HRD1-mediated METTL14 degradation regulates m6A mRNA modification to suppress ER proteotoxic liver disease.

Accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) lumen triggers an unfolded protein response (UPR) for stress adaptation, the failure of which induces cell apoptosis and tissue/organ damage. The molecular switches underlying how the UPR selects for stress adaptation over apoptosis remain unknown. Here, we discovered that accumulation of unfolded/misfolded proteins selectively induces N6-adenosine-methyltransferase-14 (METTL14) expression. METTL14 promotes C/EBP-homologous protein (CHOP) mRNA decay through its 3' UTR N6-methyladenosine (m6A) to inhibit its downstream pro-apoptotic target gene expression. UPR induces METTL14 expression by competing against the HRD1-ER-associated degradation (ERAD) machinery to block METTL14 ubiquitination and degradation. Therefore, mice with liver-specific METTL14 deletion are highly susceptible to both acute pharmacological and alpha-1 antitrypsin (AAT) deficiency-induced ER proteotoxic stress and liver injury. Further hepatic CHOP deletion protects METTL14 knockout mice from ER-stress-induced liver damage. Our study reveals a crosstalk between ER stress and mRNA m6A modification pathways, termed the ERm6A pathway, for ER stress adaptation to proteotoxicity.

Hepatic SEL1L-HRD1 ER-associated degradation regulates systemic iron homeostasis via ceruloplasmin.

Iron homeostasis is critical for cellular and organismal function and is tightly regulated to prevent toxicity or anemia due to iron excess or deficiency, respectively. However, subcellular regulatory mechanisms of iron remain largely unexplored. Here, we report that SEL1L-HRD1 protein complex of endoplasmic reticulum (ER)-associated degradation (ERAD) in hepatocytes controls systemic iron homeostasis in a ceruloplasmin (CP)-dependent, and ER stress-independent, manner. Mice with hepatocyte-specific Sel1L deficiency exhibit altered basal iron homeostasis and are sensitized to iron deficiency while resistant to iron overload. Proteomics screening for a factor linking ERAD deficiency to altered iron homeostasis identifies CP, a key ferroxidase involved in systemic iron distribution by catalyzing iron oxidation and efflux from tissues. Indeed, CP is highly unstable and a bona fide substrate of SEL1L-HRD1 ERAD. In the absence of ERAD, CP protein accumulates in the ER and is shunted to refolding, leading to elevated secretion. Providing clinical relevance of these findings, SEL1L-HRD1 ERAD is responsible for the degradation of a subset of disease-causing CP mutants, thereby attenuating their pathogenicity. Together, this study uncovers the role of SEL1L-HRD1 ERAD in systemic iron homeostasis and provides insights into protein misfolding-associated proteotoxicity.

Unique molecular signatures sustained in circulating monocytes and regulatory T cells in convalescent COVID-19 patients.

Over two years into the COVID-19 pandemic, the human immune response to SARS-CoV-2 during the active disease phase has been extensively studied. However, the long-term impact after recovery, which is critical to advance our understanding SARS-CoV-2 and COVID-19-associated long-term complications, remains largely unknown. Herein, we characterized single-cell profiles of circulating immune cells in the peripheral blood of 100 patients, including convalescent COVID-19 and sero-negative controls. Flow cytometry analyses revealed reduced frequencies of both short-lived monocytes and long-lived regulatory T (Treg) cells within the patients who have recovered from severe COVID-19. sc-RNA seq analysis identifies seven heterogeneous clusters of monocytes and nine Treg clusters featuring distinct molecular signatures in association with COVID-19 severity. Asymptomatic patients contain the most abundant clusters of monocytes and Tregs expressing high CD74 or IFN-responsive genes. In contrast, the patients recovered from a severe disease have shown two dominant inflammatory monocyte clusters featuring S100 family genes: one monocyte cluster of S100A8 & A9 coupled with high HLA-I and another cluster of S100A4 & A6 with high HLA-II genes, a specific non-classical monocyte cluster with distinct IFITM family genes, as well as a unique TGF-ß high Treg Cluster. The outpatients and seronegative controls share most of the monocyte and Treg clusters patterns with high expression of HLA genes. Surprisingly, while presumably short-lived monocytes appear to have sustained alterations over 4 months, the decreased frequencies of long-lived Tregs (high HLA-DRA and S100A6) in the outpatients restore over the tested convalescent time (≥ 4 months). Collectively, our study identifies sustained and dynamically altered monocytes and Treg clusters with distinct molecular signatures after recovery, associated with COVID-19 severity.

HRD1-ERAD controls production of the hepatokine FGF21 through CREBH polyubiquitination.

The endoplasmic reticulum-associated protein degradation (ERAD) is responsible for recognizing and retro-translocating protein substrates, misfolded or not, from the ER for cytosolic proteasomal degradation. HMG-CoA Reductase (HMGCR) Degradation protein-HRD1-was initially identified as an E3 ligase critical for ERAD. However, its physiological functions remain largely undefined. Herein, we discovered that hepatic HRD1 expression is induced in the postprandial condition upon mouse refeeding. Mice with liver-specific HRD1 deletion failed to repress FGF21 production in serum and liver even in the refeeding condition and phenocopy the FGF21 gain-of-function mice showing growth retardation, female infertility, and diurnal circadian behavior disruption. HRD1-ERAD facilitates the degradation of the liver-specific ER-tethered transcription factor CREBH to downregulate FGF21 expression. HRD1-ERAD catalyzes polyubiquitin conjugation onto CREBH at lysine 294 for its proteasomal degradation, bridging a multi-organ crosstalk in regulating growth, circadian behavior, and female fertility through regulating the CREBH-FGF21 regulatory axis.

The existence and stability of spikes in the one-dimensional Keller-Segel model with logistic growth.

It is well known that Keller-Segel models serve as a paradigm to describe the self aggregation phenomenon, which exists in a variety of biological processes such as wound healing, tumor growth, etc. In this paper, we study the existence of monotone decreasing spiky steady state and its linear stability property in the Keller-Segel model with logistic growth over one-dimensional bounded domain subject to homogeneous Neumann boundary conditions. Under the assumption that chemo-attractive coefficient is asymptotically large, we construct the single boundary spike and next show this non-constant steady state is locally linear stable via Lyapunov-Schmidt reduction method. As a consequence, the multi-symmetric spikes are obtained by reflection and periodic extension. In particular, we present the formal analysis to illustrate our rigorous theoretical results.

Endoplasmic Reticulum Stress Signaling and the Pathogenesis of Hepatocarcinoma.

Hepatocellular carcinoma (HCC), also known as hepatoma, is a primary malignancy of the liver and the third leading cause of cancer mortality globally. Although much attention has focused on HCC, its pathogenesis remains largely obscure. The endoplasmic reticulum (ER) is a cellular organelle important for regulating protein synthesis, folding, modification and trafficking, and lipid metabolism. ER stress occurs when ER homeostasis is disturbed by numerous environmental, physiological, and pathological challenges. In response to ER stress due to misfolded/unfolded protein accumulation, unfolded protein response (UPR) is activated to maintain ER function for cell survival or, in cases of excessively severe ER stress, initiation of apoptosis. The liver is especially susceptible to ER stress given its protein synthesis and detoxification functions. Experimental data suggest that ER stress and unfolded protein response are involved in HCC development, aggressiveness and response to treatment. Herein, we highlight recent findings and provide an overview of the evidence linking ER stress to the pathogenesis of HCC.

Distinct Clinical Characteristics and Risk Factors for Mortality in Female Inpatients With Coronavirus Disease 2019 (COVID-19): A Sex-stratified, Large-scale Cohort Study in Wuhan, China.

BACKGROUND: As the coronavirus disease 2019 (COVID-19) outbreak accelerates worldwide, it is important to evaluate sex-specific clinical characteristics and outcomes, which may affect public health policies. METHODS: Patients with COVID-19 admitted to Tongji Hospital between 18 January and 27 March 2020 were evaluated. Clinical features, laboratory data, complications, and outcomes were compared between females and males. Risk factors for mortality in the whole population, females, and males were determined respectively. RESULTS: There were 1667 (50.38%) females among the 3309 patients. The mortality rate was 5.9% in females but 12.7% in males. Compared with males, more females had no initial symptoms (11.1% vs 8.3%, P = .008). Complications including acute respiratory distress syndrome, acute kidney injury, septic shock, cardiac injury, and coagulation disorder were less common in females; critical illness was also significantly less common in females (31.1% vs 39.4%, P < .0001). Significantly fewer females received antibiotic treatment (P = .001), antiviral therapy (P = .025), glucocorticoids treatment (P < .0001), mechanical ventilation (P < .0001), and had intensive care unit admission (P < .0001). A lower risk of death was found in females (OR, .44; 95% CI, .34-.58) after adjusting for age and coexisting diseases. Among females, age, malignancy, chronic kidney disease, and days from onset to admission were significantly associated with mortality, while chronic kidney disease was not a risk factor in males. CONCLUSIONS: Significantly milder illness and fewer deaths were found in female COVID-19 inpatients and risk factors associated with mortality varied among males and females.

USP22 deficiency leads to myeloid leukemia upon oncogenic Kras activation through a PU.1-dependent mechanism.

Ras mutations are commonly observed in juvenile myelomonocytic leukemia (JMML) and chronic myelomonocytic leukemia (CMML). JMML and CMML transform into acute myeloid leukemia (AML) in about 10% and 50% of patients, respectively. However, how additional events cooperate with Ras to promote this transformation are largely unknown. We show that absence of the ubiquitin-specific peptidase 22 (USP22), a component of the Spt-Ada-GCN5-acetyltransferase chromatin-remodeling complex that is linked to cancer progression, unexpectedly promotes AML transformation in mice expressing oncogenic KrasG12D/+ USP22 deficiency in KrasG12D/+ mice resulted in shorter survival compared with control mice. This was due to a block in myeloid cell differentiation leading to the generation of AML. This effect was cell autonomous because mice transplanted with USP22-deficient KrasG12D/+ cells developed an aggressive disease and died rapidly. The transcriptome profile of USP22-deficient KrasG12D/+ progenitors resembled leukemic stem cells and was highly correlated with genes associated with poor prognosis in AML. We show that USP22 functions as a PU.1 deubiquitylase by positively regulating its protein stability and promoting the expression of PU.1 target genes. Reconstitution of PU.1 overexpression in USP22-deficient KrasG12D/+ progenitors rescued their differentiation. Our findings uncovered an unexpected role for USP22 in Ras-induced leukemogenesis and provide further insights into the function of USP22 in carcinogenesis.

JAK1-mediated Sirt1 phosphorylation functions as a negative feedback of the JAK1-STAT3 pathway.

The type III NAD-dependent histone deacetylase Sirt1 plays important roles in a variety of pathobiological functions through targeting either the acetylated histones or transcription factors. However, the molecular mechanisms underlying how the Sirt1 functions are regulated remain vague. Herein we identified that the Janus kinase 1 (JAK1) interacts with Sirt1 and catalyzes its phosphorylation at the tyrosine residues of 280 and 301, both of which are highly conserved and located in the histone deacetylase catalytic domain of Sirt1. IL-6 stimulation enhanced Sirt1 interaction with JAK1 and JAK1-mediated Sirt1 phosphorylation. Interestingly, JAK1-mediated Sirt1 phosphorylation did not alter Sirt1 deacetylase catalytic activity, but instead it is required for Sirt1 interaction with the downstream transcription factor STAT3. JAK1-mediated phosphorylation enhanced Sirt1 suppression of STAT3 acetylation and transcriptional activity. As a consequence, Sirt1 activation attenuates IL-6 activity in protecting cancer cells from chemotherapeutic drug-induced apoptosis. Our studies identify JAK1 as a previously unappreciated tyrosine kinase of Sirt1 and reveal a novel negative feedback of the JAK1-STAT3 pathway.

Correction to: Plexin-B1 silencing inhibits ovarian cancer cell migration and invasion.

Following publication of the original article [1], the authors reported the following error is the article.

Co-infections of HPV16/18 with other high-risk HPV types and the risk of cervical carcinogenesis: A large population-based study.

OBJECTIVE: Human papillomavirus (HPV) 16/18 genotyping is an effective method for triage of high-risk (hr) HPV-positive women in primary hrHPV screening for cervical cancer. The present study aimed to evaluate whether co-infected with other hrHPV types will affect the risk of cervical carcinogenesis in HPV16/18 positive women. METHODS: A total of 313,704 women aged ≥30 years were screened in China. Among them, 4,933 HPV16/18-positive participants underwent colposcopy-directed biopsy. The HPV genotypes were identified using the Cobas HPV genotyping system. Multinomial logistic regression was used to model different HPV16/18 infection patterns. RESULTS: The overall prevalence rates of hrHPV and HPV16/18 were 7.85% (24,456/311,382) and 1.95% (6,086/311,382) respectively. Among HPV16/18 positive individuals, 33.24% (2,023/6,086) were co-infection with multiple types. Of the 4933 women who underwent colposcopy, their HPV16/18 infection patterns were as follows: 52.38% (2,584/4,933) HVP16 only, 23.54% (1,161/4,933) HPV16 + other hrHPVs, 14.98% (739/4,933) HPV18 only, 6.83% (337/4,933) HPV18 + other hrHPVs, 1.13% (56/4,933) HPV16 + 18, 1.13% (56/4,933) HPV16 + 18+other hrHPVs. After adjusting for cofactors, compared with single HPV16 infection, the risk of developing cervical intraepithelial neoplasia (CIN) grade 3 or greater (CIN3+) was significantly lower in HPV16 + other hrHPVs group (odds ratio [OR] = 0.637, 95% confidence interval [CI] = 0.493-0.822). CONCLUSION: HPV16/18 co-infection with other hrHPVs is a common phenomenon. Different HPV16/18 infection patterns may influence the risk of cervical carcinogenesis. HPV16 co-infected with other hrHPVs appears to have a lower associated risk of CIN3+ in ≥30 years old women.

Association of age and viral factors with high-risk HPV persistence: A retrospective follow-up study.

OBJECTIVE: Cervical HR-HPV persistence is the main risk factor for cervical cancer. We aimed to investigate the association of age and viral factors with HR-HPV persistence. METHODS: From 2010 to 2017, 343,128 women underwent 390,411 tests performed by the Cervista HR-HPV assay (Data C3) and 157,123 women underwent 206,505 tests performed by the GenoArray HR-HPV assay (Data G14) in nine medical centers located in central and eastern China. We combined the test results and identified 9234 HPV-specific baseline-negative records for time-to-event analyses. The study endpoint event was defined as clearance of type/group-specific HPV. Therefore, hazard ratio (HR) < 1 indicated a higher risk of HPV persistence, which is contrary to the common meaning of HR. RESULTS: The median persistence time was 375 and 541.5 days for Data C3 and Data G14, respectively. For every 5-year increase in age, a 15% (95% confidence interval [CI], 11%-19%) decrease in the clearance rate was observed only after 400 days of infection. For each additional co-infected HPV, the HR was 1.80 (95% CI, 1.63-1.97) on infection initiation but decreased by 22% (95% CI, 18%-26%) every 100 days. The HR of infection recurrence was 0.48 (95% CI, 0.32-0.72). The findings were consistent across different populations and test methods and were robust in sensitivity analysis. CONCLUSIONS: We found a time-dependent association of age and viral factors with HPV clearance. Older age reduced HPV clearance only after 400 days of infection. Co-infection promoted HPV clearance in the beginning, but the effect attenuated and reversed as infection persisted. Recurrent same-type infection cleared slower than the previous one.

A Novel Near-Infrared Fluorescent Probe TMTP1-PEG4-ICG for in Vivo Tumor Imaging.

Molecular imaging agents are considered to be promising tracers for tumor imaging and guided therapy. TMTP1 was screened through the FliTrx bacterial peptide display system in our laboratory previously and shown to specifically target to primary tumors and metastatic foci. In this study, small peptide TMTP1 was designed to conjugate to a near-infrared fluorescent agent ICG derivative ICG-OSu through PEG4, forming the novel probe TMTP1-PEG4-ICG. It was successfully synthesized and certified. CCK-8 assay showed that it was nontoxic to normal cells and cancerous cells. Dynamics study indicated that the probe was cleared through the liver-intestine and kidney-bladder pathway. Tumor targeting capability of this probe in vitro was evaluated on 4T1, SiHa, HeLa, S12, and HaCaT cells by flow cytometry. In vivo imaging of 4T1 and HeLa tumor-bearing mice further identified the tumor homing ability. As we had expected, the probe showed excellent affinity to cancer cells not only in vitro but also in vivo, whether in murine tumor or humanized tumor. In conclusion, TMTP1-PEG4-ICG demonstrated ideal imaging effects on tumor-bearing mice model, providing new opportunities for tumor diagnostic or guiding resection.

Stabilizing a homoclinic stripe.

For a large class of reaction-diffusion systems with large diffusivity ratio, it is well known that a two-dimensional stripe (whose cross-section is a one-dimensional homoclinic spike) is unstable and breaks up into spots. Here, we study two effects that can stabilize such a homoclinic stripe. First, we consider the addition of anisotropy to the model. For the Schnakenberg model, we show that (an infinite) stripe can be stabilized if the fast-diffusing variable (substrate) is sufficiently anisotropic. Two types of instability thresholds are derived: zigzag (or bending) and break-up instabilities. The instability boundaries subdivide parameter space into three distinct zones: stable stripe, unstable stripe due to bending and unstable due to break-up instability. Numerical experiments indicate that the break-up instability is supercritical leading to a 'spotted-stripe' solution. Finally, we perform a similar analysis for the Klausmeier model of vegetation patterns on a steep hill, and examine transition from spots to stripes.This article is part of the theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 2)'.

The GTPase-activating protein GIT2 protects against colitis by negatively regulating Toll-like receptor signaling.

G protein-coupled receptor kinase-interactor 2 (GIT2) regulates thymocyte positive selection, neutrophil-direction sensing, and cell motility during immune responses by regulating the activity of the small GTPases ADP ribosylation factors (Arfs) and Ras-related C3 botulinum toxin substrate 1 (Rac1). Here, we show that Git2-deficient mice were more susceptible to dextran sodium sulfate (DSS)-induced colitis, Escherichia coli, or endotoxin-shock challenge, and a dramatic increase in proinflammatory cytokines was observed in Git2 knockout mice and macrophages. GIT2 is a previously unidentified negative regulator of Toll-like receptor (TLR)-induced NF-κB signaling. The ubiquitination of TNF receptor associated factor 6 (TRAF6) is critical for the activation of NF-κB. GIT2 terminates TLR-induced NF-κB and MAPK signaling by recruiting the deubiquitinating enzyme Cylindromatosis to inhibit the ubiquitination of TRAF6. Finally, we show that the susceptibility of Git2-deficient mice to DSS-induced colitis depends on TLR signaling. Thus, we show that GIT2 is an essential terminator of TLR signaling and that loss of GIT2 leads to uncontrolled inflammation and severe organ damage.

Smad4 is required for the development of cardiac and skeletal muscle in zebrafish.

Transforming growth factor-beta (TGF-beta) regulates cellular functions and plays key roles in development and carcinogenesis. Smad4 is the central intracellular mediator of TGF-beta signaling and plays crucial roles in tissue regeneration, cell differentiation, embryonic development, regulation of the immune system and tumor progression. To clarify the role of smad4 in development, we examined both the pattern of smad4 expression in zebrafish embryos and the effect of smad4 suppression on embryonic development using smad4-specific antisense morpholino-oligonucleotides. We show that smad4 is expressed in zebrafish embryos at all developmental stages examined and that embryonic knockdown of smad4 results in pericardial edema, decreased heartbeat and defects in the trunk structure. Additionally, these phenotypes were associated with abnormal expression of the two heart-chamber markers, cmlc2 and vmhc, as well as abnormal expression of three makers of myogenic terminal differentiation, mylz2, smyhc1 and mck. Furthermore, a notable increase in apoptosis was apparent in the smad4 knockdown embryos, while no obvious reduction in cell proliferation was observed. Collectively, these data suggest that smad4 plays an important role in heart and skeletal muscle development.

Safety of ovarian preservation in women with stage I and II cervical adenocarcinoma: a retrospective study and meta-analysis.

BACKGROUND: The safety of ovarian preservation remains uncertain in women with cervical adenocarcinoma and significant risk factors for ovarian metastases vary among different studies. OBJECTIVE: We sought to evaluate the impact of ovarian preservation on prognosis in women with cervical adenocarcinoma and to assess clinical factors associated with ovarian metastases. STUDY DESIGN: A retrospective study of 194 women with cervical adenocarcinoma was conducted and 159 women were followed up until the end of the study. To compare the impact of ovarian preservation on prognosis, women with successful follow-up were studied, including 33 women with ovarian preservation and 126 women who underwent bilateral salpingo-oophorectomy. For women who underwent radical hysterectomy, pelvic lymphadenectomy, and bilateral salpingo-oophorectomy, the risk factors for ovarian metastases were identified. A meta-analysis of the literature was carried out to further validate the findings. RESULTS: There was no significant difference in survival between women with bilateral salpingo-oophorectomy and ovarian preservation (P = .423 for disease-free survival; P = .330 for overall survival). Tumor size (>4 cm), deep cervical stromal invasion, and lymph node metastasis were significant independent prognostic factors related to poor disease-free survival, and lymph node metastasis was significantly associated with overall survival. Of 153 women with cervical adenocarcinoma who underwent bilateral salpingo-oophorectomy, a significant difference was found in the relationship between ovarian metastasis and deep cervical stromal invasion, lymph node metastasis, and parametrial invasion. The meta-analysis showed that clinical stage IIB vs I-IIA (odds ratio, 4.64; 95% confidence interval, 2.11-10.23), deep stromal invasion (odds ratio, 10.63; 95% confidence interval, 3.12-36.02), lymph node metastasis (odds ratio, 8.54; 95% confidence interval, 4.15-17.57), corpus uteri invasion (odds ratio, 7.39; 95% confidence interval, 3.69-14.78), and parametrial invasion (odds ratio, 9.72; 95% confidence interval, 4.67-20.22) were significantly related to ovarian metastasis. CONCLUSION: Ovarian preservation has no effect on prognosis in women with early-stage cervical adenocarcinoma. Risk factors for ovarian metastases were stage IIB, deep cervical stromal invasion, lymph node metastasis, corpus uteri invasion, and parametrial invasion. In women with early-stage cervical adenocarcinoma without these risk factors, ovarian conservation can be considered.

On De Giorgi's conjecture and beyond.

We consider the problem of existence of entire solutions to the Allen-Cahn equation Δu + u - u(3) = 0 in , usually regarded as a prototype for the modeling of phase transition phenomena. In particular, exploiting the link between the Allen-Cahn equation and minimal surface theory in dimensions N ≥ 9, we find a solution, u, with ∂(x(N))u > 0, such that its level sets are close to a nonplanar, minimal, entire graph. This counterexample provides a negative answer to a celebrated question by Ennio de Giorgi [De Giorgi E (1979) Proceedings of the International Meeting on Recent Methods in Nonlinear Analysis (Rome, 1978), 131-188, Pitagora, Bologna]. Our results suggest parallels of De Giorgi's conjecture for finite Morse index solutions in two and three dimensions and suggest a possible program of classification of all entire solutions.

Stability of cluster solutions in a cooperative consumer chain model.

We study a cooperative consumer chain model which consists of one producer and two consumers. It is an extension of the Schnakenberg model suggested in Gierer and Meinhardt [Kybernetik (Berlin), 12:30-39, 1972] and Schnakenberg (J Theor Biol, 81:389-400, 1979) for which there is only one producer and one consumer. In this consumer chain model there is a middle component which plays a hybrid role: it acts both as consumer and as producer. It is assumed that the producer diffuses much faster than the first consumer and the first consumer much faster than the second consumer. The system also serves as a model for a sequence of irreversible autocatalytic reactions in a container which is in contact with a well-stirred reservoir. In the small diffusion limit we construct cluster solutions in an interval which have the following properties: The spatial profile of the third component is a spike. The profile for the middle component is that of two partial spikes connected by a thin transition layer. The first component in leading order is given by a Green's function. In this profile multiple scales are involved: The spikes for the middle component are on the small scale, the spike for the third on the very small scale, the width of the transition layer for the middle component is between the small and the very small scale. The first component acts on the large scale. To the best of our knowledge, this type of spiky pattern has never before been studied rigorously. It is shown that, if the feedrates are small enough, there exist two such patterns which differ by their amplitudes.We also study the stability properties of these cluster solutions. We use a rigorous analysis to investigate the linearized operator around cluster solutions which is based on nonlocal eigenvalue problems and rigorous asymptotic analysis. The following result is established: If the time-relaxation constants are small enough, one cluster solution is stable and the other one is unstable. The instability arises through large eigenvalues of order O1. Further, there are small eigenvalues of order o1 which do not cause any instabilities. Our approach requires some new ideas: (i) The analysis of the large eigenvalues of order O1 leads to a novel system of nonlocal eigenvalue problems with inhomogeneous Robin boundary conditions whose stability properties have been investigated rigorously. (ii) The analysis of the small eigenvalues of order o1 needs a careful study of the interaction of two small length scales and is based on a suitable inner/outer expansion with rigorous error analysis. It is found that the order of these small eigenvalues is given by the smallest diffusion constant ε2(2).

Physics-driven structural docking and protein language models accelerate antibody screening and design for broad-spectrum antiviral therapy.

Therapeutic antibodies have become one of the most influential therapeutics in modern medicine to fight against infectious pathogens, cancer, and many other diseases. However, experimental screening for highly efficacious targeting antibodies is labor-intensive and of high cost, which is exacerbated by evolving antigen targets under selective pressure such as fast-mutating viral variants. As a proof-of-concept, we developed a machine learning-assisted antibody generation pipeline that greatly accelerates the screening and re-design of immunoglobulins G (IgGs) against a broad spectrum of SARS-CoV-2 coronavirus variant strains. These viruses infect human host cells via the viral spike protein binding to the host cell receptor angiotensin-converting enzyme 2 (ACE2). Using over 1300 IgG sequences derived from convalescent patient B cells that bind with spike's receptor binding domain (RBD), we first established protein structural docking models in assessing the RBD-IgG-ACE2 interaction interfaces and predicting the virus-neutralizing activity of each IgG with a confidence score. Additionally, employing Gaussian process regression (also known as Kriging) in a latent space of an antibody language model, we predicted the landscape of IgGs' activity profiles against individual coronaviral variants of concern. With functional analyses and experimental validations, we efficiently prioritized IgG candidates for neutralizing a broad spectrum of viral variants (wildtype, Delta, and Omicron) to prevent the infection of host cells in vitro and hACE2 transgenic mice in vivo. Furthermore, the computational analyses enabled rational redesigns of selective IgG clones with single amino acid substitutions at the RBD-binding interface to improve the IgG blockade efficacy for one of the severe, therapy-resistant strains - Delta (B.1.617). Our work expedites applications of artificial intelligence in antibody screening and re-design even in low-data regimes combining protein language models and Kriging for antibody sequence analysis, activity prediction, and efficacy improvement, in synergy with physics-driven protein docking models for antibody-antigen interface structure analyses and functional optimization.