Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex.

The type III-E CRISPR-Cas effector Cas7-11, with dual RNase activities for precursor CRISPR RNA (pre-crRNA) processing and crRNA-guided target RNA cleavage, is a new platform for bacterial and mammalian RNA targeting. We report the 2.5-Å resolution cryoelectron microscopy structure of Cas7-11 in complex with a crRNA and its target RNA. Cas7-11 adopts a modular architecture comprising seven domains (Cas7.1-Cas7.4, Cas11, INS, and CTE) and four interdomain linkers. The crRNA 5' tag is recognized and processed by Cas7.1, whereas the crRNA spacer hybridizes with the target RNA. Consistent with our biochemical data, the catalytic residues for programmable cleavage in Cas7.2 and Cas7.3 neighbor the scissile phosphates before the flipped-out fourth and tenth nucleotides in the target RNA, respectively. Using structural insights, we rationally engineered a compact Cas7-11 variant (Cas7-11S) for single-vector AAV packaging for transcript knockdown in human cells, enabling in vivo Cas7-11 applications.

Cyclic GMP-AMP as an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA.

The innate immune system functions as the first line of defense against invading bacteria and viruses. In this context, the cGAS/STING [cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase/STING] signaling axis perceives the nonself DNA associated with bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. In this pathway, the noncanonical cyclic dinucleotide 2',3'-cyclic GMP-AMP (2',3'-cGAMP) functions as a second messenger for signal transduction: 2',3'-cGAMP is produced by the enzyme cGAS upon its recognition of double-stranded DNA, and then the 2',3'-cGAMP is recognized by the receptor STING to induce the phosphorylation of downstream factors, including TBK1 (TANK binding kinase 1) and IRF3 (interferon regulatory factor 3). Numerous crystal structures of the components of this cGAS/STING signaling axis have been reported and these clarify the structural basis for their signal transduction mechanisms. In this review, we summarize recent progress made in the structural dissection of this signaling pathway and indicate possible directions of forthcoming research.

Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases.

RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryoelectron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement may apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses suggest not only conserved substrates for TRIM proteins but also, unexpectedly, deep evolutionary connections between TRIM proteins and RNA helicases, linking ubiquitin and RNA biology throughout animal evolution.

The physico-geometrical reaction pathway and kinetics of multistep thermal dehydration of calcium chloride dihydrate in a dry nitrogen stream.

Several inorganic hydrates exhibit reversible reactions of thermal dehydration and rehydration, which is potentially applicable to thermochemical energy storage. Detailed kinetic information on both forward and reverse reactions is essential for refining energy storage systems. In this study, factors determining the reaction pathway and kinetics of the multistep thermal dehydration of inorganic hydrates to form anhydride via intermediate hydrates were investigated as exemplified by the thermal dehydration of CaCl2·2H2O (CC-DH) in a stream of dry N2. The formation of CaCl2·H2O (CC-MH) as the intermediate hydrate is known during the thermal dehydration of CC-DH to form its anhydride (CC-AH). However, the two-step kinetic modeling based on the chemical reaction pathway considering the formation of the CC-MH intermediate failed in terms of the reaction stoichiometry and kinetic behavior of the component reaction steps. The kinetic modeling was refined by considering the physico-geometrical reaction mechanism and the self-generated reaction conditions to be a three-step reaction. The multistep reaction was explained as comprising the surface reaction of the thermal dehydration of CC-DH to CC-AH and subsequent contracting geometry-type reactions from CC-DH to CC-MH and from CC-MH to CC-AH occurring consecutively in the core of the reacting particles surrounded by the surface product layer of CC-AH. The acceleration of the linear advancement rate of the reaction interface during both contracting geometry-type reactions was revealed through multistep kinetic analysis and was described by a decrease in the water vapor pressure at the reaction interface as the previous reaction step proceeded and terminated.

Water vapor effect on the physico-geometrical reaction pathway and kinetics of the multistep thermal dehydration of calcium chloride dihydrate.

This study investigated how water vapor influences the reaction pathway and kinetics of the multistep thermal dehydration of inorganic hydrates, focusing on CaCl2·2H2O (CC-DH) transforming into its anhydride (CC-AH) via an intermediate of its monohydrate (CC-MH). In the presence of atmospheric water vapor, the thermal dehydration of CC-DH stoichiometrically proceeded through two distinct steps, resulting in the formation of CC-AH via CC-MH under isothermal conditions and linear nonisothermal conditions at a lower heating rate (ß). Irrespective of atmospheric water vapor pressure (p(H2O)), these reaction steps were kinetically characterized by a physico-geometrical consecutive process involving the surface reaction and phase boundary-controlled reaction, which was accompanied by three-dimensional shrinkage of the reaction interface. In addition, a significant induction period was observed for the second reaction step, that is, the thermal dehydration of CC-MH intermediate to form CC-AH. With increasing p(H2O), a systematic increase in the apparent Arrhenius parameters was observed for the first reaction step, that is, the thermal dehydration of CC-DH to form CC-MH, whereas the second reaction step exhibited unsystematic variations of the Arrhenius parameters. At a larger ß in the presence of atmospheric water vapor, the first and second reaction steps partially overlapped; moreover, an alternative reaction step of the thermal dehydration of CC-MH to form CaCl2·0.3H2O was observed between these reaction steps. The physico-geometrical phenomena influencing the reaction pathway and kinetics of the multistep thermal dehydration were elucidated by considering the effects of atmospheric and self-generated water vapor in a geometrically constrained reaction scheme.

Thermal dehydration of D-glucose monohydrate in solid and liquid states.

The physico-geometrical reaction pathway and kinetics of the thermal dehydration of D-glucose monohydrate (DG-MH) dramatically alter by the melting of the reactant midway through the reaction. By controlling the reaction conditions, the thermal dehydration of DG-MH was systematically traced by thermoanalytical techniques in three different reaction modes: (1) solid-state reaction, (2) switching from a solid- to liquid-state reaction, and (3) liquid-state reaction. Solid-state thermal dehydration occurred under isothermal conditions and linear nonisothermal conditions at a small heating rate (ß ≤ 1 K min-1) in a stream of dry N2. The kinetic behavior comprised the presence of an induction period and a sigmoidal mass loss process characterized by a derivative mass loss curve with a symmetrical shape under isothermal conditions, resembling the autocatalytic reaction in homogeneous kinetic processes. When DG-MH was heated at a larger ß (≥2 K min-1), the melting of DG-MH occurred midway through the thermal dehydration process, by which a core-shell structure of molten DG-MH and surface product layer of crystalline anhydride was produced. Subsequently, thermal dehydration proceeded as a complex multistep process. Furthermore, the thermal dehydration initiated at approximately the melting point of DG-MH upon the application of a certain water vapor pressure to the reaction atmosphere, and proceeded in the liquid-state, exhibiting a smooth mass loss process to form crystalline anhydride. The reaction pathway and kinetics of the thermal dehydration of DG-MH and the corresponding changes with the sample and reaction conditions are discussed on the basis of the detailed kinetic analysis.

[Mitral and Aortic Valve Replacement and Tricuspid Valve Repair in a Patient with Metal Allergy].

We report a 63-year-old woman came to our hospital with exertional dyspnea, palpitations, and abdominal distention. Echocardiography showed mitral, aortic, and tricuspid valve insufficiency, for which surgery was indicated. Twenty-six years ago, during dental therapy, she was diagnosed with metal allergy. A patch test demonstrated allergic reactions to manganese, chromium, and zinc. The patient underwent mitral and aortic valve replacement with the On-X prosthetic heart valve, which is primarily made of titanium and devoid of the allergens. She also underwent tricuspid valve repair with a Contour 3D annuloplasty ring, which is made of titanium alloy. She manifested no allergic symptoms three years after surgery. This case elucidates the importance of history taking regarding metal allergy and identification of allergens by patch testing in patients undergoing cardiac surgery involving metal device implantation.

Endocytoscopic intramucosal capillary network changes and crypt architecture abnormalities can predict relapse in patients with an ulcerative colitis Mayo endoscopic score of 1.

OBJECTIVES: Recent studies have suggested the necessity of therapeutic intervention for patients with ulcerative colitis at high risk of clinical relapse with a Mayo endoscopic score (MES) of 1. The aim of this retrospective cohort study was to demonstrate the impact of intramucosal capillary network changes and crypt architecture abnormalities to stratify the risk of relapse in patients with an MES of 1. METHODS: All included patients had an MES of ≤1 and confirmed sustained clinical remission between October 2016 and April 2019. We classified patients with an MES of 1 as "intramucosal capillary/crypt (ICC)-active" or "ICC-inactive" using endocytoscopic evaluation. We followed patients until October 2019 or until relapse; the main outcome measure was the difference in clinical relapse-free rates between ICC-active and ICC-inactive patients with an MES of 1. RESULTS: We included 224 patients and analyzed data for 218 (82 ICC-active and 54 ICC-active with an MES of 1 and 82 with an MES of 0). During follow-up, among the patients with an MES of 1, 30.5% (95% confidence interval 20.8-41.6; 25/82) of the patients relapsed in the ICC-active group and 5.6% (95% confidence interval 1.2-15.4; 3/54) of the patients relapsed in the ICC-inactive group. The ICC-inactive group had a significantly higher clinical relapse-free rate compared with the ICC-active group (P < 0.01). CONCLUSIONS: In vivo intramucosal capillary network and crypt architecture patterns stratified the risk of clinical relapse in patients with an MES of 1 (UMIN 000032580; UMIN 000036359).

Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.

Enpp1 is a membrane-bound glycoprotein that regulates bone mineralization by hydrolyzing extracellular nucleotide triphosphates to produce pyrophosphate. Enpp1 dysfunction causes human diseases characterized by ectopic calcification. Enpp1 also inhibits insulin signaling, and an Enpp1 polymorphism is associated with insulin resistance. However, the precise mechanism by which Enpp1 functions in these cellular processes remains elusive. Here, we report the crystal structures of the extracellular region of mouse Enpp1 in complex with four different nucleotide monophosphates, at resolutions of 2.7-3.2 Å. The nucleotides are accommodated in a pocket formed by an insertion loop in the catalytic domain, explaining the preference of Enpp1 for an ATP substrate. Structural mapping of disease-associated mutations indicated the functional importance of the interdomain interactions. A structural comparison of Enpp1 with Enpp2, a lysophospholipase D, revealed marked differences in the domain arrangements and active-site architectures. Notably, the Enpp1 mutant lacking the insertion loop lost the nucleotide-hydrolyzing activity but instead gained the lysophospholipid-hydrolyzing activity of Enpp2. Our findings provide structural insights into how the Enpp family proteins evolved to exert their diverse cellular functions.

Programmable RNA writing with trans-splicing.

RNA editing offers the opportunity to introduce either stable or transient modifications to nucleic acid sequence without permanent off-target effects, but installation of arbitrary edits into the transcriptome is currently infeasible. Here, we describe Programmable RNA Editing & Cleavage for Insertion, Substitution, and Erasure (PRECISE), a versatile RNA editing method for writing RNA of arbitrary length and sequence into existing pre-mRNAs via 5' or 3' trans-splicing. In trans-splicing, an exogenous template is introduced to compete with the endogenous pre-mRNA, allowing for replacement of upstream or downstream exon sequence. Using Cas7-11 cleavage of pre-mRNAs to bias towards editing outcomes, we boost the efficiency of RNA trans-splicing by 10-100 fold, achieving editing rates between 5-50% and 85% on endogenous and reporter transcripts, respectively, while maintaining high-fidelity. We demonstrate PRECISE editing across 11 distinct endogenous transcripts of widely varying expression levels, showcasing more than 50 types of edits, including all 12 possible transversions and transitions, insertions ranging from 1 to 1,863 nucleotides, and deletions. We show high efficiency replacement of exon 4 of MECP2, addressing most mutations that drive the Rett Syndrome; editing of SHANK3 transcripts, a gene involved in Autism; and replacement of exon 1 of HTT, removing the hallmark repeat expansions of Huntington's disease. Whole transcriptome sequencing reveals the high precision of PRECISE editing and lack of off-target trans-splicing activity. Furthermore, we combine payload engineering and ribozymes for protein-free, high-efficiency trans-splicing, with demonstrated efficiency in editing HTT exon 1 via AAV delivery. We show that the high activity of PRECISE editing enables editing in non-dividing neurons and patient-derived Huntington's disease fibroblasts. PRECISE editing markedly broadens the scope of genetic editing, is straightforward to deliver over existing gene editing tools like prime editing, lacks permanent off-targets, and can enable any type of genetic edit large or small, including edits not otherwise possible with existing RNA base editors, widening the spectrum of addressable diseases.

A bispecific antibody NXT007 exerts a hemostatic activity in hemophilia A monkeys enough to keep a nonhemophilic state.

BACKGROUND: Emicizumab, a factor (F) VIIIa-function mimetic bispecific antibody (BsAb) to FIXa and FX, has become an indispensable treatment option for people with hemophilia A (PwHA). However, a small proportion of PwHA still experience bleeds even under emicizumab prophylaxis, as observed in the long-term outcomes of clinical studies. A more potent BsAb may be desirable for such patients. OBJECTIVES: To identify a potent BsAb to FIXa and FX, NXT007, surpassing emicizumab by in vitro and in vivo evaluation. METHODS: New pairs of light chains for emicizumab's heavy chains were screened from phage libraries, and subsequent antibody optimization was performed. For in vitro evaluation, thrombin generation assays were performed with hemophilia A plasma. In vivo hemostatic activity was evaluated in a nonhuman primate model of acquired hemophilia A. RESULTS: NXT007 exhibited an in vitro thrombin generation activity comparable to the international standard activity of FVIII (100 IU/dL), much higher than emicizumab, when triggered by tissue factor. NXT007 also demonstrated a potent in vivo hemostatic activity at approximately 30-fold lower plasma concentrations than emicizumab's historical data. In terms of dose shift between NXT007 and emicizumab, the in vitro and in vivo results were concordant. Regarding pharmacokinetics, NXT007 showed lower in vivo clearance than those shown by typical monoclonal antibodies, suggesting that the Fc engineering to enhance FcRn binding worked well. CONCLUSION: NXT007, a potent BsAb, was successfully created. Nonclinical results suggest that NXT007 would have a potential to keep a nonhemophilic range of coagulation potential in PwHA or to realize more convenient dosing regimens than emicizumab.

Efficacy of lamivudine or entecavir against virological rebound after achieving HBV DNA negativity in chronic hepatitis B patients.

Nucleos(t)ide analogues (NAs) lead to viral suppression and undetectable hepatitis B virus (HBV) DNA in some individuals infected with HBV, but the rate of virological rebound has been unknown in such patients. We examined the prevalence of virological rebound of HBV DNA among NA-treated patients with undetectable HBV DNA. We retrospectively analyzed 303 consecutive patients [158 entecavir (ETV)- and 145 lamivudine (LAM)-treated] who achieved HBV DNA negativity, defined as HBV DNA < 3.7 log IU/mL for at least 3 months. They were followed up and their features, including their rates of viral breakthrough, were determined. Viral rebound after HBV DNA negativity was not observed in the ETV-group. Viral rebound after HBV DNA negativity occurred in 38.7% of 62 HBe antigen-positive patients in the LAM-group. On multivariate analysis, age was an independent factor for viral breakthrough among these patients (P = 0.035). Viral rebound after HBV DNA negativity occurred in 29.1% of 79 HBe antigen-negative patients in the LAM-group. Differently from LAM, ETV could inhibit HBV replication once HBV DNA negativity was achieved. In contrast, LAM could not inhibit HBV replication even if HBV negativity was achieved in the early phase. Attention should be paid to these features in clinical practice.

Clinical usefulness of doripenem (DRPM), a carbapenem antimicrobial drug, for the treatment of patients with acute cholangitis: retrospective study.

AIM: We investigated the usefulness of doripenem (DRPM), a carbapenem antimicrobial drug, for the treatment of acute cholangitis. METHODS: 28 patients who received a diagnosis of moderate or severe cholangitis were included in this investigation. 23 patients had moderate cholangitis; 5 patients had severe cholangitis. When moderate or severe cholangitis was diagnosed, administration of DRPM and endoscopic drainage were performed. The dose of DRPM was fixed at 0.5 g, 3 times daily. Evaluation of clinical findings (abdominal pain and body temperature) and blood test findings (WBC, CRP, ALT, ALP, and T-Bil) was performed before and on Day 5 after administration. RESULTS: Endoscopic drainage was successful in all patients. After administration of DRPM, a significant improvement was observed in all endpoints of both clinical findings and blood test findings (p < 0.05). No adverse events due to administration of DRPM were observed. CONCLUSION: It was suggested that administration of DRPM may be clinically useful for the treatment of moderate and severe cholangitis.

An adult case of giant congenital left atrial wall aneurysm.

Congenital left atrial wall aneurysm is a rare disorder that occurs in a wide range of age groups from infancy to adulthood. Here, we present a case of a congenital left atrial wall aneurysm that was detected in a 19-year-old man who was surgically treated. Although the patient was asymptomatic without any pre-existing conditions, chest radiography performed as part of a routine health examination detected abnormalities in the heart. Contrast-enhanced computed tomography revealed a giant aneurysm measuring 72 mm × 56 mm that extended from the posteroinferior wall of the left atrium to the posterior surface of the left ventricle. Transthoracic echocardiography revealed mild mitral regurgitation. The patient was diagnosed as having a congenital left atrial wall aneurysm associated with mild mitral regurgitation. The aneurysm was resected through median sternotomy under cardiopulmonary bypass with cardioplegic arrest. During surgery, no structural abnormalities were noted in the mitral valve. After surgery, the patient was discharged without complications. Neither recurrence of the aneurysm nor exacerbation of mitral regurgitation was observed at 1 year postoperatively. Learning objective: A congenital left atrial wall aneurysm is a rare disorder. Rupture of the aneurysm is rare. However, when they are left untreated, there are concerns regarding arrhythmias, heart failure, and systemic embolism. Thus, surgical treatment is recommended. Aneurysms are resected under cardiopulmonary bypass. In cases of aneurysms complicated by moderate or severer mitral regurgitation, mitral valve repair is necessary. The prognosis following surgical treatment is favorable.

Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses.

Programmable RNA-guided DNA nucleases perform numerous roles in prokaryotes, but the extent of their spread outside prokaryotes is unclear. Fanzors, the eukaryotic homolog of prokaryotic TnpB proteins, have been detected in genomes of eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. Here, we characterize Fanzors as RNA-programmable DNA endonucleases, using biochemical and cellular evidence. We found diverse Fanzors that frequently associate with various eukaryotic transposases. Reconstruction of Fanzors evolution revealed multiple radiations of RuvC-containing TnpB homologs in eukaryotes. Fanzor genes captured introns and proteins acquired nuclear localization signals, indicating extensive, long-term adaptation to functioning in eukaryotic cells. Fanzor nucleases contain a rearranged catalytic site of the RuvC domain, similar to a distinct subset of TnpBs, and lack collateral cleavage activity. We demonstrate that Fanzors can be harnessed for genome editing in human cells, highlighting the potential of these widespread eukaryotic RNA-guided nucleases for biotechnology applications.

Treatment strategy changes for inflammatory bowel diseases in biologic era: results from a multicenter cohort in Japan, Far East 1000.

Many molecular targeted agents, including biologics, have emerged for inflammatory bowel diseases (IBD), but their high prices have prevented their widespread use. This study aimed to reveal the changes in patient characteristics and the therapeutic strategies of IBD before and after the implementation of biologics in Japan, where the unique health insurance system allows patients with IBD and physicians to select drugs with minimum patient expenses. The analysis was performed using a prospective cohort, including IBD expert and nonexpert hospitals in Japan. In this study, patients were classified into two groups according to the year of diagnosis based on infliximab implementation as the prebiologic and biologic era groups. The characteristics of therapeutic strategies in both groups were evaluated using association analysis. This study analyzed 542 ulcerative colitis (UC) and 186 Crohn's disease (CD). The biologic era included 53.3% of patients with UC and 76.2% with CD, respectively. The age of UC (33.9 years vs. 38.8 years, P < 0.001) or CD diagnosis (24.3 years vs. 31.9 years, P < 0.001) was significantly higher in the biologic era group. The association analysis of patients with multiple drug usage histories revealed that patients in the prebiologic era group selected anti-tumor necrosis factor (TNF)-α agents, whereas those in the biologic era group preferred biologic agents with different mechanisms other than anti-TNF-α. In conclusion, this study demonstrated that both patient characteristics and treatment preferences in IBD have changed before and after biologic implementation.

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp1.

Enpp1 is an extracellular membrane-bound glycoprotein that regulates bone mineralization by hydrolyzing ATP to generate pyrophosphate. The extracellular region of mouse Enpp1 was expressed in HEK293S GnT1(-) cells, purified using the TARGET tag/P20.1-Sepharose system and crystallized. An X-ray diffraction data set was collected to 3.0 Šresolution. The crystal belonged to space group P3(1), with unit-cell parameters a = b = 105.3, c = 173.7 Å. A single-wavelength anomalous dispersion (SAD) data set was also collected to 2.7 Šresolution using a selenomethionine-labelled crystal. The experimental phases determined by the SAD method produced an interpretable electron-density map.

Six autoantibodies as potential differential biomarkers of hepatocellular carcinoma vs. liver cirrhosis and chronic hepatitis: A prospective multi-institutional study.

Serum autoantibodies respond not only to tumor-associated antigens of hepatocellular carcinoma (HCC) but also to those of liver cirrhosis (LC) and chronic hepatitis (CH). The present prospective multi-institutional study evaluated the diagnostic properties of six autoantibodies in distinguishing HCC from LC and CH. A total of 416 participants were enrolled: 149 With HCC, 76 with LC, 103 with CH and 88 healthy controls. Titers of serum autoantibodies to Sui1, RalA, p62, p53, c-myc and NY-ESO-1 were determined using enzyme-linked immunosorbent assays. All six antibodies were positive for HCC: s-Sui1-Abs (44%), s-RalA-Abs (23%), s-p62-Abs (21%), s-p53-Abs (13%), s-c-myc-Abs (11%) and s-NY-ESO-1-Abs (6%). The positivity rates of all six antibodies combined were 5% for healthy controls, 52% for CH, 58% for LC and 66% for HCC. The positivity rates of s-Sui1-Abs, s-RalA-Abs and s-p53-Abs were higher for HCC compared with those of LC and CH. However, the positivity rates of s-p62-Abs, s-c-myc-Abs and s-NY-ESO-1-Abs for HCC were not higher compared with those for LC and CH. Overall, autoantibodies were useful in differentiating patients with HCC from healthy individuals. However, they were not specific to HCC and were also present in the sera of individuals with CH and LC. These autoantibodies may be induced during the development of HCC. Clinical trial registration number: UMIN000014530 (date of registration 2011/07/11).

Molecular and clinicopathological differences between depressed and protruded T2 colorectal cancer.

BACKGROUND: Colorectal cancer (CRC) can be classified into four consensus molecular subtypes (CMS) according to genomic aberrations and gene expression profiles. CMS is expected to be useful in predicting prognosis and selecting chemotherapy regimens. However, there are still no reports on the relationship between the morphology and CMS. METHODS: This retrospective study included 55 subjects with T2 CRC undergoing surgical resection, of whom 30 had the depressed type and 25 the protruded type. In the classification of the CMS, we first defined cases with deficient mismatch repair as CMS1. And then, CMS2/3 and CMS4 were classified using an online classifier developed by Trinh et al. The staining intensity of CDX2, HTR2B, FRMD6, ZEB1, and KER and the percentage contents of CDX2, FRMD6, and KER are input into the classifier to obtain automatic output classifying the specimen as CMS2/3 or CMS4. RESULTS: According to the results yielded by the online classifier, of the 30 depressed-type cases, 15 (50%) were classified as CMS2/3 and 15 (50%) as CMS4. Of the 25 protruded-type cases, 3 (12%) were classified as CMS1 and 22 (88%) as CMS2/3. All of the T2 CRCs classified as CMS4 were depressed CRCs. More malignant pathological findings such as lymphatic invasion were associated with the depressed rather than protruded T2 CRC cases. CONCLUSIONS: Depressed-type T2 CRC had a significant association with CMS4, showing more malignant pathological findings such as lymphatic invasion than the protruded-type, which could explain the reported association between CMS4 CRC and poor prognosis.

Structure of the IscB-ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9.

Transposon-encoded IscB family proteins are RNA-guided nucleases in the OMEGA (obligate mobile element-guided activity) system, and likely ancestors of the RNA-guided nuclease Cas9 in the type II CRISPR-Cas adaptive immune system. IscB associates with its cognate ωRNA to form a ribonucleoprotein complex that cleaves double-stranded DNA targets complementary to an ωRNA guide segment. Although IscB shares the RuvC and HNH endonuclease domains with Cas9, it is much smaller than Cas9, mainly due to the lack of the α-helical nucleic-acid recognition lobe. Here, we report the cryo-electron microscopy structure of an IscB protein from the human gut metagenome (OgeuIscB) in complex with its cognate ωRNA and a target DNA, at 2.6-Å resolution. This high-resolution structure reveals the detailed architecture of the IscB-ωRNA ribonucleoprotein complex, and shows how the small IscB protein assembles with the ωRNA and mediates RNA-guided DNA cleavage. The large ωRNA scaffold structurally and functionally compensates for the recognition lobe of Cas9, and participates in the recognition of the guide RNA-target DNA heteroduplex. These findings provide insights into the mechanism of the programmable DNA cleavage by the IscB-ωRNA complex and the evolution of the type II CRISPR-Cas9 effector complexes.