Cryo-EM structure of the NLRC4CARD filament provides insights into how symmetric and asymmetric supramolecular structures drive inflammasome assembly

Inflammasomes are supramolecular signaling platforms integral to innate immune defense against invading pathogens. The NOD-like receptor (NLR) family apoptosis inhibitory protein (NAIP)·NLR family caspase-recruiting domain (CARD) domain-containing 4 (NLRC4) inflammasome recognizes intracellular bacteria and induces the polymerization of the caspase-1 protease, which in turn executes maturation of interleukin-1β (IL-1β) and pyroptosis. Several high-resolution structures of the fully assembled NAIP·NLRC4 complex are available, but these structures do not resolve the architecture of the CARD filament in atomic detail. Here, we present the cryo-EM structure of the filament assembled by the CARD of human NLRC4 (NLRC4^CARD) at 3.4 Å resolution. The structure revealed that the helical architecture of the NLRC4^CARD filament is essentially identical to that of the downstream filament assembled by the CARD of caspase-1 (casp1^CARD), but deviates from the split washer-like assembly of the NAIP·NLRC4 oligomer. Our results suggest that architectural complementarity is a major driver for the recognition between upstream and downstream CARD assemblies in inflammasomes. Furthermore, a Monte Carlo simulation of the NLRC4^CARD filament assembly rationalized why an (un)decameric NLRC4 oligomer is optimal for assembling the helical base of the NLRC4^CARD filament. Together, our results explain how symmetric and asymmetric supramolecular assemblies enable high-fidelity signaling in inflammasomes.

The allosteric activation of cGAS underpins its dynamic signaling landscape

Cyclic G/AMP synthase (cGAS) initiates type-1 interferon responses against cytosolic double-stranded (ds)DNA, which range from antiviral gene expression to apoptosis. The mechanism by which cGAS shapes this diverse signaling landscape remains poorly defined. We find that substrate-binding and dsDNA length-dependent binding are coupled to the intrinsic dimerization equilibrium of cGAS, with its N-terminal domain potentiating dimerization. Notably, increasing the dimeric fraction by raising cGAS and substrate concentrations diminishes duplex length-dependent activation, but does not negate the requirement for dsDNA. These results demonstrate that reaction context dictates the duplex length dependence, reconciling competing claims on the role of dsDNA length in cGAS activation. Overall, our study reveals how ligand-mediated allostery positions cGAS in standby, ready to tune its signaling pathway in a switch-like fashion.

The human immune system protects the body from various threats such as damaged cells or invading microbes. Many of these threats can move molecules of DNA, which are usually only found within a central compartment in the cell known as the nucleus, to the surrounding area, the cytoplasm.

An enzyme called cGAS searches for DNA in the cytoplasm of human cells. When DNA binds to cGAS it activates the enzyme to convert certain molecules (referred to as ‘substrates’) into another molecule (the ‘signal’) that triggers various immune responses to protect the body against the threat. To produce the signal, two cGAS enzymes need to work together as a single unit called a dimer.

The length of DNA molecules in the cytoplasm of cells can vary widely. It was initially thought that DNA molecules of any length binding to cGAS could activate the enzyme to a similar degree, but later studies demonstrated that this is not the case. However, it remains unclear how the length of the DNA could affect the activity of the enzyme, or why some of the earlier studies reported different findings.

Hooy and Sohn used biochemical approaches to study the human cGAS enzyme. The experiments show that cGAS can form dimers even when no DNA is present. However, when DNA bound to cGAS, the enzyme was more likely to form dimers. Longer DNA molecules were better at promoting cGAS dimers to form than shorter DNA molecules. The binding of substrates to cGAS also made it more likely that the enzyme would form dimers. These findings suggest that inside cells cGAS is primed to trigger a switch-like response when it detects DNA in the cytoplasm.

The work of Hooy and Sohn establishes a simple set of rules to predict how cGAS might respond in a given situation. Such information may aid in designing and tailoring efforts to regulate immune responses in human patients, and may provide insight into why the body responds to biological threats in different ways.

IFI16 filament formation in salivary epithelial cells shapes the anti-IFI16 immune response in Sjögren's syndrome

IFN-inducible protein 16 (IFI16) is an innate immune sensor that forms filamentous oligomers when activated by double-stranded DNA (dsDNA). Anti-IFI16 autoantibodies occur in patients with Sjögren's syndrome (SS) and associate with severe phenotypic features. We undertook this study to determine whether the structural and functional properties of IFI16 play a role in its status as an SS autoantigen. IFI16 immunostaining in labial salivary glands (LSGs) yielded striking evidence of filamentous IFI16 structures in the cytoplasm of ductal epithelial cells, representing the first microscopic description of IFI16 oligomerization in human tissues, to our knowledge. Transfection of cultured epithelial cells with dsDNA triggered the formation of cytoplasmic IFI16 filaments with similar morphology to those observed in LSGs. We found that a majority of SS anti-IFI16 autoantibodies immunoprecipitate IFI16 more effectively in the oligomeric dsDNA-bound state. Epitopes in the C-terminus of IFI16 are accessible to antibodies in the DNA-bound oligomer and are preferentially targeted by SS sera. Furthermore, cytotoxic lymphocyte granule pathways (highly enriched in the SS gland) induce striking release of IFI16•dsDNA complexes from cultured cells. Our studies reveal that IFI16 is present in a filamentous state in the target tissue of SS and suggest that this property of DNA-induced filament formation contributes to its status as an autoantigen in SS. These studies highlight the role that tissue-specific modifications and immune effector pathways might play in the selection of autoantigens in rheumatic diseases.

Abstract P2-05-07: Whole exome sequencing of extreme responders reveals low mutation burden in metastatic breast cancer

Background: Extreme responders to anticancer therapy are rarely encountered in the treatment of advanced breast cancer patients, but their treatment response have not been investigated on the whole exome level. We performed whole exome analysis to characterize genomic landscape of extreme responders in metastatic breast cancer patients.

Methods: Clinical samples were obtained from patients who showed exceptional response to anti-HER2 therapy or hormonal therapy. Non-responders were selected among those who did not respond. Matched breast tumor tissue (somatic DNA) and blood samples (germline DNA) were collected from a total of 18 responders (12 ER+, 6 HER2+) and 8 non-responders (6 ER+, 1 HER2+, 1 TNBC). Whole exome sequencing using Illumina HiSeq2500 was performed on the 26 patients (52 samples). Somatic single nucleotide variants (SNVs), indels and copy number variants (CNVs) were identified for each patient genome. Group specific somatic variants and mutation burden were statistically analyzed.

Findings: Cancer exomes were characterized by 1,455 somatic single-nucleotide variants (1,327 missense, 80 nonsense, 36 splice-site, 12 start/stop-lost), 149 insertions/deletions (108 frameshift, 41 inframe), with a median of 1 mutations per Mb (0.2 to 2.7 mutations per Mb) in all patients. Responders harbored a significantly lower non-synonymous mutation burden than non-responders (median, 27 vs. 90.5, P=0.01), and copy number variation burden was also lower (median 23 vs. 31, P=0.14). Multivariate analyses of factors influencing progression-free survival showed that high mutation burden and visceral metastases were significantly related with progression.

Interpretation: Extreme responders of metastatic breast cancer are characterized by low nonsynonymous mutational burden.

Citation Format: Sohn J, Lim SM, Kim E, Kim S, Koo JS, Kim SI, Park S, Park HS, Kwon N-J, Kim GM, Kim S. Whole exome sequencing of extreme responders reveals low mutation burden in metastatic breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-05-07.

Abstract PD6-12: Withdrawn

This abstract was withdrawn by the authors.

Abstract P1-08-03: Withdrawn

This abstract was withdrawn by the authors.

Abstract P4-22-13: Everolimus plus trastuzumab and paclitaxel as first-line therapy in women with HER2+ advanced breast cancer: Overall survival results from BOLERO-1

Background

Everolimus (EVE), an mTOR inhibitor has shown activity in HER2+ advanced breast cancer (ABC) in both preclinical and clinical studies. In the pivotal BOLERO-1 trial (NCT00876395), the progression-free survival (PFS) was not significantly different between the EVE + trastuzumab (TRAS) + paclitaxel (PAC) combination and placebo (PBO) + TRAS + PAC in the full HER2+ population (EVE, 15.0 mo vs PBO, 14.5 mo; HR=0.89; 95% CI: 0.73-1.08; p=0.1166). Although not reaching protocol defined level for statistical significance, the hormone receptor negative (HR-) subpopulation appeared to benefit from EVE, with a 7.2 mo PFS benefit vs PBO arm (EVE, 20.3 mo vs PBO, 13.1 mo; HR=0.66; 95% CI: 0.48-0.91; p=0.0049). The final exploratory overall survival (OS) analysis from the study is presented here.

Methods

In this phase 3 randomized trial, 719 women with HER2+ ABC without prior TRAS or chemotherapy in the metastatic setting were randomized 2:1 to receive either EVE (10 mg/d) or placebo (PBO) and weekly PAC+TRAS, stratified by visceral metastasis (lung, liver, peritoneal or pleural: yes vs no) and prior adjuvant or neo-adjuvant treatment with TRAS (yes vs no). As the primary objectives (PFS on full population and on HR- subpopulation) of BOLERO-1 were not met, the key secondary endpoint of OS was not formally statistically tested. However, given the results of PFS, in particular in the HR- subpopulation, a change to the OS analysis plan was made by introducing one final exploratory OS analysis at the time of study termination.

Results

At data cutoff (Dec 31, 2015), the median duration of exposure was 40.8 weeks (range: 0.6-320.4) in the EVE arm and 48.1 weeks (range: 1.1-308.0) in the PBO arm. After a median follow-up of 60.3 mo, 350 deaths were recorded in the full population, 238 (49.6%) in the EVE arm and 112 (46.9%) pts in the PBO arm. In the full population, the median OS was comparable in the EVE vs PBO arms (48.6 mo vs 50.0 mo respectively; HR = 1.13; 95% CI: 0.90-1.42). In the HR- subpopulation, 138 deaths were recorded; 88 (42.3%) pts in the EVE arm and 50 (48.5%) pts in the PBO arm. In the HR- subpopulation, the median OS in the EVE arm was longer compared to PBO arm (57.0 mo vs 41.6 mo respectively; HR = 0.83; 95% CI: 0.59-1.18). Stomatitis, diarrhea, alopecia, cough, rash, pyrexia, neutropenia, and fatigue were the most frequent adverse events (AEs) reported in EVE arm (≥35%). AEs leading to dose interruption and/or change were reported in 441 (93.4%) pts in EVE arm and 165 (69.3%) pts in the PBO arm respectively. Overall, AEs leading to treatment discontinuation were reported in 262 (55.5%) pts in EVE arm and 98 (41.2%) pts in PBO arm. Serious AEs were reported in 171 (36.2%) pts in the EVE arm and 40 (16.8%) pts in the PBO arm respectively. On treatment AE related deaths were reported for 3.6% pts in the EVE arm and 0% pts in the PBO arm.

Conclusions

The median OS was similar in the EVE vs PBO arms for overall population. However, a prolongation of 15.4 mo in median OS of HR- subpopulation was observed in the EVE arm vs PBO arm in this exploratory analysis. Pts in the EVE arm had a manageable safety, consistent with the safety profile of EVE and no new safety signals were identified.

Citation Format: Yardley D, Hurvitz S, Jiang Z-f, Toi M, Burris H, Buyse M, Slamon D, Makhson A, Elsaid A, Lerzo G, Hellerstedt B, Nuzzo F, Sohn J, Manzyuk L, Cabaribere D, Lincy J, Weimann A, Noel-Baron F, Pacaud L, Andre F. Everolimus plus trastuzumab and paclitaxel as first-line therapy in women with HER2+ advanced breast cancer: Overall survival results from BOLERO-1 [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-22-13.

Association of Antibodies to Interferon-Inducible Protein-16 With Markers of More Severe Disease in Primary Sjögren's Syndrome

OBJECTIVE

Interferon-inducible protein-16 (IFI16) is an intracellular DNA receptor involved in innate immunity. We evaluated the frequency, phenotypic characteristics, and clinical associations of anti-IFI16 antibodies in patients with primary Sjögren's syndrome (SS), and quantitated expression levels of IFI16 in SS and control salivary gland lysates.

METHODS

Anti-IFI16 antibodies were assayed by enzyme-linked immunosorbent assay using sera from patients with primary SS (n = 133) and from healthy controls (n = 47). Sera from systemic lupus erythematosus (SLE) patients (n = 132) were included as disease controls. Immunoprecipitation of in vitro transcription-translated IFI16 was used to determine which portion of IFI16 the antibodies recognized. Expression of IFI16 in salivary gland lysates was quantitated by immunoblotting.

RESULTS

Anti-IFI16 antibodies were present in the sera of 38 of 133 SS patients (29%) compared to 1 of 47 healthy controls (2.1%) (SS versus controls; P < 0.0002) and in 31 of 132 SLE controls (24%). In SS, anti-IFI16 antibodies were associated with an abnormal Schirmer's test (P = 0.003), hyperglobulinemia (P = 0.02), antinuclear antibody ≥1:320 (P = 0.01), germinal center-like structures in labial salivary gland lymphoid infiltrates (P = 0.01), and higher focus scores (3.4 versus 2.4; P = 0.005). High-titer IFI16 antibodies were directed against an epitope outside the N-terminus in 9 of 13 SS patients (69%). IFI16 was expressed in 4 of 5 (80%) of SS and 1 of 6 (17%) of control labial salivary glands.

CONCLUSION

Anti-IFI16 antibodies are a prominent specificity in primary SS and are associated with markers of severe disease. IFI16 is expressed at higher levels in SS salivary glands compared to controls. These high levels in disease target tissue may contribute to the ongoing anti-IFI16 immune response.

Abstract P1-12-09: The oncologic effect of a gonadotropin releasing hormone (GnRH) agonist for ovarian protection during breast cancer chemotherapy

Background: Recently, chemotherapy with a GnRH agonist was reported to protect against ovarian failure. This study was aimed at determining the oncologic effect of a GnRH agonist concurrent with chemotherapy for breast cancer patients.

Patients and Methods: A total of 1189 patients aged 20 to 40 years with stage I to III breast cancer who received (neo or adjuvant) chemotherapy from five hospitals in Korea from 2002 to 2012 were reviewed. A gonadotropin releasing hormone (GnRH) agonist was given to 410 patients for ovarian protection during chemotherapy (GnRH agonist group), and 779 patients received chemotherapy without ovarian protection (Chemotherapy alone group). A matching strategy was used to create matched sets of two groups by age, stage, hormone receptor status, Her2/neu status, neo or adjuvant chemotherapy, and institute.

Results: Survival analysis using Cox regression showed that the GnRH agonist group had better distant metastatic-free survival (HR=0.65, 95%CI 0.44-0.97) outcomes but similar disease free survival (HR=0.78, 95% CI 0.57-1.08) compared with the chemotherapy alone group. The survival benefit was significant for hormone receptor positive, Her2/neu negative breast cancer on distant metastasis (HR=0.44, 95% CI 0.20-0.99) and disease free survival (HR0.47 95% CI 0.23-0.93).

Conclusion: Ovarian protection using a GnRH agonist can be safely considered for premenopausal breast cancer patients for whom chemotherapy is planned.

Citation Format: Kim HJ, Lee MH, Lee JE, Park SH, Lee ES, Kang Y-J, Lee JH, Shin HN, Kim SI, Im SA, Ahn SH, Lee KS, Sohn J, Han W, Nam SJ. The oncologic effect of a gonadotropin releasing hormone (GnRH) agonist for ovarian protection during breast cancer chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-12-09.

Abstract P4-13-09: Clinical effectiveness of everolimus and exemestane in advanced breast cancer patients from Asia and Africa: First efficacy and updated safety results from the phase IIIb EVEREXES study

Background

BOLERO-2 phase III trial established the efficacy of everolimus (EVE) plus exemestane (EXE) for the treatment of postmenopausal patients with hormone receptor (HR)-positive, HER2-negative, advanced breast cancer (aBC). However, in this study only a minority (&lt;10%) of patients were recruited from African and Asia Pacific countries. Considering the potential effects of ethnic and cultural differences on treatment effectiveness, it remains compelling to confirm the safety and efficacy profile of EVE+EXE in these populations.

Methods

EVEREXES is an open-label phase IIIb, single arm, multi-center trial, which from March 2013 to October 2014 enrolled 232 post-menopausal, HR-positive and HER2-negative, aBC patients previously treated with aromatase inhibitors, across 13 countries in Asia Pacific, Middle East, North and South Africa, with a significant majority of patients being of Asian ethnicity (196, 84.5%). Its primary objective was to investigate the safety and tolerability profile of EVE+EXE. Secondary objectives were the evaluation of efficacy (assessed by PFS, ORR, and CBR based on RECIST 1.1 criteria) and change in ECOG performance status.

Results

At data cut off of 31st of January 2015, at a median follow up of 11.7 months, median PFS for the ITT population was 9.5 months [9.2-11.6 months], based on local assessment, with the observation of 1 (0.4%) CR and 35 (15.4%) PR. Regarding safety and tolerability, a majority (81.1%) of grade (G) 1/2 adverse events (AEs) was reported. In particular, the following pattern was observed in terms of % of patients who developed G1/G2/G3 mTOR-inhibition induced AEs: stomatitis (36.1, 13.7, 10.6), rash (21.6/6.2/0), fatigue (10.6, 4.4, 2.2), hyperglycemia (6.2, 11.5, 7.0), weight decrease (7.5, 7, 0.9), pneumonitis (5.7, 7, 0.9). No Grade 4 AEs related to EVE+EXE treatment were observed, with exception of one case of non infectious pneumonitis (0.4%). Median dose intensity of everolimus was 9.2 mg/day.

Conclusions

Efficacy and safety results from EVEREXES trial further confirm the role of EVE+EXE for the treatment of HR+/Her2- advanced BC patients in Eastern countries. Results were consistent with data previously reported in BOLERO-2 trial.

Citation Format: Im Y-H, Uslu R, Lee KS, Nagarkar R, Sohn J, Sevinc A, Altundag K, Chang Y-C, Abdel-Razeq H, Im S-A, Jeong J, Park HY, Arpornwirat W, Bastick P, Le TH, Ocak Arikan O, Xue HL, Canatar A, Valenti R, Kim S-B. Clinical effectiveness of everolimus and exemestane in advanced breast cancer patients from Asia and Africa: First efficacy and updated safety results from the phase IIIb EVEREXES study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-13-09.

Filament assemblies in foreign nucleic acid sensors

Helical filamentous assembly is ubiquitous in biology, but was only recently realized to be broadly employed in the innate immune system of vertebrates. Accumulating evidence suggests that the filamentous assemblies and helical oligomerization play important roles in detection of foreign nucleic acids and activation of the signaling pathways to produce antiviral and inflammatory mediators. In this review, we focus on the helical assemblies observed in the signaling pathways of RIG-I-like receptors (RLRs) and AIM2-like receptors (ALRs). We describe ligand-dependent oligomerization of receptor, receptor-dependent oligomerization of signaling adaptor molecules, and their functional implications and regulations.

The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex

The ability to recognize foreign double-stranded (ds)DNA of pathogenic origin in the intracellular environment is an essential defense mechanism of the human innate immune system. However, the molecular mechanisms underlying distinction between foreign DNA and host genomic material inside the nucleus are not understood. By combining biochemical assays and single-molecule techniques, we show that the nuclear innate immune sensor IFI16 one-dimensionally tracks long stretches of exposed foreign dsDNA to assemble into supramolecular signaling platforms. We also demonstrate that nucleosomes represent barriers that prevent IFI16 from targeting host DNA by directly interfering with these one-dimensional movements. This unique scanning-assisted assembly mechanism allows IFI16 to distinguish friend from foe and assemble into oligomers efficiently and selectively on foreign DNA.

Single-molecule imaging at high fluorophore concentrations by local activation of dye

Single-molecule fluorescence microscopy is a powerful tool for observing biomolecular interactions with high spatial and temporal resolution. Detecting fluorescent signals from individual labeled proteins above high levels of background fluorescence remains challenging, however. For this reason, the concentrations of labeled proteins in in vitro assays are often kept low compared to their in vivo concentrations. Here, we present a new fluorescence imaging technique by which single fluorescent molecules can be observed in real time at high, physiologically relevant concentrations. The technique requires a protein and its macromolecular substrate to be labeled each with a different fluorophore. Making use of short-distance energy-transfer mechanisms, only the fluorescence from those proteins that bind to their substrate is activated. This approach is demonstrated by labeling a DNA substrate with an intercalating stain, exciting the stain, and using energy transfer from the stain to activate the fluorescence of only those labeled DNA-binding proteins bound to the DNA. Such an experimental design allowed us to observe the sequence-independent interaction of Cy5-labeled interferon-inducible protein 16 with DNA and the sliding via one-dimensional diffusion of Cy5-labeled adenovirus protease on DNA in the presence of a background of hundreds of nanomolar Cy5 fluorophore.

Assembly-driven activation of the AIM2 foreign-dsDNA sensor provides a polymerization template for downstream ASC

AIM2 recognizes foreign dsDNA and assembles into the inflammasome, a filamentous supramolecular signalling platform required to launch innate immune responses. We show here that the pyrin domain of AIM2 (AIM2^PYD) drives both filament formation and dsDNA binding. In addition, the dsDNA-binding domain of AIM2 also oligomerizes and assists in filament formation. The ability to oligomerize is critical for binding dsDNA, and in turn permits the size of dsDNA to regulate the assembly of the AIM2 polymers. The AIM2^PYD oligomers define the filamentous structure, and the helical symmetry of the AIM2^PYD filament is consistent with the filament assembled by the PYD of the downstream adaptor ASC. Our results suggest that the role of AIM2^PYD is not autoinhibitory, but generating a structural template by coupling ligand binding and oligomerization is a key signal transduction mechanism in the AIM2 inflammasome.

The AIM2 inflammasome complex is essential for defence against a number of human pathogens but how it assembles upon recognition of foreign DNA remains incompletely understood. Here Morrone et al. suggest the AIM2 pyrin domain acts in both DNA binding and filament assembly to generate a structural template for complex assembly.