IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity

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Abstract

Antibodies that neutralize SARS-CoV-2, are thought to provide the most immediate and effective treatment for those severely afflicted by this virus. Because coronavirus potentially diversifies by mutation, broadly neutralizing antibodies are especially sought. Here we report a novel approach to rapid generation of potent broadly neutralizing human anti-SARS-CoV-2 antibodies. We isolated SARS-CoV-2 Spike protein-specific memory B cells by panning from the blood of convalescent human subjects after infection with SARS-CoV-2, sequenced and expressed Ig genes from individual B cells as human monoclonal antibodies (mAbs). All of 43 human mAbs generated in this way neutralized SARS-CoV-2. Eighteen of the 43 human mAbs exhibited half-maximal inhibitory concentration (IC50s) of 6.7 x10-12 M to 6.7x10-15 M for spike pseudotyped virus. Seven of the human mAbs also neutralized with IC50<6.7 x10-12 M viruses pseudotyped with mutant spike proteins (including receptor binding domain mutants and the S1 C-terminal D614G mutant). Neutralization of the Wuhan Hu-1 founder strain and of some variants decreased when coding sequences were reverted to germline, suggesting that potency of neutralization was acquired by somatic hypermutation and selection of B cells. The results indicate that infection with SARS-CoV-2 evokes high affinity B cell responses, some products of which are broadly neutralizing and others highly strain-specific. We also identify variants that would potentially resist immunity evoked by infection with the Wuhan Hu-1 founder strain or by vaccines developed with products of that strain, suggesting evolutionary courses SARS-CoV-2 could take.

Authors

Mayara Garcia de Mattos Barbosa, Hui Liu, Daniel Huynh, Greg Shelley, Evan T. Keller, Brian T. Emmer, Emily J. Sherman, David Ginsburg, Andrew A. Kennedy, Andrew W. Tai, Christiane E. Wobus, Carmen Mirabelli, Thomas M. Lanigan, Milagros Samaniego, Wenzhao Meng, Aaron M. Rosenfeld, Eline T. Luning Prak, Jeffrey L. Platt, Marilia Cascalho

PALLD mutation in a European family conveys a stromal predisposition for familial pancreatic cancer

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Abstract

Background and aims: Pancreatic cancer is one of the deadliest cancers, still with low long term survival rates. Despite recent advances in treatment, it is extremely important to screen high-risk individuals in order to establish preventive and early detection measures and, in some cases, molecular driven therapeutic options. Familial pancreatic cancer (FPC) accounts for 4%-10% of pancreatic cancers. Several germline mutations are known to be related with an increased risk and might offer novel screening and therapy options. In this study, our goal was to discover the identity of a familial pancreatic cancer gene in two members of a family with FPC. Methods: Whole exome sequencing and PCR confirmation was performed on the surgical specimen and peripheral blood of an index patient and her sister in a family with high incidence of pancreatic cancer, to identify somatic and germline mutations associated with familial pancreatic cancer. Compartment-specific gene expression data and immunohistochemistry was used to characterize PALLD expression. Results: A germline mutation of the PALLD gene (NM_001166108.1:c.G154A:p.D52N) was detected in the index patient with pancreatic cancer. The identical PALLD mutation was identified in the tumor tissue of her sister. Whole genome sequencing showed similar somatic mutation patterns between the two sisters. Apart from the PALLD mutation, commonly mutated genes that characterize PDAC (KRAS and CDKN2A) were found in both tumor samples. However, the two patients harbored different somatic KRAS mutations (respectively G12D in the index patient and G12V in the index patient’s sister). Analysis for PALLD mutation in the healthy siblings of the two sisters was negative, indicating that the identified PALLD mutation might have a disease specific impact. Of note, compartment-specific gene expression data and IHC suggested a predominant role in cancer associated fibroblasts (CAFs). Conclusion: We identified a germline mutation of the palladin (PALLD) gene in two siblings in Europe, affected by familial pancreatic cancer, with a predominant function in the tumor stroma.

Authors

Lucia Liotta, Sebastian Lange, H. Carlo Maurer, Kenneth P. Olive, Rickmer Braren, Nicole Pfarr, Alexander Muckenhuber, Moritz Jesinghaus, Wilko Weichert, Katja Steiger, Sebastian Burger, Helmut Friess, Roland M. Schmid, Hana Alguel, Philipp Jost, Juliane Ramser, Christine Fischer, Anne S. Quante, Maximilian Reichert, Michael Quante

DMV Extrasynaptic NMDA Receptors Regulate Caloric Intake in Rats

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Abstract

Acute high fat diet (HFD) exposure induces a brief period of hyperphagia before caloric balance is restored. Previous studies have demonstrated this period of regulation is associated with activation of synaptic NMDA receptors (NMDARs) on dorsal motor nucleus of the vagus (DMV) neurons, which increases vagal control of gastric functions. Our aim was to test the hypothesis that activation of DMV NMDARs occurs subsequent to activation of extrasynaptic NMDA receptors (NMDARex). Sprague-Dawley rats were fed control or HFD for 3-5 days prior to experimentation. Whole cell patch clamp recordings from gastric-projecting DMV neurons, in vivo recordings of gastric motility, tone, compliance, and emptying, as well as food intake studies were used to assess the effects of NMDAR antagonism on caloric regulation. Following acute HFD exposure, inhibition of NMDARex prevented the NMDARs-mediated increase in glutamatergic transmission to DMV neurons, as well as the increase in gastric tone and motility, while chronic NMDARex inhibition attenuated the regulation of caloric intake. Following acute HFD exposure, the regulation of food intake involves NMDARs-mediated currents, which occur in response to NMDARex activation. Understanding these events may provide a mechanistic basis for hyperphagia and identify potential novel therapeutic targets for the treatment of obesity.

Authors

Courtney Clyburn, R. Alberto Travagli, Amy C. Arnold, Kirsteen N. Browning

Efficacy of AAV9-mediated SGPL1 gene transfer in a mouse model of S1P lyase insufficiency syndrome

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Abstract

Sphingosine-1-phosphate lyase insufficiency syndrome (SPLIS) is a rare metabolic disorder caused by inactivating mutations in SGPL1, which is required for the final step of sphingolipid metabolism. SPLIS features include steroid-resistant nephrotic syndrome (SRNS) and impairment of neurological, endocrine, and hematopoietic systems. Many affected individuals die within the first two years. No targeted therapy for SPLIS is available. We hypothesized that SGPL1 gene replacement would address the root cause of SPLIS, thereby serving as a universal treatment for the condition. As proof of concept, we evaluated the efficacy of adeno-associated virus 9-mediated transfer of human SGPL1 (AAV-SPL) given to newborn Sgpl1 KO mice that model SPLIS and die in the first weeks of life. Treatment dramatically prolonged survival and prevented nephrosis, neurodevelopmental delay, anemia, and hypercholesterolemia. STAT3 pathway activation and elevated pro-inflammatory and fibrogenic cytokines observed in KO kidneys were attenuated by treatment. Plasma and tissue sphingolipids were reduced in treated compared to untreated KO pups. SGPL1 expression and activity were measurable for at least 40 weeks. In summary, early AAV-SPL treatment prevents nephrosis, lipidosis and neurological impairment in a mouse model of SPLIS. Our results suggest that SGPL1 gene replacement holds promise as a durable and universal targeted treatment for SPLIS.

Authors

Piming Zhao, Gizachew B. Tassew, Joanna Y. Lee, Babak Oskouian, Denise P. Muñoz, Jeffrey B. Hodgin, Gordon L. Watson, Felicia Tang, Jen-Yeu Wang, Jinghui Luo, Yingbao Yang, Sarah M. King, Ronald M. Krauss, Nancy Keller, Julie D. Saba

Importance of lymph node immune responses in MSI-H/dMMR colorectal cancer

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Abstract

Patients with colorectal cancers (CRCs) generally exhibit improved survival through intensive lymph node (LN) dissection. However, recent progress in cancer immunotherapy revisits the potential importance of regional LNs, where T cells are primed to attack tumor cells. To elucidate the role of regional LN, we investigated the immunological status of non-metastatic regional LN lymphocytes (LNLs) in comparison with those in the tumor microenvironment (tumor-infiltrating lymphocytes; TILs) using flow cytometry and next-generation sequencing. LNLs comprised an intermediate level of the effector T cell population between peripheral blood lymphocytes (PBLs) and TILs. Significant overlap of the T-cell receptor (TCR) repertoire was observed in microsatellite instability-high (MSI-H)/mismatch repair deficient (dMMR) CRCs with high tumor mutation burden (TMB), although limited TCRs were shared between non-metastatic LNs and primary tumors in microsatellite stable (MSS)/MMR proficient (pMMR) CRC patients with low TMB. In line with the overlap of the TCR repertoire, an excessive LN dissection did not provide a positive impact on long-term prognosis in our MSI-H/dMMR CRC cohort (n =130). We propose that regional LNs play an important role in antitumor immunity, particularly in MSI-H/dMMR CRCs with high TMB, requiring to be careful of excessive non-metastatic LN dissection in MSI-H/dMMR CRC patients.

Authors

Koji Inamori, Yosuke Togashi, Shota Fukuoka, Kiwamu Akagi, Kouetsu Ogasawara, Takuma Irie, Daisuke Motooka, Yoichi Kobayashi, Daisuke Sugiyama, Motohiro Kojima, Norihiko Shiiya, Shota Nakamura, Shoichi Maruyama, Yutaka Suzuki, Masaaki Ito, Hiroyoshi Nishikawa

LIN28B induces a differentiation program through CDX2 in colon cancer

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Abstract

Most colorectal cancers (CRCs) are moderately-differentiated or well-differentiated, a status that is preserved even in metastatic tumors. However, the molecular mechanisms underlying CRC differentiation remain to be elucidated. Herein, we unravel a novel post-transcriptional regulatory mechanism via a previously unappreciated LIN28B-CDX2 signaling axis that plays a critical role in mediating CRC differentiation. Owing to a large number of mRNA targets, the mRNA-binding protein LIN28B has diverse functions in development, metabolism, tissue regeneration and tumorigenesis. Our RNA-binding protein immunoprecipitation (RIP) assay revealed LIN28B directly binds CDX2 mRNA, which is a pivotal homeobox transcription factor in normal intestinal epithelial cell identity and differentiation. Furthermore, LIN28B overexpression results in enhanced CDX2 expression to promote both differentiation in subcutaneous xenograft tumors generated from CRC cells and metastatic tumor colonization through mesenchymal-epithelial transition in CRC liver metastasis mouse models. Chromatin immunoprecipitation (ChIP) sequence for CDX2 identified Alpha-Methylacyl-CoA racemase (AMACR) as a novel transcriptional target of CDX2 in the context of LIN28B overexpression. We also found AMACR enhances intestinal alkaline phosphatase (ALPi) activity, which is known as a key component of intestinal differentiation, through the upregulation of butyric acid. Overall, we demonstrate that LIN28B promotes CRC differentiation through CDX2-AMACR axis.

Authors

Kensuke Suzuki, Yasunori Masuike, Rei Mizuno, Uma M Sachdeva, Priya Chatterji, Sarah F. Andres, Wenping Sun, Andres J Klein-Szanto, Sepideh Besharati, Helen E Remotti, Michael P Verzi, Anil K. Rustgi

REP1-deficiency causes systemic dysfunction of lipid metabolism and oxidative stress in choroideremia

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Abstract

Choroideremia (CHM) is a X-linked recessive chorioretinal dystrophy caused by mutations in CHM, encoding for Rab escort protein 1 (REP1). Loss of functional REP1 leads to the accumulation of unprenylated Rab proteins and defective intracellular protein trafficking, the putative cause for photoreceptor, retinal pigment epithelium (RPE) and choroidal degeneration. CHM is ubiquitously expressed, but adequate prenylation is considered to be achieved, outside the retina, through the isoform REP2. Recently, the possibility of systemic features in CHM has been debated, hence, in this study whole metabolomic analysis of plasma samples from 25 CHM patients versus age and gender matched controls was performed. Results showed plasma alterations in oxidative stress-related metabolites, coupled with alterations in tryptophan metabolism leading to significantly raised serotonin levels. Lipid metabolism was disrupted with decreased branched fatty acids and acylcarnitines, suggestive of dysfunctional lipid oxidation, and imbalances of several sphingolipids and glycerophospholipids. Targeted lipidomics of the chmru848 zebrafish provided further evidence for dysfunction, with the use of Fenofibrates over Simvastatin circumventing the prenylation pathway to improve the lipid profile and increase survival. This study provides strong evidence for systemic manifestations of CHM and proposes novel pathomechanisms and targets for therapeutic consideration.

Authors

Dulce Lima Cunha, Rose Richardson, Dhani Tracey-White, Alessandro Abbouda, Andreas Mitsios, Verena Horneffer-van der Sluis, Panteleimon Takis, Nicholas Owen, Jane Skinner, Ailsa A. Welch, Mariya Moosajee

Patterns and persistence of SARS-CoV-2 IgG antibodies in Chicago to monitor COVID-19 exposure

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Abstract

Background: Estimates of seroprevalence to SARS-CoV-2 vary widely and may influence vaccination response. We ascertained IgG levels across a single US metropolitan site, Chicago, from June 2020 through December 2020. Methods: Participants (n=7935) were recruited through electronic advertising and received materials for a self-sampled dried blood spot assay through the mail or a minimal contact in person method. IgG to the receptor binding domain of SARS-CoV-2 was measured using an established highly sensitive and highly specific assay. Results: Overall seroprevalence was 17.9%, with no significant difference between method of contact. Only 2.5% of participants reported having had a diagnosis of COVID-19 based on virus detection, consistent with a 7-fold greater exposure to SARS-CoV-2 measured by serology than detected by viral testing. The range of IgG level observed in seropositive participants from this community survey overlapped with the range of IgG levels associated with COVID-19 cases having a documented positive PCR positive test. From a subset of those who participated in repeat testing, half of seropositive individuals retained detectable antibodies for 3-4 months. Conclusions: Quantitative IgG measurements with a highly specific and sensitive assay indicate more widespread exposure to SARS-CoV-2 than observed by viral testing. The range of IgG concentration produced from these asymptomatic exposures is similar to IgG levels occurring after documented non-hospitalized COVID-19, which is considerably lower than that produced from hospitalized COVID-19 cases. The differing ranges of IgG response, coupled with the rate of decay of antibodies, may influence response to subsequent viral exposure and vaccine.

Authors

Alexis R. Demonbreun, Thomas W. McDade, Lorenzo L. Pesce, Lauren A. Vaught, Nina L. Reiser, Elena Bogdanovic, Matthew P. Velez, Ryan R. Hsieh, Lacy M. Simons, Rana Saber, Daniel T. Ryan, Michael G. Ison, Judd F. Hultquist, John T. Wilkins, Richard T. D'Aquila, Brian Mustanski, Elizabeth M. McNally

Identification of a novel series of hair-cell MET channel blockers that protect against aminoglycoside-induced ototoxicity

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Abstract

To identify small molecules that shield mammalian sensory hair cells from the ototoxic side effects of aminoglycoside antibiotics we screened 10,240 compounds, selecting those that protected against neomycin and gentamicin in zebrafish lateral-line hair cells and, when retested in mouse cochlear cultures, prevented gentamicin-induced death of outer hair cells (OHCs). Of 64 compounds that protected zebrafish hair cells, 8 protect OHCs from gentamicin in vitro. These hits share structural features and all block, to varying degrees, the OHC’s mechano-electrical transducer (MET) channel, a known route of aminoglycoside entry into hair cells. Further characterisation of one of the strongest MET-channel blockers, UoS-7692, revealed it additionally protects against kanamycin and tobramycin, and does not abrogate the bactericidal activity of gentamicin. UoS-7692 behaves, like the aminoglycosides, as a permeant blocker of the MET channel, significantly reduces gentamicin-Texas Red loading into OHCs, and preserves lateral-line function in neomycin-treated zebrafish. Trans-tympanic injection of UoS-7692 protects mouse OHCs from furosemide-kanamycin exposure in vivo and partially preserves hearing. The results confirm the hair-cell MET channel as a viable target for the identification of compounds that protect the cochlea from aminoglycosides, and provide a series of hit compounds that will inform the design of future otoprotectants.

Authors

Emma J. Kenyon, Nerissa K. Kirkwood, Siân R. Kitcher, Richard J. Goodyear, Marco Derudas, Daire M. Cantillon, Sarah Baxendale, Antonio de la Vega de León, Virginia N. Mahieu, Richard T. Osgood, Charlotte Donald Wilson, James C. Bull, Simon J. Waddell, Tanya T. Whitfield, Simon E. Ward, Corné J. Kros, Guy P. Richardson.

Gut-derived acetate promotes B10 cells with anti-inflammatory effects

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Abstract

Autoimmune diseases are characterized by a breakdown of immune tolerance partly due to environmental factors. The short-chain fatty acid acetate, derived mostly from gut microbial fermentation of dietary fiber, promotes anti-inflammatory regulatory T cells and protects mice from type 1 diabetes, colitis and allergies. Here, we show that the effects of acetate extend to another important immune subset involved in tolerance, the IL-10 producing regulatory B cells (B10 cells). Acetate directly promoted B10 cell differentiation from mouse B1a cells both in vivo and in vitro. These effects were linked to metabolic changes through the increased production of acetyl-CoA, which fueled the tricarboxylic acid cycle and promoted post-translational lysine acetylation. Acetate also promoted B10 cells from human blood cell through similar mechanisms. Finally, we identified that dietary fiber supplementation in healthy individuals was associated with increased blood B10 cells. Direct delivery of acetate or indirectly via acetate-producing diets or -bacteria might be a promising approach to restore B10 cells in non-communicable diseases.

Authors

Claire I. Daïen, Jian Tan, Rachel Audo, Julie Mielle, Lake-Ee Quek, James R. Krycer, Alexandra S. Angelatos, Martha Duares, Gabriela V. Pinget, Duan Ni, Remy Robert, Md Jahangir Alam, Carmen Balguerías Amián, Frederic Sierro, Arvind Parmar, Gary J. Perkins, Sumaiya Hoque, Alison K. Gosby, Stephen J. Simpson, Rosilene V. Ribeiro, Charles R. Mackay, Laurence Macia