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Chronic hepatitis B virus (HBV) infection is a major risk factor for the development of liver diseases including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). HBV has the multifunctional protein, HBV X protein (HBx, 154 residues), which plays key roles in HBV replication and liver disease development. Interaction of HBx through its BH3-like motif with the anti-apoptotic protein Bcl-xL leads to HBV replication and induction of apoptosis, resulting in HCC development. Our previous nuclear magnetic resonance (NMR) study revealed that the HBx BH3-like motif peptide (residues 101–136) binds to the common BH3-binding groove of Bcl-xL. Importantly, a C-terminal-truncated HBx, e.g., residues 1–120 of HBx, is strongly associated with the increased risk of HBV-related HCC development. However, the interaction mode between the C-terminal-truncated HBx and Bcl-xL remains unclear. To elucidate this interaction mode, the C-terminal-deleted HBx BH3-like motif peptide (residues 101–120) was used as a model peptide in this study. To facilitate the NMR analysis, we prepared a fusion protein of HBx(101–120) and Bcl-xL connected with five repeats of the glycine-serine dipeptide as a linker. Here, we report the 1H, 13C, and 15N resonance assignments of the fusion protein. This is the first step for the elucidation of the pathogenesis of liver diseases caused by the interaction between the C-terminal-truncated HBx and Bcl-xL.

Glutathione peroxidase 4 (GPx4) behaves as an antioxidant enzyme capable of directly reducing peroxidized phospholipids within cell membranes. Recently, GPx4 has attracted attention as a target molecule for cancer therapy because it induces the immortalization of cancer cells suppressing ferroptosis. In this study, to analyze the function and structure of GPx4 by solution NMR, we performed resonance assignments of GPx4 and assigned almost all backbone 1H, 13C, and 15N resonances and most of the side chain 1H and 13C resonances. Using these assignments, the secondary structure of GPx4 was analyzed by the TALOS + program. GPx4 has six helices and seven strands. Then, the backbone dynamics were examined by the {1H}-15N heteronuclear NOE experiment. GPx4 was found to be rigid except for a short loop region. These results will provide bases for functional analysis and the first solution structure determination of GPx4.

BACKGROUND Postoperative prolonged air leakage is a frequent complication after lung resection. We have developed a new sealant based on a hydrophobically modified Alaska pollock-derived gelatin (ApGltn) sealant. The purpose of this study was to evaluate the adhesive strength of the ApGltn sealant in comparison with a fibrin sealant using a new spray system in ex vivo and in vivo models. METHODS Pleural defects in ex vivo and in vivo porcine models were created, to which the ApGltn sealant or the fibrin sealant was applied. The pressure resistance was assessed with a stepwise increase in airway pressure to confirm air leakage from the sealing site. Tissue samples covered with each sealant were obtained for histologic assessment. RESULTS In the ex vivo experiment, the leak pressures of the ApGltn sealant were significantly greater than those of the fibrin sealant (102.94 ± 15.6 cm H2O and 28.37 ± 5.1 cm H2O, respectively) (P < .01). In the in vivo experiment, the leak pressures of the ApGltn sealant were also significantly greater than those of the fibrin sealant (68.82 ± 18.04 cm H2O and 43.33 ± 7.13 cm H2O, respectively) (P = .043). The histologic examination confirmed that the ApGltn sealant adhered tightly to both the pleura and the surface of the pleural defect. CONCLUSIONS The ApGltn sealant has sufficiently high adhesive quality in ex vivo and in vivo porcine lungs, which could be considered suitable and effective for use in the prevention of air leakage from the lungs.

Background Silicone stents are options for airway stenosis or obstruction. Generally, silicone stent placement needs rigid bronchoscopy, but manipulation of a rigid bronchoscope has technical difficulties in some cases. The objective of this clinical case report is to highlight silicone stent placement with a rigid bronchoscope successfully achieved by changing the insertion from the mouth to the tracheostoma in a patient with postpneumonectomy syndrome. Case presentation A 47-year-old man underwent right-side pneumonectomy 30 years previously, and he had an intubation tube inserted through a tracheostoma for 29 years to maintain the lumen for bronchial stenosis due to postpneumonectomy syndrome. A granuloma grew at the distal end of intubation tube, and he had labored breathing with stridor. Rigid bronchoscopy for silicone stent placement via the mouth failed because of airway curvature. We sequentially tried rigid bronchoscopy via the tracheostoma as an alternative, and we could easily insert the scope into the left secondary carina and place the silicone stent. Conclusion Although strong airway curvature with tracheostomy is an uncommon situation, we succeeded silicone stent placement using a rigid bronchoscope via the tracheostoma. Insertion of a rigid bronchoscope via the tracheostoma instead of via the mouth could be an option.

Decreased pulmonary function and poor deglutition are a major risk factor for poststroke aspiration pneumonia. We analyzed the benefits of pulmonary training on pulmonary function, deglutition, and quality of life (QOL) in community-dwelling, frail elderly people with chronic stroke.This study was designed as an open, randomized, controlled pilot trial. The participants, who were frail older adults with a history of stroke, were randomized to 2 rehabilitation groups: intervention group (The intervention group showed significant improvement in %MIP (95% CI, 2.9-31.6;These results suggest that the addition of pulmonary training including home pulmonary exercise to a standard rehabilitation program could improve pulmonary function, deglutition, and QOL in frail elderly people with chronic stroke.

Matrin-3 is a multifunctional protein that binds to both DNA and RNA. Its DNA-binding activity is linked to the formation of the nuclear matrix and transcriptional regulation, while its RNA-binding activity is linked to mRNA metabolism including splicing, transport, stabilization, and degradation. Correspondingly, Matrin-3 has two zinc finger domains for DNA binding and two consecutive RNA recognition motif (RRM) domains for RNA binding. Matrin-3 has been reported to cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) when its disordered region contains pathogenic mutations. Simultaneously, it has been shown that the RNA-binding activity of Matrin-3 mediated by its RRM domains, affects the formation of insoluble cytoplasmic granules, which are related to the pathogenic mechanism of ALS/FTD. Thus, the effect of the RRM domains on the phase separation of condensed protein/RNA mixtures has to be clarified for a comprehensive understanding of ALS/FTD. Here, we report the 1H, 15N, and 13C resonance assignments of the two RNA binding domains and their solution structures. The resonance assignments and the solution structures obtained in this work will contribute to the elucidation of the molecular basis of Matrin-3 in the pathogenic mechanism of ALS and/or FTD.

Shinsuke Kitazawa, Ashoka Indranatha Wijesinghe, Naoki Maki, Takahiro Yanagihara, Yusuke Saeki, Naohiro Kobayashi, Shinji Kikuchi, Yukinobu Goto, Hideo Ichimura, Yukio Sato Department of General Thoracic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, JapanCorrespondence: Yukio SatoDepartment of General Thoracic Surgery, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8575, JapanTel +81 29 853 3210Fax +81 29 853 7991Email ysato@md.tsukuba.ac.jpPurpose: In performing surgery for lung cancer, emphysema is a risk factor related to postoperative respiratory complications (PRC). However, few studies have addressed the risk of radiological emphysematous volume affecting PRC. The aim of this study was to investigate the relationship between emphysematous volume as measured on 3-dimensional computed tomography and PRC.Patients and Methods: We reviewed 342 lung cancer patients undergoing lobectomy between 2013 and 2018. The percentage of low attenuation area (LAA%) was defined as the percentage of the lung area showing attenuation of − 950 Hounsfield units or lower. Preoperative factors including age, sex, body mass index, smoking index, respiratory function, tumour histology, and LAA% were evaluated. PRC included pneumonia, atelectasis, prolonged air leakage, empyema, hypoxia, ischemic bronchitis, bronchopleural fistula, and exacerbation of interstitial pneumonia. Uni- and multivariable analyses were performed to investigate the relationship between independent clinical variables and postoperative adverse events.Results: Median LAA% was 5.0% (range, 0– 40%) and PRC was observed in 50 patients (14.6%). Patients who presented with PRC showed significantly high LAA% compared to those without complications (median: 8.1% vs 3.8%; p < 0.001). Based on univariable analysis, age, sex, smoking index, percentage of forced expiratory volume in 1 s (FEV1.0%), histology, and LAA% were significant predictors for PRC. Multivariable analysis revealed higher LAA% as a significant risk factor for PRC (odds ratio = 1.040; 95% confidence interval, 1.001– 1.080; p = 0.046).Conclusion: In addition to respiratory function with spirometry, LAA% can be used as a predictor of PRC.Keywords: lung cancer, emphysema, radiology and other imaging, respiratory function tests, thoracic surgery

Gaussia luciferase (GLuc 18.2kDa; 168 residues) is a marine copepod luciferase that emits a bright blue light when oxidizing coelenterazine (CTZ). It is a helical protein where two homologous sequential repeats form two anti-parallel bundles, each made of four helices. We previously identified a hydrophobic cavity as a prime candidate for the catalytic site, but Gluc’s fast bioluminescence reaction hampered a detailed analysis. Here, we used azacoelenterazine, a non-oxidizable coelenterazine analog, as a probe to investigate its binding mode to GLuc. Interestingly, the biochemical studies of GLuc inhibition by azacoelenterazine also led us to find that salt, and monovalent anions, are required for GLuc’s bioluminescence, which seems reasonable for a sea-dwelling creature. The NMR-based investigation, using chemical shift perturbations monitored by 15NH-HSQC, suggested that CTZ binds to residue in or near the hydrophobic cavity. Of note is that these NMR data are in line with a recent structural prediction of GLuc, hypothesizing that large structural changes occur in regions remote from the hydrophobic cavity upon the addition of CTZ. Interestingly, these results point toward a unique mode of catalysis to achieve CTZ oxidative decarboxylation.

SURP domains are exclusively found in splicing-related proteins in all eukaryotes. SF3A1, a component of the U2 snRNP, has two tandem SURP domains, SURP1, and SURP2. SURP2 is permanently associated with a specific short region of SF3A3 within the SF3A protein complex whereas, SURP1 binds to the splicing factor SF1 for recruitment of U2 snRNP to the early spliceosomal complex, from which SF1 is dissociated during complex conversion. Here, we determined the solution structure of the complex of SURP1 and the human SF1 fragment using nuclear magnetic resonance (NMR) methods. SURP1 adopts the canonical topology of α1-α2-3

Background The incidence rate of kinking of the middle lobe bronchus following right upper lobectomy is higher compared to that with residual lung bronchus following other lobectomies. Bronchial kinking was presumed to be caused by the displacement of the residual lung lobes, but its etiology is unclear. Moreover, prevention methods and effective treatments have not yet been established. The purpose of this study was to investigate the risk factors and etiology of middle lobe bronchus kinking and discuss prevention methods. Methods Patients who underwent right upper lobectomy in our hospital were retrospectively evaluated. Patient clinical characteristics, lung function, and lung lobe volume, surgical procedure were analyzed in association with the incidence of middle lobe bronchus kinking. The association between the displacement of residual lung lobes after operation and the incidence of middle lobe bronchus kinking was analyzed to assess the etiology. Results A total of 175 patients were enrolled in the risk analysis. Middle lobe bronchus kinking was observed in 5 patients (2.9%). The low percentage of forced expiratory volume percentage in 1 second (P=0.021), the low volume ratio of the right middle lobe (RML) to the right thoracic cavity (RTC) (P=0.016), and the low volume ratio of RML to right upper lobe (RML/RUL) (P=0.006) were significant risk factors of middle lobe bronchus kinking. In the patients who underwent CT at 6 months after surgery, the degree of the cranial displacement of RML was associated with the incidence of middle lobe bronchus kinking (P=0.025). Conclusions The risk of middle lobe bronchus kinking could be assessed preoperatively by calculating the volume ratio of RML/RTC and RML/RUL. The displacement of RML could be associated with the incidence of middle lobe bronchus kinking.

OBJECTIVES Postoperative prolonged air leakage is a frequent complication following lung resection. We have shown the high adhesive quality of a newly developed sealant based on a hydrophobically modified Alaska pollock-derived gelatin (ApGltn) sealant in acute in vivo settings. The purpose of this study was to investigate the long-term efficacy and safety of ApGltn sealant using rats as a preclinical model. METHODS An air leakage rat model with a 5-mm pleural defect was created, to which ApGltn sealant or fibrin sealant was applied. In both groups, the rats were evaluated on days 1, 7, 14 and 28. In the ApGltn sealant group, days 56 and 84 were added to evaluate absorption as sealant was still present on day 28. The number of rats in each subgroup was 4 (for a total of 40). Lung specimens and blood samples were obtained for histological and haematological assessment. RESULTS No findings suggesting infection or air leakage were observed. ApGltn sealant was absorbed from day 56 to day 84. Histologically, although neutrophil and lymphocyte infiltrations on the lung side did not differ between groups, those on the sealant side were significantly less in the ApGltn sealant group. Blood sample tests revealed no significant findings suggesting inflammation or organ damage in either group. CONCLUSIONS ApGltn sealant showed long-term sealing efficacy and safety with mild inflammation in a pulmonary air leakage rat model. ApGltn sealant is expected to be a safe and effective sealant for clinical applications.

Background Pleural adhesions are often troublesome in lung surgeries. In some dense pleural adhesions, blood vessels between lung and chest wall (BVLC) are found during surgery. Theoretically, BVLC would increase the amount of blood flow just below the visceral pleura and could allow blood vessels beneath the pleural surface to be clearly visualized on CT. In this study, we investigated whether it was possible to identify the typical CT findings of cases with BVLC. Methods Medical records and imaging findings of 186 patients who underwent surgery for lung tumors in our institution were retrospectively reviewed. Results BVLC was found in 56 patients, of whom 44 (79%) had findings on preoperative CT that indicated increase of micro-vessels just below pleura. In the 21 patients with BVLC of ≥1 mm vessel diameter, the same CT findings were recognized in 19 cases (90%). Conclusion Our results indicate that the CT finding of increased micro-vessels just below pleura has the potential to be used as a novel predictor of pleural adhesion.

Ubiquitin-like with PHD and RING finger domain-containing protein 1 (UHRF1)-dependent DNA methylation is essential for maintaining cell fate during cell proliferation. Developmental pluripotency-associated 3 (DPPA3) is an intrinsically disordered protein that specifically interacts with UHRF1 and promotes passive DNA demethylation by inhibiting UHRF1 chromatin localization. However, the molecular basis of how DPPA3 interacts with and inhibits UHRF1 remains unclear. We aimed to determine the structure of the mouse UHRF1 plant homeodomain (PHD) complexed with DPPA3 using nuclear magnetic resonance. Induced α-helices in DPPA3 upon binding of UHRF1 PHD contribute to stable complex formation with multifaceted interactions, unlike canonical ligand proteins of the PHD domain. Mutations in the binding interface and unfolding of the DPPA3 helical structure inhibited binding to UHRF1 and its chromatin localization. Our results provide structural insights into the mechanism and specificity underlying the inhibition of UHRF1 by DPPA3.

Background The preoperative predictors of quality of life (QOL) in patients who undergo lung resection for lung cancer are poorly known. Here, we investigated these predictors in such patients using two QOL measures. Methods In this single‐institutional prospective cohort study, we administered the EQ‐5D‐5 levels (EQ‐5D‐5L) from January 2015, and the European Organization for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire with 30 items from April 2015 to April 2018 preoperatively (Pre) and at one month postoperatively (M1), and one year postoperatively (Y1). General health status was measured by the EQ‐5D visual analogue scale (VAS) and EORTC global health status/QOL (GHS) scores. Multivariable linear regression analyses were used to explore the preoperative predictors of QOL at Y1. Results A total of 223 patients were included in the study. The EQ‐5D VAS and EORTC GHS scores, at Pre, M1, and Y1, were 80 ± 15, 77 ± 15, and 84 ± 11; and 74 ± 19, 65 ± 20, and 78 ± 17, respectively. In the multivariable analyses, the albumin level, preoperative VAS score, and preoperative pain/discomfort and anxiety/depression were identified as predictors by the EQ‐5D VAS score. The preoperative EORTC GHS score, absence of diabetes mellitus, preoperative cognitive function score, and preoperative symptom score of pain were identified as predictors by the EORTC GHS score. Conclusions The EQ‐5D VAS and EORTC GHS scores traced similar trajectories of QOL. In both QOL measures, preoperative pain was found as a common predictor. These predictors may help improve patient/survivor care in the future., We investigated the preoperative predictors of QOL in surgical patients with lung cancer. General health status/QOL was measured by EQ‐5D VAS and EORTC GHS scores. Multivariable linear regression analyses were used. Although each QOL measure detected some preoperative predictors, preoperative pain was a common predictor in both, one year after surgery. Predictors detected in this study were possible targets for patient/survivor care.

Gaussia luciferase (GLuc) is a small luciferase (18.2 kDa; 168 residues) and is thus attracting much attention as a reporter protein, but the lack of structural information is hampering further application. Here, we report the first solution structure of a fully active, recombinant GLuc determined by heteronuclear multidimensional NMR. We obtained a natively folded GLuc by bacterial expression and efficient refolding using a Solubility Enhancement Petide (SEP) tag. Almost perfect assignments of GLuc’s 1H, 13C and 15N backbone signals were obtained. GLuc structure was determined using CYANA, which automatically identified over 2500 NOEs of which > 570 were long-range. GLuc is an all-alpha-helix protein made of nine helices. The region spanning residues 10–18, 36–81, 96–145 and containing eight out of the nine helices was determined with a Cα-atom RMSD of 1.39 Å ± 0.39 Å. The structure of GLuc is novel and unique. Two homologous sequential repeats form two anti-parallel bundles made by 4 helices and tied together by three disulfide bonds. The N-terminal helix 1 is grabbed by these 4 helices. Further, we found a hydrophobic cavity where several residues responsible for bioluminescence were identified in previous mutational studies, and we thus hypothesize that this is a catalytic cavity, where the hydrophobic coelenterazine binds and the bioluminescence reaction takes place.

Rie Koga, Mami Yamamoto, Takahiro Kosugi, Naohiro Kobayashi, Toshihiko Sugiki, Toshimichi Fujiwara, Nobuyasu Koga, Robust folding of a de novo designed ideal protein even with most of the core mutated to valine. Proceedings of the National Academy of Sciences. 117 (49), 31149-31156 (2020). DOI: 10.1073/pnas.2002120117., Protein design provides a stringent test for our understanding of protein folding. We previously described principles for designing ideal protein structures stabilized by consistent local and nonlocal interactions, based on a set of rules relating local backbone structures to tertiary packing motifs. The principles have made possible the design of protein structures having various topologies with high thermal stability. Whereas nonlocal interactions such as tight hydrophobic core packing have traditionally been considered to be crucial for protein folding and stability, the rules proposed by our previous studies suggest the importance of local backbone structures to protein folding. In this study, we investigated the robustness of folding of de novo designed proteins to the reduction of the hydrophobic core, by extensive mutation of large hydrophobic residues (Leu, Ile) to smaller ones (Val) for one of the designs. Surprisingly, even after 10 Leu and Ile residues were mutated to Val, this mutant with the core mostly filled with Val was found to not be in a molten globule state and fold into the same backbone structure as the original design, with high stability. These results indicate the importance of local backbone structures to the folding ability and high thermal stability of designed proteins and suggest a method for engineering thermally stabilized natural proteins.

Left cardiac sympathetic denervation is a procedure used to prevent ventricular arrhythmias that remain refractory despite medical treatments. This procedure usually involves the resection of the lower side of the stellate ganglion, which is an uncommon surgical technique due to the limited situations in which it can be applied. Here, we report a case of refractory ventricular arrhythmias and a description of its successful treatment with the method of left cardiac sympathetic denervation using video-assisted thoracotomy.

Endobronchial‐invasive lung cancers are generally diagnosed at advanced stages and may require emergency treatment for airway obstruction. Stent implantation is a common intervention for such obstructed airways but certain subsets of patients cannot receive adequate treatment without respiratory support. Veno‐venous extracorporeal membrane oxygenation (ECMO) is a salvage therapy for respiratory failure but its usefulness in managing patients with advanced lung cancer remains unclear given the poor prognosis. In recent years, molecular targeted agents for patients with driver mutations offer rapid responses and may be administered even while under critical care. In this report, we describe the case of 39‐year‐old female who presented to our emergency department with severe respiratory distress. A computed tomography scan revealed a large mediastinal tumor invading the tracheal carina causing severe stenosis of the left main bronchus and right main pulmonary artery. ECMO support was required as the respiratory condition remained unstable despite high pressure ventilation. Under ECMO support, the patient underwent bronchial stent implantation and was successfully weaned off ECMO. The tumor was histologically diagnosed as pulmonary adenocarcinoma with anaplastic lymphoma kinase gene rearrangement. Treatment with a tyrosine kinase inhibitor, alectinib, induced a marked tumor reduction within a short period. The patient recovered well and is now in remission one year later. This case indicates that intensive respiratory support with ECMO may become a bridge through the critical period for selected patients with respiratory failure secondary to advanced lung cancer. Key points Significant findings of this study ECMO was important to maintain oxygenation during airway intervention for acute respiratory failure due to critical lung adenocarcinoma with ALK gene rearrangement. What this study adds With the development of targeted therapies and the improvement in therapeutic bronchoscopy, intensive respiratory support with ECMO may be helpful especially in selected lung cancer patients with oncogenic driver mutations., Respiratory support with extracorporeal membrane oxygenation (ECMO) in managing patients with advanced lung cancer remains unclear given the poor prognosis. Targeted agents for patients with driver mutations offer rapid responses and may be administered even while under critical care. In some patients with critical lung cancer, ECMO may become a bridge through the critical period with respect to effective anti‐cancer therapies.

In humans, YTH (YT521-B homology) domain containing protein 2 (YTHDC2) plays a crucial role in the phase-shift from mitosis to meiosis. YTH domains bind to methylated adenosine nucleotides such as m6A. In a phylogenic tree, the YTH domain of YTHDC2 (YTH2) and that of the YTH containing protein YTHDC1 (YTH1) belong to the same sub-group. However, the binding affinity of m6A differs between these proteins. Here, we report 1H, 13C and 15N resonance assignment of YTH2 and its solution structure to examine the difference of the structural architecture and the dynamic properties of YTH1 and YTH2. YTH2 adopts a β1-α1-β2-α2-β3-β4-β5-α3-β6-α4 topology, which was also observed in YTH1. However, the β4-β5 loops of YTH1 and YTH2 are distinct in length and amino acid composition. Our data revealed that, unlike in YTH1, the structure of m6A-binding pocket of YTH2 formed by the β4-β5 loop is stabilized by electrostatic interaction. This assignment and the structural information for YTH2 will provide the insight on the further functional research of YTHDC2.

This study evaluated the relationship between three-dimensional (3D) mean computed tomography (CT) attenuation values of ground-glass nodules (GGN) and pathological invasiveness in early lung adenocarcinoma. The diagnostic accuracy of 3D CT attenuation values was compared with that of two-dimensional (2D) CT attenuation values and standardised uptake value on positron-emission tomography (PET).Surgical and radiological data from 96 pure or part-solid GGNs of20 mm were analysed retrospectively. Mean 2D and 3D CT attenuation values of the tumours were obtained with semi-automated volumetric software. Pathological invasiveness was diagnosed according to the International Association for the Study of Lung Cancer (IASLC))/American Thoracic Society (ATS)/European Respiratory Society (ERS) classification. Pre-invasive lesions and minimally invasive adenocarcinomas were classified as non-invasive adenocarcinoma. Univariate and multivariate analyses determined relationships between pathological invasiveness and clinical/radiological findings. Receiver operating characteristic (ROC) analysis was performed to determine the optimal cut-off value for detecting invasive adenocarcinoma.A total of 66 non-invasive and 30 invasive adenocarcinoma cases between 2010 and 2016 were analysed. Univariate analysis revealed four tumour invasiveness-associated predictors: maximum diameter, SUVmax, mean 2D CT attenuation value, and mean 3D CT attenuation value (p0.05). Multivariate analysis revealed that the maximum diameter, SUVmax, and mean 3D CT attenuation value were significant predictors of pathological invasiveness (p=0.023, 0.022, 0.004). The area under the ROC curve to predict invasive adenocarcinoma for mean 3D CT attenuation value was 0.838 and the cut-off value was -489 HU.The mean 3D CT attenuation value could distinguish pre-invasive lesions and minimally invasive adenocarcinoma from invasive adenocarcinoma.

NMR studies can provide unique information about protein conformations in solution. In CASP14, three reference structures provided by solution NMR methods were available (T1027, T1029, and T1055), as well as a fourth data set of NMR-derived contacts for an integral membrane protein (T1088). For the three targets with NMR-based structures, the best prediction results ranged from very good (GDT_TS=0.90, for T1055) to poor (GDT_TS=0.47, for T1029). We explored the basis of these results by comparing all CASP14 prediction models against experimental NMR data. For T1027, NMR data reveal extensive internal dynamics, presenting a unique challenge for protein structure prediction methods. The analysis of T1029 motivated exploration of a novel method of "inverse structure determination", in which an AlphaFold2 model was used to guide NMR data analysis. NMR data provided to CASP predictor groups for target T1088, a 238-residue integral membrane porin, was also used to assess several NMR-assisted prediction methods. Most groups involved in this exercise generated similar beta-barrel models, with good agreement with the experimental data. However, as was also observed in CASP13, some pure prediction groups that did not use any NMR data generated models for T1088 that better fit the NMR data than the models generated using these experimental data. These results demonstrate the remarkable power of modern methods to predict structures of proteins with accuracies rivaling solution NMR structures, and that it is now possible to reliably use prediction models to guide and complement experimental NMR data analysis. This article is protected by copyright. All rights reserved.

MAFB is a transcription factor specifically expressed in macrophages. Tumor associated macrophages (TAMs) play a key role in the tumor microenvironment (TME) by inducing immunosuppression, angiogenesis, tumor invasion, and metastasis. However, finding a suitable specific biomarker and target for TAMs is challenging. Our previous study1 suggested that MAFB could be a suitable marker for tumor-associated macrophages (TAMs) besides MAFB is expressed in anti-inflammatory alternatively activated M2 macrophages in vitro. In the current study, in a cohort of patients with lung adenocarcinoma (n = 120), increased MAFB expression was related to increased metastasis and poor overall survival rate. Our findings indicate that MAFB can be used as a prognostic marker for assessing metastatic potential in patients with lung adenocarcinoma. Further, we showed that MAFB expression was positively correlated with the expression of CD204 and CD68 in hepatocarcinoma, colon and pancreatic cancers. We demonstrated that MAFB could be used as a biomarker for TAMs and consequently, for assessing severity in various human cancers, including lung, liver, colon, and pancreatic cancers, according to the immunohistochemical analysis of the expression of MAFB, CD68, and CD204. In addition, we showed that MAFB was expressed in TAMs expressing Programmed cell death protein-1 and/or Programmed cell death ligand 1 (TAM PD-1+ and TAM PD-L1+) cells in lung adenocarcinoma and Lewis lung carcinoma (LLC) mouse model. These findings indicate that MAFB can be a potential target for drug development against TAM PD-1+ and TAM PD-L1+ cells. In summary, transcriptional factor MAFB can be used as a specific biomarker, prognostic marker, and a potential target for cancer immunotherapy against TAMs.