The Global Phosphorylation Landscape of SARS-CoV-2 Infection.

The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.

Stability and failure rate during 3 years of fixed retention: A follow-up of an randomized clinical trial on adolescents with four different lingual retainers.

OBJECTIVE: To evaluate stability outcomes and failure rates associated with four types of lingual retainers: (1) dead-soft wire, (2) multistrand stainless steel (SS) wire, (3) CAD/CAM nitinol, and (4) connected bonding pads (CBPs) after 3 years of retention. METHODS: This study enrolled 96 patients (66 females, 30 males) with a median age of 19 years with four types of lingual retainers: (1) 0.016 × 0.022-inch dead-soft wire, (2) 0.0215-inch five-strand SS wire, (3) 0.014 × 0.014-inch CAD/CAM nitinol wire, and (4) CBPs. The irregularity index, intercanine distances, and arch lengths were obtained and used to evaluate mandibular stability. Failure rates were also assessed during this study. Data were statistically analysed. RESULTS: Irregularity increased, whereas intercanine width and arch length decreased after 3 years of retention. The greatest irregularity was associated with the CBPs and the least with the CAD/CAM retainers. Changes in stability measurements were significantly higher in the dead-soft wire and CBPs than those in the CAD/CAM nitinol and multistrand SS wires. Parallel to these changes, the frequency of failure yielded similar results with the same significance between the groups. The failure rate of CBPs, in contrast to the CAD/CAM nitinol and multistrand SS wires, was significantly higher in the right quadrant (P < .05). CONCLUSION: After taking the 3-year results into consideration, CAD/CAM nitinol and multistrand SS wires were found to be more successful than the others in maintaining mandibular stability. The most failures were observed with CBPs after 3 years of retention.

Use of Leukocyte-rich and Platelet-rich Fibrin (L-PRF) Adjunct to Surgical Debridement in the Treatment of Stage 2 and 3 Medication-Related Osteonecrosis of the Jaw.

Medication-related osteonecrosis of the jaw (MRONJ) is characterized by exposed necrotic bone persisting for more than 8 weeks in the maxillofacial region in patients using antiresorptive or antiangiogenetic drugs for several treatment options like bone metastasis or osteoporosis. There are several treatment options studied in scientific literature, and one of them with promising results is using platelet concentrates adjunct to surgical therapy. The aim of this study is to examine the therapeutic effect of leukocyte and platelet-rich fibrin (L-PRF) on patients with MRONJ. This 2-centered study investigated patients referred to oral and maxillofacial surgery departments of 2 university clinics between the years 2014 and 2020 with the diagnosis of MRONJ. Demographic data, the indication of the drug usage, drug type, duration, administration route, and systemic comorbidities of the patients were recorded. L-PRF was applied to 20 osteonecrotic lesions of 19 patients following surgical debridement. The male/female ratio was 5/14. Except 1 of the patients, all of the indications of medication were neoplasia-related. The mean follow-up period of patients was 27.9±9.2 months. Most common antirezorptive drug was zoledronate (84.2%). Complete resolution was observed in 16 necrosis sites (80%). It could be concluded that the use of L-PRF may represent an important adjunct in the surgical management of MRONJ.

Effect of Residual Bone Height and Implant Macro-Design on Primary Stability in Sinus Floor Elevation: An Ex Vivo Study.

The objective was to evaluate the influence of residual bone height (RBH) and implant macro-design on the primary stability (PS) of implants using a simultaneous sinus floor elevation (SFE) and implant insertion model. Fresh bovine rib samples that resembled type-IV density that were confirmed by computerized tomography were prepared to represent 4 groups of varying RBHs (3, 6, 9, 15 mm). To simulate simultaneous implant insertion with SFE, 120 implants in different macro-designs (group R: NobelReplace; group P: NobelParallel; group A: NobelActive, Nobel Biocare, Gothenburg, Sweden) were randomly inserted at RBHs of 3, 6, 9, and 15 mm in each rib. The implant stability quotient (ISQ) was measured immediately after implant insertion. RBH and implant macro-design have an impact on ISQ values (P < .001). ISQ values were the highest with RBH of 15 mm, followed by RBHs of 9, 6, and 3 mm. (P < .001). There was no statistically significant difference between different implant macro-designs at RBHs of 3 and 15 mm regarding ISQ values (P = .111, P = .551). ISQ values of group P were higher than those of group R and group A at an RBH of 6 mm (P = .049, P = .029). ISQ values were also higher in group P compared to group A at an RBH of 9 mm (P = .006). A higher PS may be expected in sites with higher RBH, regardless of the macro-design. In addition, cylindric implant design may enhance the PS at RBHs of 6 and 9 mm in simultaneous implant insertion with SFE.

Integrating biological pathways and genomic profiles with ChiBE 2.

BACKGROUND: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets. RESULTS: ChiBE is a free, open-source software tool for visualizing, querying, and analyzing human biological pathways in BioPAX format. The recently released version 2 can search for neighborhoods, paths between molecules, and common regulators/targets of molecules, on large integrated cellular networks in the Pathway Commons database as well as in local BioPAX models. Resulting networks can be automatically laid out for visualization using a graphically rich, process-centric notation. Profiling data from the cBioPortal for Cancer Genomics and expression data from the Gene Expression Omnibus can be overlaid on these networks. CONCLUSIONS: ChiBE's new capabilities are organized around a genomics-oriented workflow and offer a unique comprehensive pathway analysis solution for genomics researchers. The software is freely available at http://code.google.com/p/chibe.

Early treatment of unilateral temporomandibular joint ankylosis: a multidisciplinary approach.

Ankylosis of temporomandibular joint is a condition in which partial or complete immobilization of mandible occurs because of fusion between mandibular condyle and skull base. This condition can be treated orthodontically, surgically, or therapeutically or by prosthodontic rehabilitation. A 10-year-old female patient presented to the Department of Oral and Maxillofacial Surgery, Gazi University Faculty of Dentistry, with limited mouth opening. She got injury in the face when she was 5 years old. Extraoral and intraoral examination findings were facial asymmetry on the left side, micrognathic mandible, and 19-mm mouth opening. After radiographic examination, ankylosis (Shawney type I) on the left side was revealed, and the patient was referred to Department of Orthodontics. After orthodontic clinical examination, we create following multidisciplinary treatment approach: (1) acrylic posterior bite block with spring application, (2) interpositional arthroplasty operation, and (3) physiotherapy (passive mouth-opening exercises). After the follow-up of 9 months, significant improvement (5 mm) was noticed in the opening of the mouth, and we decided to remove appliance and operate on the patient. Surgical procedure was performed under general anesthesia via blinded nasotracheal intubation. To prevent postoperative relapse, temporal fascia was interpositioned and sutured. Passive mouth-opening exercises were started 10 days after the surgery. Thirty-one-millimeter mouth opening was reached after the surgery and passive mouth-opening exercises. Patient's routine controls have been continued for 2 years.

Transoral endoscopic assisted reduction and internal fixation of mandibular condylar neck fractures with short condylar segment.

This study aimed to assess the reliability and safety of transoral endoscopic-assisted reduction internal fixation (TERIF) for treating short-segment condylar neck fractures (CNF), including hardware removal. Patients with displaced CNF and short condylar segments treated using TERIF were included in the study. Clinical evaluation covered dental occlusion, range of mouth opening, deviation during mouth opening, protrusion, laterotrusion, pain, and chewing. Radiological evaluation was used to assess fracture displacement, angulation, head dislocation, postoperative reduction, fixation stability, and bone healing. The same technique was used to treat 15 patients with 18 CNF and short condylar segments. Hardware removal was performed for nine fractures in eight patients after fracture healing using the same approach. All patients regained satisfactory, pain-free mouth opening with no deviation and complete bone healing. Computed tomographic images displayed adequate reduction and stable fixation during the follow-up period for all patients. No temporary or permanent facial nerve impairment occurred in any of the patients. TERIF is a reliable and safe treatment for CNF with short condylar segments, even in the presence of head dislocation, medial override, and malunited fractures; hardware can be safely removed after healing using the same approach.

Mediator kinase inhibition impedes transcriptional plasticity and prevents resistance to ERK/MAPK-targeted therapy in KRAS-mutant cancers.

Acquired resistance remains a major challenge for therapies targeting oncogene activated pathways. KRAS is the most frequently mutated oncogene in human cancers, yet strategies targeting its downstream signaling kinases have failed to produce durable treatment responses. Here, we developed multiple models of acquired resistance to dual-mechanism ERK/MAPK inhibitors across KRAS-mutant pancreatic, colorectal, and lung cancers, and then probed the long-term events enabling survival against this class of drugs. These studies revealed that resistance emerges secondary to large-scale transcriptional adaptations that are diverse and cell line-specific. Transcriptional reprogramming extends beyond the well-established early response, and instead represents a dynamic, evolved process that is refined to attain a stably resistant phenotype. Mechanistic and translational studies reveal that resistance to dual-mechanism ERK/MAPK inhibition is broadly susceptible to manipulation of the epigenetic machinery, and that Mediator kinase, in particular, can be co-targeted at a bottleneck point to prevent diverse, cell line-specific resistance programs.

A foundational atlas of autism protein interactions reveals molecular convergence.

Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.

Utilization of Sunflower Oil-based Oleogel forDeep-Fried Coated Chicken Products.

This study aimed to examine the effect of using oleogel as a frying medium on the quality of coated and deep-fried chicken products. Sunflower oil-based oleogels prepared with 0.5%, 1%, 1.5% and 2% carnauba wax were produced for deep frying of coated chicken products and were compared to sunflower and commercial frying oil based on palm oil. The increased carnauba wax concentration in the oleogel decreased the pH, oil, oil absorbance and TBARS value of coated chicken (p < 0.05). Samples deepfried with oleogels containing 1.5% and 2% carnauba wax had the lowest pH values. In addition, since the oil absorption during deep-frying was significantly reduced in these groups (1.5 and 2%), the fat contents of coated products were also lower (p < 0.05). The use of oleogel as a frying medium did not cause a significant change in the color values of the coated chicken products. However, the increased carnauba wax concentration in the oleogel increased the hardness of coated chicken (p < 0.05). As a result, sunflower oilbased oleogels with a carnauba wax content of 1.5% and higher which is healthier in terms of saturated fat content can be used as frying media and can be improved the quality of coated and deep-fried chicken products.

Mediator Kinase Inhibition Impedes Transcriptional Plasticity and Prevents Resistance to ERK/MAPK-Targeted Therapy in KRAS-Mutant Cancers.

Acquired resistance remains a major challenge for therapies targeting oncogene activated pathways. KRAS is the most frequently mutated oncogene in human cancers, yet strategies targeting its downstream signaling kinases have failed to produce durable treatment responses. Here, we developed multiple models of acquired resistance to dual-mechanism ERK/MAPK inhibitors across KRAS-mutant pancreatic, colorectal, and lung cancers, and then probed the long-term events enabling survival against this class of drugs. These studies revealed that resistance emerges secondary to large-scale transcriptional adaptations that are diverse and cell line-specific. Transcriptional reprogramming extends beyond the well-established early response, and instead represents a dynamic, evolved process that is refined to attain a stably resistant phenotype. Mechanistic and translational studies reveal that resistance to dual-mechanism ERK/MAPK inhibition is broadly susceptible to manipulation of the epigenetic machinery, and that Mediator kinase, in particular, can be co-targeted at a bottleneck point to prevent diverse, cell line-specific resistance programs.

Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches.

Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.

Antibiotic prescribing habits of the clinicians dealing with dental implant surgery in Turkey: a questionnaire study.

PURPOSE: Although various prophylactic and/or postoperative systemic antibiotic regimens have been suggested to minimize failure after dental implant placement and postoperative infection, the role of antibiotics in implant dentistry is still controversial. The purposes of this questionnaire study were to determine the current antibiotic prescribing habits of clinicians in conjunction with dental implant placement and to understand whether any consensus has been reached among implant surgery performing clinicians. METHODS: An electronic questionnaire was sent by electronic mail to all members of the Turkish Dental Society. The questions were related to whether antibiotics were routinely prescribed either pre- or/and postoperatively during routine dental implant placement. The respondents were also asked to specify their workplace and education. The results were analyzed using SPSS software. Descriptive and chi-square analyses were used to compare categorical data; Kruskal-Wallis test was used to compare the quantitative data by category. RESULTS: A total of 429 members responded to the questionnaire. The clinicians having more experience had a greater tendency to prescribe preoperative antibiotics (p < 0.001), but there was no statistically significant difference between the postoperative antibiotic prescription choice of the clinician according to the clinicians' experience (p > 0.05). A total of 175 of the clinicians preferred to prescribe preoperative antibiotics when there was systemic comorbidity; 99 of the clinicians preferred to prescribe antibiotics before every implant surgery. The aminopenicillins were the most commonly prescribed antibiotics by the clinicians. A total of 38.58% of the respondents (n = 130) who were prescribing preoperative antibiotics, 2000 mg aminopenicillin was given 1 h before the surgical procedure. Dentists and solo private practitioners were prescribing more preoperative antibiotics (p < 0,05). CONCLUSIONS: There was no consensus among clinicians regarding the use of antibiotics in association with routine dental implant placement. Aminopenicillins were the most commonly prescribed antibiotics for both pre- and postoperatively. Furthermore, most of the antibiotic regimens being used are not in accordance with the current published data.

The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2.

The mapping of SARS-CoV-2 human protein-protein interactions by Gordon and colleagues revealed druggable targets that are hijacked by the virus. Here, we highlight several oncogenic pathways identified at the host-virus interface of SARS-CoV-2 to enable cancer biologists to apply their knowledge for rapid drug repurposing to treat COVID-19, and help inform the response to potential long-term complications of the disease.

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.

An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption 1,2 . There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.

Label propagation defines signaling networks associated with recurrently mutated cancer genes.

Human tumors have distinct profiles of genomic alterations, and each of these alterations has the potential to cause unique changes to cellular homeostasis. Detailed analyses of these changes could reveal downstream effects of genomic alterations, contributing to our understanding of their roles in tumor development and progression. Across a range of tumor types, including bladder, lung, and endometrial carcinoma, we determined genes that are frequently altered in The Cancer Genome Atlas patient populations, then examined the effects of these alterations on signaling and regulatory pathways. To achieve this, we used a label propagation-based methodology to generate networks from gene expression signatures associated with defined mutations. Individual networks offered a large-scale view of signaling changes represented by gene signatures, which in turn reflected the scope of molecular events that are perturbed in the presence of a given genomic alteration. Comparing different networks to one another revealed common biological pathways impacted by distinct genomic alterations, highlighting the concept that tumors can dysregulate key pathways through multiple, seemingly unrelated mechanisms. Finally, altered genes inducing common changes to the signaling network were used to search for genomic markers of drug response, connecting shared perturbations to differential drug sensitivity.

Genomically informed small-molecule drugs overcome resistance to a sustained-release formulation of an engineered death receptor agonist in patient-derived tumor models.

Extrinsic pathway agonists have failed repeatedly in the clinic for three core reasons: Inefficient ligand-induced receptor multimerization, poor pharmacokinetic properties, and tumor intrinsic resistance. Here, we address these factors by (i) using a highly potent death receptor agonist (DRA), (ii) developing an injectable depot for sustained DRA delivery, and (iii) leveraging a CRISPR-Cas9 knockout screen in DRA-resistant colorectal cancer (CRC) cells to identify functional drivers of resistance. Pharmacological blockade of XIAP and BCL-XL by targeted small-molecule drugs strongly enhanced the antitumor activity of DRA in CRC cell lines. Recombinant fusion of the DRA to a thermally responsive elastin-like polypeptide (ELP) creates a gel-like depot upon subcutaneous injection that abolishes tumors in DRA-sensitive Colo205 mouse xenografts. Combination of ELPdepot-DRA with BCL-XL and/or XIAP inhibitors led to tumor growth inhibition and extended survival in DRA-resistant patient-derived xenografts. This strategy provides a precision medicine approach to overcome similar challenges with other protein-based cancer therapies.

Systematic mapping of BCL-2 gene dependencies in cancer reveals molecular determinants of BH3 mimetic sensitivity.

While inhibitors of BCL-2 family proteins (BH3 mimetics) have shown promise as anti-cancer agents, the various dependencies or co-dependencies of diverse cancers on BCL-2 genes remain poorly understood. Here we develop a drug screening approach to define the sensitivity of cancer cells from ten tissue types to all possible combinations of selective BCL-2, BCL-XL, and MCL-1 inhibitors and discover that most cell lines depend on at least one combination for survival. We demonstrate that expression levels of BCL-2 genes predict single mimetic sensitivity, whereas EMT status predicts synergistic dependence on BCL-XL+MCL-1. Lastly, we use a CRISPR/Cas9 screen to discover that BFL-1 and BCL-w promote resistance to all tested combinations of BCL-2, BCL-XL, and MCL-1 inhibitors. Together, these results provide a roadmap for rationally targeting BCL-2 family dependencies in diverse human cancers and motivate the development of selective BFL-1 and BCL-w inhibitors to overcome intrinsic resistance to BH3 mimetics.