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Molecular basis for antibody recognition of multiple drug-peptide/MHC complexes

Maso, Lorenzo; Rajak, Epsa; Bang, Injin; Koide, Akiko; Hattori, Takamitsu; Neel, Benjamin G; Koide, Shohei
The HapImmuneTM platform exploits covalent inhibitors as haptens for creating major histocompatibility complex (MHC)-presented tumor-specific neoantigens by design, combining targeted therapies with immunotherapy for the treatment of drug-resistant cancers. A HapImmune antibody, R023, recognizes multiple sotorasib-conjugated KRAS(G12C) peptides presented by different human leukocyte antigens (HLAs). This high specificity to sotorasib, coupled with broad HLA-binding capability, enables such antibodies, when reformatted as T cell engagers, to potently and selectively kill sotorasib-resistant KRAS(G12C) cancer cells expressing different HLAs upon sotorasib treatment. The loosening of HLA restriction could increase the patient population that can benefit from this therapeutic approach. To understand the molecular basis for its unconventional binding capability, we used single-particle cryogenic electron microscopy to determine the structures of R023 bound to multiple sotorasib-peptide conjugates presented by different HLAs. R023 forms a pocket for sotorasib between the VH and VL domains, binds HLAs in an unconventional, angled way, with VL making most contacts with them, and makes few contacts with the peptide moieties. This binding mode enables the antibody to accommodate different hapten-peptide conjugates and to adjust its conformation to different HLAs presenting hapten-peptides. Deep mutational scanning validated the structures and revealed distinct levels of mutation tolerance by sotorasib- and HLA-binding residues. Together, our structural information and sequence landscape analysis reveal key features for achieving MHC-restricted recognition of multiple hapten-peptide antigens, which will inform the development of next-generation therapeutic antibodies.
PMID: 38781214
ISSN: 1091-6490
CID: 5654922

Proton-coupled transport mechanism of the efflux pump NorA

Li, Jianping; Li, Yan; Koide, Akiko; Kuang, Huihui; Torres, Victor J; Koide, Shohei; Wang, Da-Neng; Traaseth, Nathaniel J
Efflux pump antiporters confer drug resistance to bacteria by coupling proton import with the expulsion of antibiotics from the cytoplasm. Despite efforts there remains a lack of understanding as to how acid/base chemistry drives drug efflux. Here, we uncover the proton-coupling mechanism of the Staphylococcus aureus efflux pump NorA by elucidating structures in various protonation states of two essential acidic residues using cryo-EM. Protonation of Glu222 and Asp307 within the C-terminal domain stabilized the inward-occluded conformation by forming hydrogen bonds between the acidic residues and a single helix within the N-terminal domain responsible for occluding the substrate binding pocket. Remarkably, deprotonation of both Glu222 and Asp307 is needed to release interdomain tethering interactions, leading to opening of the pocket for antibiotic entry. Hence, the two acidic residues serve as a "belt and suspenders" protection mechanism to prevent simultaneous binding of protons and drug that enforce NorA coupling stoichiometry and confer antibiotic resistance.
PMCID:11130294
PMID: 38802368
ISSN: 2041-1723
CID: 5663352

Efficacy and safety of guselkumab in patients with active psoriatic arthritis who had inadequate efficacy and/or intolerance to one prior tumor necrosis factor inhibitor: study protocol for SOLSTICE, a phase 3B, multicenter, randomized, double-blind, placebo-controlled study

Ogdie, Alexis; Merola, Joseph F; Mease, Philip J; Ritchlin, Christopher T; Scher, Jose U; Lafferty, Kimberly Parnell; Chan, Daphne; Chakravarty, Soumya D; Langholff, Wayne; Wang, Yanli; Choi, Olivia; Krol, Yevgeniy; Gottlieb, Alice B
BACKGROUND:Tumor necrosis factor inhibitors (TNFi) are frequently chosen as the first biologic for patients with psoriatic arthritis (PsA). Given that many patients with PsA are TNFi inadequate responders (TNF-IR; either inadequate efficacy or intolerance), treatments utilizing alternative mechanisms of action are needed. In phase 3 studies, the fully human interleukin (IL)-23p19 subunit-inhibitor, guselkumab, was efficacious in patients with active PsA, including TNFi-IR. Efficacy was generally consistent between TNFi-naïve and TNFi-experienced cohorts; however, in the latter, higher response rates have been observed with the Q4W dosing regimen relative to the Q8W dosing regimen for some endpoints, suggesting the need to evaluate whether more frequent dosing may provide an incremental clinical benefit for TNFi-IR patients. METHODS:The phase 3b SOLSTICE study will assess guselkumab efficacy and safety in TNFi-IR PsA patients. Eligibility criteria include a PsA diagnosis for ≥ 6 months; active disease (≥ 3 swollen, ≥ 3 tender joints, C-reactive protein ≥ 0.3 mg/dL); and inadequate efficacy with, and/or intolerance to, one prior TNFi. Participants will be randomized 1:1:1 to guselkumab Q4W or Q8W or placebo→guselkumab Q4W (at Week 24). The primary endpoint is the proportion of patients achieving ≥ 20% improvement in the American College of Rheumatology criteria (ACR20) at Week 24. Major secondary endpoints include ACR50, ACR70; an Investigator's Global Assessment (IGA) of psoriasis score of 0/1 plus ≥ 2-grade reduction and ≥ 90% improvement in Psoriasis Area and Severity Index (both among patients with ≥ 3% body surface area affected by psoriasis and baseline IGA ≥ 2); minimal/very low disease activity; and changes from baseline in Health Assessment Questionnaire-Disability Index, the 36-item Short-Form Health Survey Physical Component Summary, and Functional Assessment of Chronic Illness Therapy-Fatigue scores. The target sample size (N = 450) is estimated to provide > 90% power in detecting differences between each guselkumab group and the placebo group for the primary endpoint assuming a 2-sided α = 0.05. Cochran-Mantel-Haenszel testing and analyses of covariance will be used to compare efficacy for binary and continuous endpoints, respectively. DISCUSSION/CONCLUSIONS:Findings from the phase 3b SOLSTICE study, the design of which was informed by results from previously conducted phase 3 studies, is expected to provide important efficacy and safety information on guselkumab therapy in TNFi-IR patients with PsA. TRIAL REGISTRATION/BACKGROUND:This trial was registered at ClinicalTrials.gov, NCT04936308, on 23 June 2021.
PMCID:11106968
PMID: 38773563
ISSN: 2520-1026
CID: 5654512

Risk of kidney failure in patients with inflammatory bowel disease undergoing colectomy: a nationwide cohort study

Yang, Yuanhang; Ludvigsson, Jonas F; Forss, Anders; Faucon, Anne-Laure; Faye, Adam S; Olén, Ola; Sjölander, Arvid; Carrero, Juan J
BACKGROUND:Inflammatory bowel disease (IBD) is frequently accompanied by kidney complications. Potential triggers or subpopulations at high-risk of kidney problems are not well elucidated. We hypothesized that surgical interventions, specifically colectomy, might in part explain this risk. METHODS:Nationwide Swedish cohort study comprising 82,051 individuals with biopsy-proven IBD diagnosed during 1965-2017, with follow-up until 2019. We investigated the association between incident colectomy (time-varying exposure) and future risk of acute kidney injury (AKI) and kidney failure (diagnosis of end-stage kidney disease or death due to chronic kidney disease) using Cox proportional hazard models. We also examined the impact of partial vs. total colectomy and the presence/duration of a stoma. Covariates included demographics, education level, and selected comorbidities. RESULTS:Over a median follow-up of 14 years, 16,479 individuals underwent colectomy, and 2,556 AKI and 1,146 kidney failure events occurred. Colectomy was associated with an increased relative risk of both AKI (adjusted hazard ratio [aHR] 2.37; 95%CI 2.17-2.58) and kidney failure (1.54; 1.34-1.76). Compared to pre-colectomy periods, undergoing total colectomy and colectomy with prolonged stoma showed higher risks of both kidney outcomes versus partial colectomy or colectomy with a temporary stoma, respectively. Subgroup analyses suggested higher risks in patients with ulcerative colitis. CONCLUSIONS:In people with IBD, rates of AKI and kidney failure are higher among those undergoing colectomy, particularly among those following total colectomy, or colectomy with a prolonged stoma. This study identifies a high-risk population that may benefit from established protocols for kidney function monitoring/surveillance and referral to nephrologist care.
PMID: 38777172
ISSN: 1542-7714
CID: 5654722

Safety of Immunosuppression in A Prospective Cohort of Inflammatory Bowel Disease Patients with a HIstoRy of CancEr: SAPPHIRE Registry

Itzkowitz, Steven H; Jiang, Yue; Villagra, Cristina; Colombel, Jean-Frederic; Sultan, Keith; Lukin, Dana J; Faleck, David M; Scherl, Ellen; Chang, Shannon; Chen, LeaAnn; Katz, Seymour; Kwah, Joann; Swaminath, Arun; Petralia, Francesca; Sharpless, Virginia; Sachar, David; Jandorf, Lina; Axelrad, Jordan E; ,
BACKGROUND AND AIMS/OBJECTIVE:In patients with inflammatory bowel disease (IBD) and a history of cancer, retrospective studies suggest that exposure to immunosuppressive agents does not increase the risk of incident (recurrent or new) cancer compared to unexposed patients. SAPPHIRE is a prospective registry aimed at addressing this issue. METHODS:Since 2016, patients with IBD and confirmed index cancer prior to enrollment were followed annually. Patients receiving chemotherapy or radiation at enrollment, or recurrent cancer within five years were excluded. Primary outcome was development of incident cancer related to exposure to immunosuppressive medications. RESULTS:Among 305 patients (47% male, 88% white), median age at IBD diagnosis and cancer were 32 and 52 years, respectively. Index cancers were solid organ (46%), dermatologic (32%), gastrointestinal (13%), and hematologic (9%). During median follow-up of 4.8 years, 210 (69%) were exposed to immunosuppressive therapy and 46 (15%) developed incident cancers (25 new, 21 recurrent). In unadjusted analysis, the crude rate of incident cancer in unexposed patients was 2.58/100 person-years versus 4.78/100 PY (relative risk 1.85, 95% CI 0.92-3.73) for immunosuppression exposed patients. In a proportional hazards model adjusting for sex, smoking history, age and stage at index malignancy, and non-melanoma skin cancer, no significant association was found between receipt of immunosuppression and incident cancer (adjusted hazard ratio, aHR, 1.41, 95% CI: 0.69-2.90), or with any major drug class. CONCLUSION/CONCLUSIONS:In this interim analysis of patients with IBD and a history of cancer, despite numerically elevated aHRs, we did not find a statistically significant association between subsequent exposure to immunosuppressive therapies and development of incident cancers.
PMID: 38768673
ISSN: 1542-7714
CID: 5654242

Metabolic coordination between skin epithelium and type 17 immunity sustains chronic skin inflammation

Subudhi, Ipsita; Konieczny, Piotr; Prystupa, Aleksandr; Castillo, Rochelle L; Sze-Tu, Erica; Xing, Yue; Rosenblum, Daniel; Reznikov, Ilana; Sidhu, Ikjot; Loomis, Cynthia; Lu, Catherine P; Anandasabapathy, Niroshana; Suárez-Fariñas, Mayte; Gudjonsson, Johann E; Tsirigos, Aristotelis; Scher, Jose U; Naik, Shruti
Inflammatory epithelial diseases are spurred by the concomitant dysregulation of immune and epithelial cells. How these two dysregulated cellular compartments simultaneously sustain their heightened metabolic demands is unclear. Single-cell and spatial transcriptomics (ST), along with immunofluorescence, revealed that hypoxia-inducible factor 1α (HIF1α), downstream of IL-17 signaling, drove psoriatic epithelial remodeling. Blocking HIF1α in human psoriatic lesions ex vivo impaired glycolysis and phenocopied anti-IL-17 therapy. In a murine model of skin inflammation, epidermal-specific loss of HIF1α or its target gene, glucose transporter 1, ameliorated epidermal, immune, vascular, and neuronal pathology. Mechanistically, glycolysis autonomously fueled epithelial pathology and enhanced lactate production, which augmented the γδ T17 cell response. RORγt-driven genetic deletion or pharmacological inhibition of either lactate-producing enzymes or lactate transporters attenuated epithelial pathology and IL-17A expression in vivo. Our findings identify a metabolic hierarchy between epithelial and immune compartments and the consequent coordination of metabolic processes that sustain inflammatory disease.
PMID: 38772365
ISSN: 1097-4180
CID: 5654422

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation

Sargsian, Shushan; Mondragón-Palomino, Octavio; Lejeune, Alannah; Ercelen, Defne; Jin, Wen-Bing; Varghese, Alan; Lim, Yvonne A L; Guo, Chun-Jun; Loke, P'ng; Cadwell, Ken
BACKGROUND:Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, display microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes with immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. In this study, we aimed to further characterize the functional properties of these bacteria. RESULTS:Clostridiales isolates were profiled for their ability to perform 57 enzymatic reactions and produce short-chain fatty acids (SCFAs) and hydrogen sulfide, revealing that these bacteria were capable of a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T-cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching. CONCLUSION/CONCLUSIONS:We identified Clostridiales species that are sufficient to induce high levels of Tregs. We also identified a set of metabolic activities linked with Treg differentiation and Trichuris egg hatching mediated by these newly isolated bacteria. Altogether, this study provides functional insights into the microbiotas of individuals residing in a helminth-endemic region. Video Abstract.
PMID: 38730492
ISSN: 2049-2618
CID: 5656072

Use of Phage Display and Other Molecular Display Methods for the Development of Monobodies

Koide, Akiko; Koide, Shohei
Synthetic binding proteins are human-made binding proteins that use non-antibody proteins as the starting scaffold. Molecular display technologies, such as phage display, enable the construction of large combinatorial libraries and their efficient sorting and, thus, are crucial for the development of synthetic binding proteins. Monobodies are the founding system of a set of synthetic binding proteins based on the fibronectin type III (FN3) domain. Since the original report in 1998, the monobody and related FN3-based systems have steadily been refined, and current methods are capable of rapidly generating potent and selective binding molecules to even challenging targets. The FN3 domain is small (∼90 amino acids) and autonomous and is structurally similar to the conventional immunoglobulin (Ig) domain. Unlike the Ig domain, however, the FN3 lacks a disulfide bond but is highly stable. These attributes of FN3 present unique opportunities and challenges in the design of phage and other display systems, combinatorial libraries, and library sorting strategies. This article reviews key technological innovations in the establishment of our monobody development pipeline, with an emphasis on phage display methodology. These give insights into the molecular mechanisms underlying molecular display technologies and protein-protein interactions, which should be broadly applicable to diverse systems intended for generating high-performance binding proteins.
PMID: 37137569
ISSN: 1559-6095
CID: 5509082

Inflammatory Memory in Chronic Skin Disease

Daccache, Joseph A.; Naik, Shruti
Inflammation is a hallmark of remitting-relapsing dermatological diseases. Although a large emphasis has been placed on adaptive immune cells as mediators of relapse, evidence in epithelial and innate immune biology suggests that disease memory is widespread. In this study, we bring to the fore the concept of inflammatory memory or nonspecific training of long-lived cells in the skin, highlighting the epigenetic and other mechanisms that propagate memory at the cellular level. We place these findings in the context of psoriasis, a prototypic flaring disease known to have localized memory, and underscore the importance of targeting memory to limit disease flares.
SCOPUS:85191304722
ISSN: 2667-0267
CID: 5659962

Histological remission in inflammatory bowel disease and female fertility: A nationwide study

Mårild, Karl; Söderling, Jonas; Stephansson, Olof; Axelrad, Jordan; Halfvarson, Jonas; ,; Bröms, Gabriella; Marsal, Jan; Olén, Ola; Ludvigsson, Jonas F
BACKGROUND & AIMS/OBJECTIVE:Inflammatory bowel disease (IBD) is linked to reduced female fertility, but it is unclear how fertility rates vary by histological disease activity. METHODS:Nationwide IBD cohort of Swedish women aged 15-44 years. We examined fertility rates during periods with vs. without histological inflammation (n=21,046; follow-up: 1990-2016) and during periods with vs. without clinical activity (IBD-related hospitalization, surgery, or treatment escalation) (n=24,995; follow-up: 2006-2020). Accounting for socio-demographics and comorbidities, we used Poisson regression to estimate adjusted fertility rate ratios (aFRRs) for live-births conceived during 12-month-periods of histological inflammation (vs. histological remission) and 3-month-periods of clinically active IBD (vs. quiescent IBD). RESULTS:During periods with vs. without histological inflammation, there were 6.35 (95%CI=5.98-6.73) and 7.09 (95%CI=6.48-7.70) live-births conceived per 100 person-years of follow-up, respectively, or one fewer child per fourteen women with 10 years of histological inflammation (aFRR=0.90; 95%CI=0.81-1.00). In women with histological inflammation fertility was similarly reduced in ulcerative colitis (UC, aFRR=0.89 [95%CI=0.78-1.02]) and Crohn's disease (CD, aFRR=0.86 [95%CI=0.72-1.04]). Clinical IBD activity was associated with an aFRR of 0.76 (95%CI=0.72-0.79) or one fewer child per six women with 10 years of clinical activity. Fertility was reduced in clinically active UC (aFRR=0.75 [95%CI=0.70-0.81]) and CD (aFRR=0.76 [95%CI=0.70-0.82]). Finally, also among women with clinically quiescent IBD, histological inflammation (vs. histological remission) was associated with reduced fertility (aFRR=0.85 [95%CI=0.73-0.98]). CONCLUSIONS:An association between histological and clinical activity and reduced female fertility in CD and UC was found. Notably, histological inflammation was linked to reduced fertility also in women with clinically quiescent IBD.
PMID: 38331202
ISSN: 1528-0012
CID: 5632422