Heavy-chain CDR3-engineered B cells facilitate in vivo evaluation of HIV-1 vaccine candidates.

V2-glycan/apex broadly neutralizing antibodies (bnAbs) recognize a closed quaternary epitope of the HIV-1 envelope glycoprotein (Env). This closed structure is necessary to elicit apex antibodies and useful to guide the maturation of other bnAb classes. To compare antigens designed to maintain this conformation, we evaluated apex-specific responses in mice engrafted with a diverse repertoire of B cells expressing the HCDR3 of the apex bnAb VRC26.25. Engineered B cells affinity matured, guiding the improvement of VRC26.25 itself. We found that soluble Env (SOSIP) variants differed significantly in their ability to raise anti-apex responses. A transmembrane SOSIP (SOSIP-TM) delivered as an mRNA-lipid nanoparticle elicited more potent neutralizing responses than multimerized SOSIP proteins. Importantly, SOSIP-TM elicited neutralizing sera from B cells engineered with the predicted VRC26.25-HCDR3 progenitor, which also affinity matured. Our data show that HCDR3-edited B cells facilitate efficient in vivo comparisons of Env antigens and highlight the potential of an HCDR3-focused vaccine approach.

Orchestrated intron retention regulates normal granulocyte differentiation.

Intron retention (IR) is widely recognized as a consequence of mis-splicing that leads to failed excision of intronic sequences from pre-messenger RNAs. Our bioinformatic analyses of transcriptomic and proteomic data of normal white blood cell differentiation reveal IR as a physiological mechanism of gene expression control. IR regulates the expression of 86 functionally related genes, including those that determine the nuclear shape that is unique to granulocytes. Retention of introns in specific genes is associated with downregulation of splicing factors and higher GC content. IR, conserved between human and mouse, led to reduced mRNA and protein levels by triggering the nonsense-mediated decay (NMD) pathway. In contrast to the prevalent view that NMD is limited to mRNAs encoding aberrant proteins, our data establish that IR coupled with NMD is a conserved mechanism in normal granulopoiesis. Physiological IR may provide an energetically favorable level of dynamic gene expression control prior to sustained gene translation.

Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma.

Phyllodes tumours (PTs) are rare fibroepithelial lesions of the breast that are classified as benign, borderline, or malignant. As little is known about the molecular underpinnings of PTs, current diagnosis relies on histological examination. However, accurate classification is often difficult, particularly for distinguishing borderline from malignant PTs. Furthermore, PTs can be misdiagnosed as other tumour types with shared histological features, such as fibroadenoma and metaplastic breast cancers. As DNA methylation is a recognised hallmark of many cancers, we hypothesised that DNA methylation could provide novel biomarkers for diagnosis and tumour stratification in PTs, whilst also allowing insight into the molecular aetiology of this otherwise understudied tumour. We generated whole-genome methylation data using the Illumina EPIC microarray in a novel PT cohort (n = 33) and curated methylation microarray data from published datasets including PTs and other potentially histopathologically similar tumours (total n = 817 samples). Analyses revealed that PTs have a unique methylome compared to normal breast tissue and to potentially histopathologically similar tumours (metaplastic breast cancer, fibroadenoma and sarcomas), with PT-specific methylation changes enriched in gene sets involved in KRAS signalling and epithelial-mesenchymal transition. Next, we identified 53 differentially methylated regions (DMRs) (false discovery rate < 0.05) that specifically delineated malignant from non-malignant PTs. The top DMR in both discovery and validation cohorts was hypermethylation at the HSD17B8 CpG island promoter. Matched PT single-cell expression data showed that HSD17B8 had minimal expression in fibroblast (putative tumour) cells. Finally, we created a methylation classifier to distinguish PTs from metaplastic breast cancer samples, where we revealed a likely misdiagnosis for two TCGA metaplastic breast cancer samples. In conclusion, DNA methylation alterations are associated with PT histopathology and hold the potential to improve our understanding of PT molecular aetiology, diagnostics, and risk stratification. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Multi-Level Thrombotic/Embolic Burden and Its Role in Sex-Related Outcomes in Acute Limb Ischemia (ALI).

INTRODUCTION: The impact of sex upon outcomes in acute limb ischemia (ALI) remains disputed. We aim to quantify the effect of sex upon amputation-free survival (AFS) after a percutaneous-first approach for ALI. METHODS: Two-center retrospective review of ALI managed via a percutaneous-first approach. Demographics, comorbidities, and clinical characteristics were analyzed (Table I). The Kaplan-Meier and Cox regression were used to estimate AFS, limb-salvage and overall survival. RESULTS: Over nine years, 170 patients (87, 51% males; median age 67 IQR 59, 77 years) presented with ALI. Rutherford Classification was I in 56 (33%); IIa in 85 (50%); IIb in 20 (12%) and III in 9 (5%). Thirty-day mortality, major amputation rate and fasciotomy rates were 8% (N=13); 6.5% (N=11), and 4.7% (N=8), respectively. Among revascularized limbs, 92% were patent at 30 days. Length of stay was 7 (IQR 3-11) days. Complications included 13 bleeding episodes (8%), 4 cases of atrial fibrillation (2%), and 3 re-thrombosis/clot extension events (1.7%). No differences were noted in complication rates when stratified by sex. Females were older than males (median age 70 IQR 62, 79 vs 65 IQR 56, 76 years; p=0.02) and more likely to present with atrial fibrillation (20.5% vs 8%, p 0.02); and hyperlipidemia (72% vs 57%, p = 0.04). Females also more frequently presented with multi-level thrombotic/embolic burden compared to males (56% vs 43%; p=0.03), and required both aspiration thrombectomy and thrombolysis (27% versus 14%; p 0.02). Kaplan-Meier estimated median AFS, limb salvage, and overall survival were 425 (IQR 140, 824 days); 314 (IQR 72, 727 days); and 342 (IQR 112, 762 days). When stratified by sex, females had worse survival (median 270 IQR 92, 636 versus 406 IQR 140, 937 days; p=0.005); and limb salvage (median 241 IQR 88, 636 versus 363 IQR 49, 822 days; p=0.04) compared to males. Univariate Cox regression showed female sex (HR = 1.46 95% CI 1.04-2.05; p=0.03); multi-level thrombotic/embolic burden (HR 1.64 95% CI 1.17-2.31; p=0.004) and Rutherford Class (HR 1.37 95% CI 1.08-1.73; p=0.009) predicted major amputation/death. By multivariable Cox regression, multi-level thrombotic/embolic burden (HR 1.54 95% CI 1.09-2.17; p=0.01), Rutherford Class (HR 1.34 95% CI 1.07-1.69; p=0.01), and female Sex (HR = 1.45 95% CI 1.03-2.05; p=0.03) were each independently predictive of major amputation/death. CONCLUSIONS: A percutaneous-first strategy is safe and efficacious in the overall ALI population. Similar to prior works, female versus male ALI patients in our cohort have higher rates of mortality and major amputation. In our multivariable model, multi-level thrombotic/embolic burden was independently associated with a greater than 45% increased hazard of major amputation/ death at last follow up. Further prospective analysis is warranted to elucidate the underlying factors contributing to the higher prevalence of multi-level thrombotic/embolic burden in female ALI patients, and to further define the optimal percutaneous-first approach for ALI in consideration of patient sex and extent of clot burden.

Mesothelin antigen density influences anti-mesothelin chimeric antigen receptor T cell cytotoxicity.

BACKGROUND AIMS: Several anti-mesothelin (MSLN) chimeric antigen receptor (CAR) T cells are in phase 1/2 clinical trials to treat solid-organ malignancies. The effect of MSLN antigen density on MSLN CAR cytotoxicity against tumor cells has not been examined previously, nor are there data regarding the effect of agents that increase MSLN antigen density on anti-MSLN CAR T cell efficacy. METHODS: MSLN antigen density was measured on a panel of pancreatic cancer and mesothelioma cell lines by flow cytometry. In parallel, the cytotoxicity and specificity of two anti-MSLN CAR T cells (m912 and SS1) were compared against these cell lines using a real-time impedance-based assay. The effect of two MSLN 'sheddase' inhibitors (lanabecestat and TMI-1) that increase MSLN surface expression was also tested in combination with CAR T cells. RESULTS: SS1 CAR T cells were more cytotoxic compared with m912 CAR T cells against cell lines that expressed fewer than ∼170 000 MSLN molecules/cell. A comparison of the m912 and amatuximab (humanized SS1) antibodies identified that amatuximab could detect and bind to lower levels of MSLN on pancreatic cancer and mesothelioma cell lines, suggesting that superior antibody/scFv affinity was the reason for the SS1 CAR's superior cytotoxicity. The cytotoxicity of m912 CAR T cells was improved in the presence of sheddase inhibitors, which increased MSLN antigen density. CONCLUSIONS: These data highlight the value of assessing CAR constructs against a panel of cells expressing varying degrees of target tumor antigen as occurs in human tumors. Furthermore, the problem of low antigen density may be overcome by concomitant administration of drugs that inhibit enzymatic shedding of MSLN.

Cutdown is Associated with Higher 30-day Unplanned Readmissions and Wound Complications than Percutaneous Access for EVAR.

BACKGROUND: A 2023 Cochrane review showed no difference in bleeding/wound infection complications, short-term mortality and aneurysm exclusion between the percutaneous and cut-down approach for femoral access in endovascular aortic aneurysm repair (EVAR). In contrast, single-center studies have shown bilateral cutdown resulting in higher readmission rates due to higher rates of groin wound infections. Whether 30-day readmission rates vary by type of access during EVAR procedures is unknown. The goal of this study was to ascertain which femoral access approach for EVAR is associated with the lowest risk of 30-day readmission. METHODS: The Targeted Vascular Module from the American College of Surgeons National Surgical Quality Improvement Program was queried to identify patients undergoing EVAR for aortic disease from 2012-2021. All ruptures and other emergency cases were excluded. Cohorts were divided into bilateral cutdown, unilateral cutdown, failed percutaneous attempt converted to open and successful percutaneous access. The primary 30-day outcomes were unplanned readmission and wound complications. Univariate analyses were performed using the Fisher's exact test, Chi-Square test and the Student's t-test. Multivariable analysis was performed using logistic regression. RESULTS: From 2012 to 2021, 14,002 patients met study criteria. Most (7,395 [53%]) underwent completely percutaneous access, 5,616 (40%) underwent bilateral cutdown, 849 (6%) underwent unilateral cutdown, and 146 (1%) had a failed percutaneous access which was converted to open. Unplanned readmissions by access strategy included 7.6% for bilateral cutdown, 7.3% for unilateral cutdown, 7.8% for attempted percutaneous converted to cutdown, and 5.7% for completely percutaneous access (P < 0.001, Figure 1). After multivariable analysis, unplanned readmissions compared to percutaneous access yielded: percutaneous converted to cutdown adjusted odds ratio (AOR): 1.38, 95% CI [0.76-2.53], P = 0.29; unilateral cutdown AOR: 1.18, 95% CI [0.92-1.51], P = 0.20; bilateral cutdown AOR: 1.26, 95% CI [1.09-1.43], P = 0.001. Bilateral cutdown was also associated with higher wound complications compared to percutaneous access (AOR: 4.41, CI [2.86-6.79], P < 0.001), as was unilateral cutdown (AOR: 3.04, CI [1.46-6.32], P = 0.003). CONCLUSIONS: Patients undergoing cutdown for EVAR are at higher risk for 30-day readmission compared to completely percutaneous access. If patient anatomy allows for percutaneous EVAR, this access option should be prioritized.

A signal-seeking Phase 2 study of olaparib and durvalumab in advanced solid cancers with homologous recombination repair gene alterations.

PURPOSE: To determine the safety and efficacy of PARP plus PD-L1 inhibition (olaparib + durvalumab, O + D) in patients with advanced solid, predominantly rare cancers harbouring homologous recombination repair (HRR) defects. PATIENTS AND METHODS: In total, 48 patients were treated with O + D, 16 with BRCA1/2 alterations (group 1) and 32 with other select HRR alterations (group 2). Overall, 32 (66%) patients had rare or less common cancers. The primary objective of this single-arm Phase II trial was a progression-free survival rate at 6 months (PFS6). Post hoc exploratory analyses were conducted on archival tumour tissue and serial bloods. RESULTS: The PFS6 rate was 35% and 38% with durable objective tumour responses (OTR) in 3(19%) and 3(9%) in groups 1 and 2, respectively. Rare cancers achieving an OTR included cholangiocarcinoma, perivascular epithelioid cell (PEComa), neuroendocrine, gallbladder and endometrial cancer. O + D was safe, with five serious adverse events related to the study drug(s) in 3 (6%) patients. A higher proportion of CD38 high B cells in the blood and higher CD40 expression in tumour was prognostic of survival. CONCLUSIONS: O + D demonstrated no new toxicity concerns and yielded a clinically meaningful PFS6 rate and durable OTRs across several cancers with HRR defects, including rare cancers.

Mutations derived from horseshoe bat ACE2 orthologs enhance ACE2-Fc neutralization of SARS-CoV-2.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein mediates infection of cells expressing angiotensin-converting enzyme 2 (ACE2). ACE2 is also the viral receptor of SARS-CoV (SARS-CoV-1), a related coronavirus that emerged in 2002-2003. Horseshoe bats (genus Rhinolophus) are presumed to be the original reservoir of both viruses, and a SARS-like coronavirus, RaTG13, closely related to SARS-CoV-2, has been identified in one horseshoe-bat species. Here we characterize the ability of the S-protein receptor-binding domains (RBDs) of SARS-CoV-1, SARS-CoV-2, pangolin coronavirus (PgCoV), RaTG13, and LyRa11, a bat virus similar to SARS-CoV-1, to bind a range of ACE2 orthologs. We observed that the PgCoV RBD bound human ACE2 at least as efficiently as the SARS-CoV-2 RBD, and that both RBDs bound pangolin ACE2 efficiently. We also observed a high level of variability in binding to closely related horseshoe-bat ACE2 orthologs consistent with the heterogeneity of their RBD-binding regions. However five consensus horseshoe-bat ACE2 residues enhanced ACE2 binding to the SARS-CoV-2 RBD and neutralization of SARS-CoV-2 pseudoviruses by an enzymatically inactive immunoadhesin form of human ACE2 (hACE2-NN-Fc). Two of these mutations impaired neutralization of SARS-CoV-1 pseudoviruses. An hACE2-NN-Fc variant bearing all five mutations neutralized both SARS-CoV-2 pseudovirus and infectious virus more efficiently than wild-type hACE2-NN-Fc. These data suggest that SARS-CoV-1 and -2 originate from distinct bat species, and identify a more potently neutralizing form of soluble ACE2.

Cloud-based fusion imaging improves operative metrics during fenestrated endovascular aneurysm repair.

OBJECTIVE: Endovascular treatment of complex aortic pathology has been associated with increases in procedural-related metrics, including the operative time and radiation exposure. Three-dimensional fusion imaging technology has decreased the radiation dose and iodinated contrast use during endovascular aneurysm repair. The aim of the present study was to report our institutional experience with the use of a cloud-based fusion imaging platform during fenestrated endovascular aneurysm repair (FEVAR). METHODS: A retrospective review of a prospectively maintained aortic database was performed to identify all patients who had undergone FEVAR with commercially available devices (Zenith Fenestrated; Cook Medical Inc, Bloomington, IN) between 2013 and 2020 and all endovascular aneurysm repairs performed using Cydar EV Intelligent Maps (Cydar Medical, Cambridge, UK). The Cydar EV cohort was reviewed further to select all FEVARs performed with overlay map guidance. The patient demographic, clinical, and procedure metrics were analyzed, with a comparative analysis of FEVAR performed without and with the Cydar EV imaging platform. Patients were excluded from comparative analysis if the data were incomplete in the dataset or they had a documented history of prior open or endovascular abdominal aortic aneurysm repair. RESULTS: During the 7-year study period, 191 FEVARs had been performed. The Cydar EV imaging platform was implemented in 2018 and used in 124 complex endovascular aneurysm repairs, including 69 consecutive FEVARs. A complete dataset was available for 137 FEVARs. With exclusion to select for de novo FEVAR, a comparative analysis was performed of 53 FEVAR without and 63 with Cydar EV imaging guidance. The cohorts were similar in patient demographics, medical comorbidities, and aortic aneurysm characteristics. No significant difference was noted between the two groups for major adverse postoperative events, length of stay, or length of intensive care unit stay. The use of Cydar EV resulted in nonsignificant decreases in the mean fluoroscopy time (69.3 ± 28 minutes vs 66.2 ± 33 minutes; P = .598) and operative time (204.4 ± 64 minutes vs 186 ± 105 minutes; P = .278). A statistically significant decrease was found in the iodinated contrast volume (105 ± 44 mL vs 83 ± 32 mL; P = .005), patient radiation exposure using the dose area product (1,049,841 mGy/cm2 vs 630,990 mGy/cm2; P < .001) and cumulative air kerma levels (4518 mGy vs 3084 mGy; P = .02) for patients undergoing FEVAR with Cydar EV guidance. CONCLUSIONS: At our aortic center, we have observed a trend toward shorter operative times and significant reductions in both iodinated contrast use and radiation exposure during FEVAR using the Cydar EV intelligent maps. Intelligent map guidance improved the efficiency of complex endovascular aneurysm repair, providing a safer intervention for both patient and practitioner.

The 4-1BBζ costimulatory domain in chimeric antigen receptors enhances CD8+ T-cell functionality following T-cell receptor stimulation.

BACKGROUND: Chimeric antigen receptor (CAR) T-cells have revolutionized the treatment of CD19- and B-cell maturation antigen-positive haematological malignancies. However, the effect of a CAR construct on the function of T-cells stimulated via their endogenous T-cell receptors (TCRs) has yet to be comprehensively investigated. METHODS: Experiments were performed to systematically assess TCR signalling and function in CAR T-cells using anti-mesothelin human CAR T-cells as a model system. CAR T-cells expressing the CD28 or 4-1BB costimulatory endodomains were manufactured and compared to both untransduced T-cells and CAR T-cells with a non-functional endodomain. These cell products were treated with staphylococcal enterotoxin B to stimulate the TCR, and in vitro functional assays were performed by flow cytometry. RESULTS: Increased proliferation, CD69 expression and IFNγ production were identified in CD8+ 4-1BBζ CAR T-cells compared to control untransduced CD8+ T-cells. These functional differences were associated with higher levels of phosphorylated ZAP70 after stimulation. In addition, these functional differences were associated with a differing immunophenotype, with a more than two-fold increase in central memory cells in CD8+ 4-1BBζ CAR T-cell products. CONCLUSION: Our data indicate that the 4-1BBζ CAR enhances CD8+ TCR-mediated function. This could be beneficial if the TCR targets epitopes on malignant tissues or infectious agents, but detrimental if the TCR targets autoantigens.

Clinical course and management of children with IgA vasculitis with nephritis.

BACKGROUND: IgA vasculitis is the most common vasculitis in children and is often complicated by acute nephritis (IgAVN). Risk of chronic kidney disease (CKD) among children with IgAVN remains unknown. This study aimed to describe the clinical management and kidney outcomes in a large cohort of children with IgAVN. METHODS: This observational cohort study used the PEDSnet database to identify children diagnosed with IgAV between January 1, 2009, and February 29, 2020. Demographic and clinical characteristics were compared among children with and without kidney involvement. For children followed by nephrology, clinical course, and management patterns were described. Patients were divided into four categories based on treatment: observation, renin-angiotensin-aldosterone system (RAAS) blockade, corticosteroids, and other immunosuppression, and outcomes were compared among these groups. RESULTS: A total of 6802 children had a diagnosis of IgAV, of whom 1139 (16.7%) were followed by nephrology for at least 2 visits over a median follow-up period of 1.7 years [0.4,4.2]. Conservative management was the most predominant practice pattern, consisting of observation in 57% and RAAS blockade in 6%. Steroid monotherapy was used in 29% and other immunosuppression regimens in 8%. Children receiving immunosuppression had higher rates of proteinuria and hypertension compared to those managed with observation (p < 0.001). At the end of follow-up, 2.6 and 0.5% developed CKD and kidney failure, respectively. CONCLUSIONS: Kidney outcomes over a limited follow-up period were favorable in a large cohort of children with IgAV. Immunosuppressive medications were used in those with more severe presentations and may have contributed to improved outcomes. A higher resolution version of the Graphical abstract is available as Supplementary information.

28-Year Experience with Ruptured and Symptomatic Type I-III Thoracoabdominal Aortic Aneurysms at a Large Tertiary Referral Center.

BACKGROUND: Given the relative rarity of ruptured and symptomatic type I-III thoracoabdominal aortic aneurysms (TAAA), data is scarce with regard the outcomes of those who survive to repair. The goal of this study was to determine short and long-term outcomes after open repair of type I-III TAAA surgery for ruptured and symptomatic TAAA and compare the results to elective TAAA repairs. METHODS: All open type I-III TAAA repairs performed from 1987 to 2015 were evaluated using an institutional database. Charts were retrospectively evaluated for perioperative outcomes: major adverse event (MAE), in-hospital death, spinal cord ischemia (SCI) and long-term survival. Ruptured, symptomatic and elective repair cohorts were created for comparison. Univariate analysis was performed using the Fisher's exact test for categorical variables and analysis of variance (ANOVA) for continuous variables. Logistic regression was used for in-hospital endpoints; survival analysis was performed with Cox proportional hazards modelling and Kaplan-Meier techniques. RESULTS: Five hundred-sixteen patients had an open type I-III TAAA repair during the study period. Fifty-nine (11.4%) were performed for rupture and 51 (9.9%) were performed for symptomatic aneurysms (RAs). Ruptured and symptomatic groups were more likely to be older, female, and have larger presenting aortic diameters. Most of the ruptured and symptomatic cases were transferred from an outside facility (59.3% and 54.9%, respectively). Intraoperatively, the elective cohort was more likely to receive left heart bypass as an operative adjunct; ruptures were less likely to receive a renal bypass, and operative time was highest for the elective cohort. Perioperative mortality was 18.6% for ruptured, 2.0% for symptomatic, and 7.4% for elective indications. Ruptures were most likely to require new hemodialysis after repair (20.3% vs. 10.3% for elective, P = 0.02). On adjusted analysis, ruptures were more likely to suffer from perioperative death (adjusted odds ratio [AOR]: 4.5, 95% confidence interval (CI): 1.7-11.4) and MAEs (AOR: 2.8, 95% CI: 1.4-5.4). Ruptured and symptomatic aneurysms were not independently associated with SCI; however, preoperative hemodynamic instability was predictive (AOR: 8.7, 95% CI: 1.7-44.2). Both rupture and symptomatic cases were associated with decreased survival on Kaplan-Meier analysis with 5-year survival for ruptures at 35%, symptomatic at 47.7% and elective at 63.7%, P < 0.001. Adjusted hazards of death were 1.2 (95% CI: 0.9-1.8) in the symptomatic cohort and 2.3 (95% CI: 1.5-3.7) in the ruptured cohort. CONCLUSIONS: Open ruptured and symptomatic type I-III TAAA repairs can be performed with acceptable morbidity and mortality. Most symptomatic and rupture repairs were performed after transfer from another institution. Postoperative SCI is most strongly related to the preoperative hemodynamic status of the patient.

CTCF as a regulator of alternative splicing: new tricks for an old player.

Three decades of research have established the CCCTC-binding factor (CTCF) as a ubiquitously expressed chromatin organizing factor and master regulator of gene expression. A new role for CTCF as a regulator of alternative splicing (AS) has now emerged. CTCF has been directly and indirectly linked to the modulation of AS at the individual transcript and at the transcriptome-wide level. The emerging role of CTCF-mediated regulation of AS involves diverse mechanisms; including transcriptional elongation, DNA methylation, chromatin architecture, histone modifications, and regulation of splicing factor expression and assembly. CTCF thereby appears to not only co-ordinate gene expression regulation but contributes to the modulation of transcriptomic complexity. In this review, we highlight previous discoveries regarding the role of CTCF in AS. In addition, we summarize detailed mechanisms by which CTCF mediates AS regulation. We propose opportunities for further research designed to examine the possible fate of CTCF-mediated alternatively spliced genes and associated biological consequences. CTCF has been widely acknowledged as the 'master weaver of the genome'. Given its multiple connections, further characterization of CTCF's emerging role in splicing regulation might extend its functional repertoire towards a 'conductor of the splicing orchestra'.

Mapping oncogenic protein interactions for precision medicine.

Normal protein-protein interactions (normPPIs) occur with high fidelity to regulate almost every physiological process. In cancer, this highly organised and precisely regulated network is disrupted, hijacked or reprogrammed resulting in oncogenic protein-protein interactions (oncoPPIs). OncoPPIs, which can result from genomic alterations, are a hallmark of many types of cancers. Recent technological advances in the field of mass spectrometry (MS)-based interactomics, structural biology and drug discovery have prompted scientists to identify and characterise oncoPPIs. Disruption of oncoPPI interfaces has become a major focus of drug discovery programs and has resulted in the use of PPI-specific drugs clinically. However, due to several technical hurdles, studies to build a reference oncoPPI map for various cancer types have not been undertaken. Therefore, there is an urgent need for experimental workflows to overcome the existing challenges in studying oncoPPIs in various cancers and to build comprehensive reference maps. Here, we discuss the important hurdles for characterising oncoPPIs and propose a three-phase multidisciplinary workflow to identify and characterise oncoPPIs. Systematic identification of cancer-type-specific oncogenic interactions will spur new opportunities for PPI-focused drug discovery projects and precision medicine.

Decolonization to Reduce Postdischarge Infection Risk among MRSA Carriers.

BACKGROUND: Hospitalized patients who are colonized with methicillin-resistant Staphylococcus aureus (MRSA) are at high risk for infection after discharge. METHODS: We conducted a multicenter, randomized, controlled trial of postdischarge hygiene education, as compared with education plus decolonization, in patients colonized with MRSA (carriers). Decolonization involved chlorhexidine mouthwash, baths or showers with chlorhexidine, and nasal mupirocin for 5 days twice per month for 6 months. Participants were followed for 1 year. The primary outcome was MRSA infection as defined according to Centers for Disease Control and Prevention (CDC) criteria. Secondary outcomes included MRSA infection determined on the basis of clinical judgment, infection from any cause, and infection-related hospitalization. All analyses were performed with the use of proportional-hazards models in the per-protocol population (all participants who underwent randomization, met the inclusion criteria, and survived beyond the recruitment hospitalization) and as-treated population (participants stratified according to adherence). RESULTS: In the per-protocol population, MRSA infection occurred in 98 of 1063 participants (9.2%) in the education group and in 67 of 1058 (6.3%) in the decolonization group; 84.8% of the MRSA infections led to hospitalization. Infection from any cause occurred in 23.7% of the participants in the education group and 19.6% of those in the decolonization group; 85.8% of the infections led to hospitalization. The hazard of MRSA infection was significantly lower in the decolonization group than in the education group (hazard ratio, 0.70; 95% confidence interval [CI], 0.52 to 0.96; P=0.03; number needed to treat to prevent one infection, 30; 95% CI, 18 to 230); this lower hazard led to a lower risk of hospitalization due to MRSA infection (hazard ratio, 0.71; 95% CI, 0.51 to 0.99). The decolonization group had lower likelihoods of clinically judged infection from any cause (hazard ratio, 0.83; 95% CI, 0.70 to 0.99) and infection-related hospitalization (hazard ratio, 0.76; 95% CI, 0.62 to 0.93); treatment effects for secondary outcomes should be interpreted with caution owing to a lack of prespecified adjustment for multiple comparisons. In as-treated analyses, participants in the decolonization group who adhered fully to the regimen had 44% fewer MRSA infections than the education group (hazard ratio, 0.56; 95% CI, 0.36 to 0.86) and had 40% fewer infections from any cause (hazard ratio, 0.60; 95% CI, 0.46 to 0.78). Side effects (all mild) occurred in 4.2% of the participants. CONCLUSIONS: Postdischarge MRSA decolonization with chlorhexidine and mupirocin led to a 30% lower risk of MRSA infection than education alone. (Funded by the AHRQ Healthcare-Associated Infections Program and others; ClinicalTrials.gov number, NCT01209234 .).

Sprouty and Spred temporally regulate ERK1/2-signaling to suppress TGFß-induced lens EMT.

Epithelial-mesenchymal transition (EMT) of lens epithelial cells (LECs) principally contributes to the pathogenesis of fibrotic cataract. Sprouty (Spry) and Spred proteins are receptor tyrosine kinase (RTK) antagonists that can regulate RTK-mediated signaling pathways, such as the MAPK/ERK1/2-signaling pathway. The present study examines the ability of Spry and Spred to inhibit TGFß-induced EMT in LECs. LECs explanted from postnatal-day-21 Wistar rats were transduced with adenoviral vectors coding for Spry1, Spry2 or Spred2, and subsequently treated with or without TGFß2. Immunofluorescent labeling of explants for the epithelial membrane marker ß-catenin, and the mesenchymal marker alpha-smooth muscle actin (α-sma), were used to characterize the progression of EMT. Western blotting was used to quantify levels of α-sma and ERK1/2-signaling. Overexpression of Spry or Spred in LECs was sufficient to suppress EMT in response to TGFß, including a block to cell elongation, ß-catenin delocalization and α-sma accumulation. Spry and Spred were also shown to significantly block ERK1/2 phosphorylation for up to 18 h of TGFß treatment but did not impair the earlier activation of ERK1/2 at 20 min. These findings suggest that Spry and Spred may not directly impact ERK1/2-signaling activated by the serine/threonine kinase TGFß receptor, but may selectively target later ERK1/2-signaling driven by downstream RTK-mediated signaling. Taken together, our data establish Spry and Spred antagonists as potent negative regulators of TGFß-induced EMT that can regulate ERK1/2-signaling in a temporal manner. A greater understanding of how Spry and Spred regulate the complex signaling interactions that underlie TGFß-induced EMT will be essential to facilitate the development of novel therapeutics for different pathologies driven by EMT, including fibrotic forms of cataract.

Structure-function relationships explain CTCF zinc finger mutation phenotypes in cancer.

CCCTC-binding factor (CTCF) plays fundamental roles in transcriptional regulation and chromatin architecture maintenance. CTCF is also a tumour suppressor frequently mutated in cancer, however, the structural and functional impact of mutations have not been examined. We performed molecular and structural characterisation of five cancer-specific CTCF missense zinc finger (ZF) mutations occurring within key intra- and inter-ZF residues. Functional characterisation of CTCF ZF mutations revealed a complete (L309P, R339W, R377H) or intermediate (R339Q) abrogation as well as an enhancement (G420D) of the anti-proliferative effects of CTCF. DNA binding at select sites was disrupted and transcriptional regulatory activities abrogated. Molecular docking and molecular dynamics confirmed that mutations in residues specifically contacting DNA bases or backbone exhibited loss of DNA binding. However, R339Q and G420D were stabilised by the formation of new primary DNA bonds, contributing to gain-of-function. Our data confirm that a spectrum of loss-, change- and gain-of-function impacts on CTCF zinc fingers are observed in cell growth regulation and gene regulatory activities. Hence, diverse cellular phenotypes of mutant CTCF are clearly explained by examining structure-function relationships.

Approved gene therapies in Australia: coming to a store near you.

Gene therapy has been promising paradigm-shifting advances in medical science for over two decades. Broadly, it is defined as a human therapy in which an existing defective gene function is added to, replaced, edited or disrupted to achieve a clinical benefit, up to and including a potential lifelong cure. Although originally set out to treat monogenic disorders, gene therapy has since been utilised to treat neoplasia, cardiovascular and neurodegenerative diseases, as well as infections. The realisation of this therapy has been dependent on the achievement of fundamental milestones in medicine, from determining the human genome sequence to identifying effective vehicles for the gene of interest, ultimately facilitating gene delivery in humans. In this review, six approved gene and cell therapies available in Australia are described. Their efficacy, adverse effects, limitations and eligibility are discussed, as well as an overview of cost and future directions.

An improved production and purification protocol for recombinant soluble human fibroblast activation protein alpha.

Fibroblast activation protein alpha (FAP) is a cell-surface expressed type II glycoprotein that has a unique proteolytic activity. FAP has active soluble forms that retain the extracellular portion but lack the transmembrane domain and cytoplasmic tail. FAP expression is normally very low in adult tissue but is highly expressed by activated fibroblasts in sites of tissue remodelling. Thus, FAP is a potential biomarker and pharmacological target in liver fibrosis, atherosclerosis, cardiac fibrosis, arthritis and cancer. Understanding the biological significance of FAP by investigating protein structure, interactions and activities requires reliable methods for the production and purification of abundant pure and stable protein. We describe an improved production and purification protocol for His6-tagged recombinant soluble human FAP. A modified baculovirus expression construct was generated using the pFastBac1 vector and the gp67 secretion signal to produce abundant active soluble recombinant human FAP (residues 27-760) in insect cells. The FAP purification protocol employed ammonium sulphate precipitation, ion exchange chromatography, immobilised metal affinity chromatography and ultrafiltration. High purity was achieved, as judged by gel electrophoresis and specific activity. The purified 82 kDa FAP protein was specifically inhibited by a FAP selective inhibitor, ARI-3099, and was inhibited by zinc with an IC50 of 25 µM. Our approach could be adopted for producing the soluble portions of other type II transmembrane glycoproteins to study their structure and function.

Ctcf haploinsufficiency mediates intron retention in a tissue-specific manner.

CTCF is a master regulator of gene transcription and chromatin organisation with occupancy at thousands of DNA target sites genome-wide. While CTCF is essential for cell survival, CTCF haploinsufficiency is associated with tumour development and hypermethylation. Increasing evidence demonstrates CTCF as a key player in several mechanisms regulating alternative splicing (AS), however, the genome-wide impact of Ctcf dosage on AS has not been investigated. We examined the effect of Ctcf haploinsufficiency on gene expression and AS in five tissues from Ctcf hemizygous (Ctcf+/-) mice. Reduced Ctcf levels caused distinct tissue-specific differences in gene expression and AS in all tissues. An increase in intron retention (IR) was observed in Ctcf+/- liver and kidney. In liver, this specifically impacted genes associated with cytoskeletal organisation, splicing and metabolism. Strikingly, most differentially retained introns were short, with a high GC content and enriched in Ctcf binding sites in their proximal upstream genomic region. This study provides new insights into the effects of CTCF haploinsufficiency on organ transcriptomes and the role of CTCF in AS regulation.