAP knockdown with morpholinos on early brain development in zebrafish. Also reviewed is the role of PACAP at several stages of reproduction as assessed in mice with a disrupted PACAP gene. New data are presented to analyze PACAP's action in energy homeostasis (body mass, food intake, endocrine parameters) using female PACAP-null mice. The evidence suggests PACAP is important for brain development in zebrafish and is required for normal reproduction, but not for body mass or food intake in mice maintained near thermoneutrality.

Role of two genes encoding PACAP in early brain development in zebrafish.

To study the role of pituitary adenylate cyclase-activating polypeptide (PACAP) in early brain development, we examined PACAP and its receptors for first expression and then separately knocked down the two forms of PACAP in zebrafish where development is rapid and observable. We injected morpholinos (antisense oligonucleotides) into fertilized eggs to block PACAP. Morphological changes in the brain were observed in embryos at 27 h post fertilization (hpf). Using in situ hybridization of early brain marker genes, we found that the most striking effects were an increase in pax2.1 expression in eye stalks associated with absence of either form of PACAP or an increase in eng2 and fgf8 in the midbrain-hindbrain boundary after loss of PACAP2. These marker genes are among the earliest factors in the formation of the midbrain-hindbrain boundary, an early organizing center. We suggest that PACAP is a target gene with feedback inhibition on pax2.1, eng2, or fgf8 in specific brain areas. In the hindbrain, the absence of either form of PACAP had little effect, as shown by expression of ephA4 and meis1.1. During midbrain development, our evidence suggests that PACAP1 can activate mbx. In both the diencephalon and/or forebrain, lack of PACAP1 or PACAP2 led to an increase in fgf8, again suggesting a suppressive effect of PACAP during development on these important genes that help to define cells in the forebrain. The early expression of transcripts for PACAP and its receptors by 0.5-6 hpf make both PACAP1 and PACAP2 candidates for factors that influence brain development.

Contaminant effects on the teleost fish thyroid.

Numerous environmentally relevant chemicals, including polychlorinated hydrocarbons, polycyclic aromatic hydrocarbons, organochlorine pesticides, chlorinated paraffins, organophosphorous pesticides, carbamate pesticides, cyanide compounds, methyl bromide, phenols, ammonia, metals, acid loads, sex steroids, and pharmaceuticals, exert acute or chronic effects on the thyroid cascade in the approximately 40 teleost fish species tested to date. Thyroid endpoints, therefore, serve as biomarkers of exposure to environmental pollutants. However, the mechanisms underlying thyroid changes and their physiological consequences are poorly understood because the thyroid cascade may respond indirectly and it has considerable capacity to compensate for abuses that otherwise would disrupt thyroid hormone homeostasis. Indeed, a xenobiotic-induced change in fish thyroid function has yet to be conclusively causally linked to decreased fitness or survival. Other complications in interpretation arise from the diversity of test conditions employed and the often indiscriminate use of numerous thyroid endpoints. Future work should be directed toward standardizing test conditions and thyroid endpoints and investigating causal links between thyroid changes and fish growth, reproduction, and development. Development may be particularly susceptible to thyroid disruption, and thyroid endpoints appropriate for early life stages need to be applied.

Cloning and localization of three forms of gonadotropin-releasing hormone, including the novel whitefish form, in a salmonid, Coregonus clupeaformis.

Cells containing different GnRH peptides currently are thought to have distinct locations and functions in the brain. Lake whitefish is the first salmonid species to have three forms of GnRH peptide in contrast to later-evolving salmonids (salmon and trout) in which only two forms have been identified. Our objective was to isolate the cDNAs that code for these transcripts and to localize the transcripts for the three forms of GnRH in adult lake whitefish brain. Also, we provide phylogenetic analysis of these three whitefish genes based on their preprohormone sequence. From whitefish we isolated cDNAs encoding chicken (c)GnRH-II, salmon (s)GnRH, and the novel whitefish (wf)GnRH. The three cDNAs each encode only one GnRH and are placed in separate groups with phylogenetic analysis. A combination of in situ hybridization and immunocytochemistry with two antisera revealed neurons that expressed protein and/or mRNA for cGnRH-II in the midbrain and hindbrain; sGnRH in the olfactory nerve and bulb, ventral telencephalon, and preoptic area; and wfGnRH in the same latter two brain regions and the hypothalamus. Thus, in the anterior brain, cells containing sGnRH and wfGnRH were in the same brain areas but not at identical locations in the ventral telencephalon and preoptic area. Based on our results, we speculate that both sGnRH and wfGnRH have gonadotropin-releasing roles in the lake whitefish brain.

Six novel gonadotropin-releasing hormones are encoded as triplets on each of two genes in the protochordate, Ciona intestinalis.

GnRH is the key regulator of the reproductive axis in vertebrates, but little is known about GnRH before the origin of vertebrates. We have identified two genes encoding GnRH in a protochordate, Ciona intestinalis, thought to be related to the ancestral animal that gave rise to vertebrates. Each gene, Ci-gnrh1 and Ci-gnrh2, encodes in tandem three GnRH peptides, each of which is unique compared with known forms. Ci-gnrh1 encodes three peptides and contains no introns, whereas Ci-gnrh2 encodes three more peptides but has two introns. This is the first report in which more than one GnRH peptide is encoded on a single gene. The Ciona genes reveal consensus promoter elements that are conserved compared with human GNRH1. Both tunicate genes are expressed as mRNA early and throughout development, measured at the stages of four-cell, gastrulation, tail release, and tail resorption. In a closely related tunicate species, Ciona savignyi, we used in silico analysis to identify two similar genes encoding six peptides, only one of which is unique compared with C. intestinalis. Immunohistochemistry showed that at least one GnRH peptide was in the nerve net that surrounds the dorsal strand. Synthetic forms of the seven novel tunicate peptides induced release of gametes in adult tunicates. In contrast, the peptides did not activate the human GnRH-I receptor or cause release of LH in a rat pituitary cell assay. These data provide insight into the structural evolution of the GnRH peptides and their genes and show a functional role for GnRH in tunicate spawning.

Pituitary adenylate cyclase-activating polypeptide and growth hormone-releasing hormone-like peptide in sturgeon, whitefish, grayling, flounder and halibut: cDNA sequence, exon skipping and evolution.

To better understand the evolution of pituitary adenylate cyclase-activating polypeptide (PACAP) and growth hormone-releasing hormone (GHRH), we isolated the cDNAs encoding these peptides from the brains of five species of fish: sturgeon, whitefish, grayling, flounder and halibut. Both hormones are encoded in tandem in full-length cDNAs. We compared the phylogenetic relationship among these and other known sequences encoding PACAP. In closely related species, transcripts encoding PACAP and GHRH are strongly conserved in the hormone coding regions, moderately conserved in the signal peptide, cryptic peptide and 3'-untranslated regions, but are most varied in the 5'-untranslated regions.Next, we compared the deduced amino acid sequences for the peptides to known sequences. Sturgeon and whitefish have a PACAP(38) peptide sequence that is 92% conserved compared to human PACAP(38), the highest for a fish reported to date. GHRH is the lesser conserved of the two peptides with only 39% to 45% conservation between fish and human.Each of the five fish species had a second cDNA encoding a short precursor lacking GHRH(1-32), the bioactive portion of GHRH. This suggests that exon skipping in GHRH-PACAP transcripts may be an important mechanism for regulating the ratio of PACAP to GHRH peptides.

Transcription and translation of the salmon gonadotropin-releasing hormone genes in brain and gonads of sexually maturing rainbow trout (Oncorhynchus mykiss).

Rainbow trout sexually mature at the end of Year 3. The form of GnRH that controls gonadotropin release in trout is salmon GnRH (sGnRH). In the tetraploid rainbow trout, two genes encode an identical sGnRH peptide. The sGnRH gene-1 produces one mRNA, whereas sGnRH gene-2 can produce more than one. This study asks whether the transcripts and their protein products are expressed in the brain and gonads and whether the pattern correlates with sexual maturity over the final year leading to first spawning. Brain sGnRH mRNA and protein were continuously present throughout the third year. We show for the first time that the long sGnRH-2 mRNA transcript is expressed in neural tissue and not exclusively in gonadal tissue. Expression of the long sGnRH-2 mRNA in the brain coincides with high levels of sGnRH peptide in the brain during a time of increased gonadal growth. Thus, the long sGnRH-2 mRNA in the brain may act to regulate sGnRH production in a stage-specific rather than a tissue-specific manner. In gonads, local sGnRH is thought to play an autocrine/paracrine role in regulating gonadal maturation and spawning. In the maturing gonads, sGnRH gene-1 and -2 are expressed intermittently. Strikingly, sGnRH peptide was not detected in the gonads at any time during Year 3. These results suggest that either the sGnRH transcripts in the gonads are not translated into protein or, if translated, the protein is rapidly released, resulting in gonadal content below 1 fM per fish.

Three forms of gonadotropin-releasing hormone, including a novel form, in a basal salmonid, Coregonus clupeaformis.

Multiple forms of GnRH within individual brains may have different functions. However, some vertebrates such as salmonids continue to reproduce even though they have lost or do not express 1 of the 3 forms of GnRH found in most other teleosts. We examined a basal salmonid, lake whitefish, to determine the mechanism by which a reduction in the number of GnRH forms occurs. We identified for the first time 3 distinct GnRHs in a salmonid. One form is novel and is designated whitefish GnRH. The primary structure is pGlu-His-Trp-Ser-Tyr-Gly-Met-Asn-Pro-Gly-NH(2). HPLC and RIA were used for purification followed by Edman degradation for sequence determination. Mass spectroscopy was used to confirm the sequence and amidation of the peptide. The other 2 forms, salmon GnRH and chicken GnRH-II, are identical to the 2 forms found in salmon, which evolved later than whitefish. Synthetic whitefish GnRH is biologically active, as it increased mRNA expression of growth hormone and the alpha-subunit for LH and thyroid-stimulating hormone in dispersed fish pituitary cells. Our data support the hypothesis that the ancestral salmonid had a third GnRH form when the genome doubled (tetraploidization), but the third form was lost later in some salmonids due to chromosomal rearrangements. We suggest that the salmon GnRH form compensated for the loss of the third form.