A point mutation in the nucleotide exchange factor eIF2B constitutively activates the integrated stress response by allosteric modulation

In eukaryotic cells, stressors reprogram the cellular proteome by activating the integrated stress response (ISR). In its canonical form, stress-sensing kinases phosphorylate the eukaryotic translation initiation factor eIF2 (eIF2-P), which ultimately leads to reduced levels of ternary complex required for initiation of mRNA translation. Previously we showed that translational control is primarily exerted through a conformational switch in eIF2's nucleotide exchange factor, eIF2B, which shifts from its active A-State conformation to its inhibited I-State conformation upon eIF2-P binding, resulting in reduced nucleotide exchange on eIF2 (Schoof et al. 2021). Here, we show functionally and structurally how a single histidine to aspartate point mutation in eIF2B's β subunit (H160D) mimics the effects of eIF2-P binding by promoting an I-State like conformation, resulting in eIF2-P independent activation of the ISR. These findings corroborate our previously proposed A/I-State model of allosteric ISR regulation.

Viral evasion of the integrated stress response through antagonism of eIF2-P binding to eIF2B

Viral infection triggers activation of the integrated stress response (ISR). In response to viral double-stranded RNA (dsRNA), RNA-activated protein kinase (PKR) phosphorylates the translation initiation factor eIF2, converting it from a translation initiator into a potent translation inhibitor and this restricts the synthesis of viral proteins. Phosphorylated eIF2 (eIF2-P) inhibits translation by binding to eIF2's dedicated, heterodecameric nucleotide exchange factor eIF2B and conformationally inactivating it. We show that the NSs protein of Sandfly Fever Sicilian virus (SFSV) allows the virus to evade the ISR. Mechanistically, NSs tightly binds to eIF2B (KD = 30 nM), blocks eIF2-P binding, and rescues eIF2B GEF activity. Cryo-EM structures demonstrate that SFSV NSs and eIF2-P directly compete, with the primary NSs contacts to eIF2Bα mediated by five 'aromatic fingers'. NSs binding preserves eIF2B activity by maintaining eIF2B's conformation in its active A-State.

eIF2B conformation and assembly state regulate the integrated stress response

The integrated stress response (ISR) is activated by phosphorylation of the translation initiation factor eIF2 in response to various stress conditions. Phosphorylated eIF2 (eIF2-P) inhibits eIF2’s nucleotide exchange factor eIF2B, a twofold symmetric heterodecamer assembled from subcomplexes. Here, we monitor and manipulate eIF2B assembly in vitro and in vivo. In the absence of eIF2B’s α-subunit, the ISR is induced because unassembled eIF2B tetramer subcomplexes accumulate in cells. Upon addition of the small-molecule ISR inhibitor ISRIB, eIF2B tetramers assemble into active octamers. Surprisingly, ISRIB inhibits the ISR even in the context of fully assembled eIF2B decamers, revealing allosteric communication between the physically distant eIF2, eIF2-P, and ISRIB binding sites. Cryo-electron microscopy structures suggest a rocking motion in eIF2B that couples these binding sites. eIF2-P binding converts eIF2B decamers into ‘conjoined tetramers’ with diminished substrate binding and enzymatic activity. Canonical eIF2-P-driven ISR activation thus arises due to this change in eIF2B’s conformational state.

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo-electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.

GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control

Ribosome-associated quality control (RQC) pathways protect cells from toxicity caused by incomplete protein products resulting from translation of damaged or problematic mRNAs. Extensive work in yeast has identified highly conserved mechanisms that lead to degradation of faulty mRNA and partially synthesized polypeptides. Here we used CRISPR-Cas9-based screening to search for additional RQC strategies in mammals. We found that failed translation leads to specific inhibition of translation initiation on that message. This negative feedback loop is mediated by two translation inhibitors, GIGYF2 and 4EHP. Model substrates and growth-based assays established that inhibition of additional rounds of translation acts in concert with known RQC pathways to prevent buildup of toxic proteins. Inability to block translation of faulty mRNAs and subsequent accumulation of partially synthesized polypeptides could explain the neurodevelopmental and neuropsychiatric disorders observed in mice and humans with compromised GIGYF2 function.

An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation

Without an effective prophylactic solution, infections from SARS-CoV-2 continue to rise worldwide with devastating health and economic costs. SARS-CoV-2 gains entry into host cells via an interaction between its Spike protein and the host cell receptor angiotensin converting enzyme 2 (ACE2). Disruption of this interaction confers potent neutralization of viral entry, providing an avenue for vaccine design and for therapeutic antibodies. Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. By screening a yeast surface-displayed library of synthetic nanobody sequences, we identified a panel of nanobodies that bind to multiple epitopes on Spike and block ACE2 interaction via two distinct mechanisms. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for SARS-CoV-2 Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains stability and function after aerosolization, lyophilization, and heat treatment. These properties may enable aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia, promising to yield a widely deployable, patient-friendly prophylactic and/or early infection therapeutic agent to stem the worst pandemic in a century.

Chromatin accessibility dynamics across C. elegans development and ageing

An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here, we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one Caenorhabditis elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, more than 1000 promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements changes during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

Abstract B65: Milky spots are required for ovarian cancer metastatic colonization of peritoneal adipose depots

Introduction: In ovarian cancer, attachment of cells to the omentum represents a rate-limiting step in metastasis formation. Thus, there is significant interest in identifying the tissue microenvironments involved in cancer cell colonization of this preferred metastatic site. The omentum is composed of translucent membranes and adipose, which contains immune structures known as milky spots. Two general models of omental colonization can be discerned from the published literature. In the “milky spot-driven” model, cancer cell lodging is due to factors produced by milky spots which serve as a colonization niche1. In contrast, the “adipose-driven” model proposes that adipocyte-derived factors are solely responsible for cancer cell lodging2. By taking advantage of peritoneal adipose deposits which either contain or lack milky spots, we set forth to test the hypothesis that these unusual immune structures are required for cancer cell colonization of adipose-rich tissues such as the omentum.

Methods: Ovarian cancer cell migration, lodging and growth was assessed in a panel of peritoneal fat depots which either contain milky spots (omentum, splenoportal fat) or lack them (uterine fat, mesentery, and gonadal fat). The presence or absence of milky spots was confirmed by histology and immunohistochemistry (IHC) for CD45. Ovarian cancer cell lodging was evaluated via experimental metastasis assays using SKOV3ip.1 (human) or ID8 (mouse) ovarian cancer cells injected into Athymic Nude or C57BL/6 mice, respectively. At 7 days post injection (dpi) peritoneal fat depots were harvested and evaluated for the presence of cancer cells using histology and pan-cytokeratin IHC. The relative chemoattractant ability of tissue-conditioned media was evaluated by transwell migration assays using SKOV3ip.1 and ID8 cells.

Results: The presence of milky spots in omental and splenoportal fat and their absence in uterine, gonadal, and mesenteric fat was confirmed by histology and IHC. In metastasis assays, cancer foci were observed in omental and splenoportal milky spots at 7 dpi. In contrast, cancer cells were never observed in adipose that lacked milky spots; even at 63 dpi. Consistent with this, conditioned media from milky-spot containing tissues had a significantly increased ability to promote ovarian cancer cells migration .

Conclusions: In sum, our findings show that milky spots are an absolute requirement for cancer cell lodging on peritoneal adipose. Consistent with this, migration assays show that the presence of milky spots causes a significant enhancement in the ability of peritoneal adipose to promote directed migration. Taken together, these finding suggest that while adipose may secrete a general chemoattrative signal, additional contributions from the milky spots are required for localization and invasion. Current experiments include investigating the chemoattractant(s) used by the milky spots to attract cancer cells and the cell type(s) responsible for their secretion.

Competing interests: The authors declare no competing interests.

References: 1. Sorensen et al. 2009. Immunol Res.; 2. Nieman et al. 2011. Nat Med.

Work was supported by grants from the DOD (W81XWH-09-1-0127), NCI/NIH (2RO1CA089569), Elsa U. Pardee Foundation; A Rivkin Center for Ovarian Cancer Research Pilot Study Award, and Section of Urology funds (The University of Chicago)

Citation Format: Robert Clark, Venkatesh Krishnan, Michael Schoof, Irving Rodriguez, Marina Chekmareva, Betty Theriault, Carrie Rinker-Schaeffer. Milky spots are required for ovarian cancer metastatic colonization of peritoneal adipose depots. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr B65.

Abstract B33: Omental milky spots serve as a niche for ovarian cancer metastatic colonization

Introduction: Metastatic ovarian cancer remains an urgent clinical problem. The homing and invasion of cancer cells into the omentum, the preferred site of ovarian cancer metastasis, is a rate-limiting step in disease progression. We have recently shown that immune cell-containing structures known as milky spots are required for colonization of the omental adipose. Experiments were designed using well-established ovarian cancer models and experimental metastasis assays to answer the following questions: Does cancer cell localization depend upon the immune composition of the milky spots? Do cancer cells utilize the native milky spot microenvironment, or does it undergo remodeling during colonization? Answers to these questions will be the foundation for mechanism-based studies aimed at identifying ovarian cancer-omental interactions that can be targeted therapeutically.

Methods: Mouse strains with varying immune-competency were used to: 1) test the effect of immune composition on volume of milky spots within the omentum; 2) determine the requirement of specific immune cell types on ovarian cancer cell lodging and invasion into milky spots; and assess the effect of ovarian cancer cell lodging on milky spot composition. Strains included: C57BL/6 (immunocompetent), Athymic Nude (T cell deficient), Beige Nude (NK and T cell deficient), Rag1-/- (no mature T or B cells, no CD3+ or T cell receptor a-b positive cells), and Igh6-/- (lack mature B cells). Experimental metastasis assays used intraperitoneal injection of 1 x 106 ID8 (mouse) or SKOV3ip.1 (human) ovarian cancer cells into C57BL/6 mice, or immunodeficient mice, respectively. Milky spot volume in naïve omenta was calculated from digital whole-mounts constructed from Giemsa-stained tissue sections. Milky spot composition was evaluated using immunohistochemistry (IHC) for lymphocytes (CD45), T cells (CD3), B cells (B220), macrophages (F4/80), and endothelial cells (CD31).

Results: ID8 and SKOV3ip.1 ovarian cancer cells localized to and proliferated in the milky spots. Studies using a panel of immune-deficient mice showed that the mouse genetic background does not alter omental milky spot number and size, nor does it affect ovarian cancer colonization. Analysis of digital whole mounts found no difference in the volume of milky spots in omenta from C57BL/6, Athymic Nude, Beige Nude, Rag1-/-, Igh6-/- mice. IHC of naïve omenta show the presence of B cells, T cells, and macrophages consistent with the genotype of the mouse. Abundant endothelial cells were present in milky spots corresponding to the dense vasculature that is a conserved feature of milky spots. Finally, evaluation of milky spot composition during metastatic colonization showed an influx of macrophages 24 hours and 3 days post injection (dpi). Staining for activated macrophages in metastases increased from week 1 to week 5; staining persisted until the experimental endpoint.

Conclusions: Targeting the host tissue microenviroment is crucial to contain or reduce cancer spread, prolonging patient life. Use of genetic models ruled out a requirement of B, T, and NK cells in ovarian cancer cell homing to milky spots suggesting a role for macrophages in this process. A preliminary study indicates a temporal increase in activated macrophages upon cancer colonization. We speculate that cancer cells co-opt the normal developmental role of macrophages to promote their own growth.

Work was supported by grants from the DOD (W81XWH-09-1-0127), NCI/NIH (2RO1CA089569), and Elsa U. Pardee Foundation; A Rivkin Center for Ovarian Cancer Research Pilot Study Award, and funds from the Section of Urology (The University of Chicago)

Citation Format: Venkatesh Krishnan, Robert Clark, Michael Schoof, Irving Rodriguez, Marina Chekmareva, Carrie Rinker-Schaeffer. Omental milky spots serve as a niche for ovarian cancer metastatic colonization. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr B33.

[Selected medico-sociologic aspects of contact behavior in an urban population with special reference to the relation of neurotic disorders]

The quality and quantity of interpersonal relations were investigated by a special questionnaire to discover the connexion of psychonervous disorders with the contact behaviour. The psychonervous disorder was measured by a screening method, which examines the neurotic status. 361 patients of an urban population were asked by the questionnaire. 309 questionnaires of the probably neurotic patients and non neurotic patients were analyzed with respect to the differences between the two groups patients. Probably neurotic patients felt more stressed. They are more directed to the family members. The contact behaviour of the probably neurotic patients is more restrained in profession and also in free time than the behaviour of the non neurotic patients. The fewer agreement between reality and desire of the contact behaviour is typical for the probably neurotic patients. The intention of the conclusions was to help them to develop a feeling of interpersonal contentment.

Psychiatric disorders of abused women at a shelter

Thirty physically abused women were randomly selected from the population of a local women's shelter and evaluated by psychiatric interview and psychiatric rating scales. High prevalences of major depression disorder (37%) and PTSD (47%) were determined. Furthermore, these disorders were found to be positively associated. These results suggest the need for immediate availability of psychiatric services at such shelters along with further study of their populations and possible intervention strategies.