Publications by authors named "Tomoyuki Tanaka"

205 Publications

Clonal Dynamics and clinical implications of Post-Remission Clonal Hematopoiesis in Acute Myeloid Leukemia (AML).

Blood 2021 Jun 3. Epub 2021 Jun 3.

The University of Texas MD Anderson Cancer Center, Houston, Texas, United States.

While clonal hematopoiesis (CH) can precede the development of acute myeloid leukemia (AML), it can also persist after achieving remission. Long-term clonal dynamics and clinical implications of persistent CH are not well understood. Here, we studied the prevalence, dynamics and clinical implications of post-remission CH in 164 AML patients who attained complete remission after induction chemotherapies. Post-remission CH was identified in 79 (49%) patients. Post-remission CH persisted long-term in 91% of the trackable patients despite treatment with various types of consolidation and maintenance therapies. Post-remission CH was eradicated in 20 out of 21 (95%) patients who underwent allogeneic stem cell transplant. While patients with post-remission CH as a group had comparable hematopoiesis with those without it, patients with persistent TET2 mutations showed significant neutropenia long-term. Post-remission CH had little impact on relapse risk, non-relapse mortality, and incidence of atherosclerotic cardiovascular disease, although the clinical impact of post-CR CH was heterogeneous among different mutations. These data suggest that while residual clonal hematopoietic stem cells (HSCs) are generally resistant to consolidation and maintenance therapies, they retain the ability to maintain normal hematopoiesis and have little impact on clinical outcomes, although larger study is needed to dissect the gene-specific heterogeneity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1182/blood.2020010483DOI Listing
June 2021

Iridium-Catalyzed Isomerization/Cycloisomerization/Aromatization of -Allyl--sulfonyl--(λ-silylethynyl)aniline Derivatives to Give Substituted Indole Derivatives.

Org Lett 2021 Jun 25;23(11):4284-4288. Epub 2021 May 25.

Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka 565-0871, Japan.

We have developed a one-iridium-catalyst system that transforms -allyl--sulfonyl-2-(silylalkynyl)aniline derivatives, which are 1,7-enynes in which both multiple bonds have a heteroatom, to the corresponding substituted indole derivatives via isomerization/cycloisomerization/aromatization. This strategy provides an atom-economical and straightforward synthetic approach to a series of valuable indoles having vinyl and silylmethyl groups at the 2- and 3-positions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.orglett.1c01231DOI Listing
June 2021

Leukemia stemness and co-occurring mutations drive resistance to IDH inhibitors in acute myeloid leukemia.

Nat Commun 2021 05 10;12(1):2607. Epub 2021 May 10.

Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Allosteric inhibitors of mutant IDH1 or IDH2 induce terminal differentiation of the mutant leukemic blasts and provide durable clinical responses in approximately 40% of acute myeloid leukemia (AML) patients with the mutations. However, primary resistance and acquired resistance to the drugs are major clinical issues. To understand the molecular underpinnings of clinical resistance to IDH inhibitors (IDHi), we perform multipronged genomic analyses (DNA sequencing, RNA sequencing and cytosine methylation profiling) in longitudinally collected specimens from 60 IDH1- or IDH2-mutant AML patients treated with the inhibitors. The analysis reveals that leukemia stemness is a major driver of primary resistance to IDHi, whereas selection of mutations in RUNX1/CEBPA or RAS-RTK pathway genes is the main driver of acquired resistance to IDHi, along with BCOR, homologous IDH gene, and TET2. These data suggest that targeting stemness and certain high-risk co-occurring mutations may overcome resistance to IDHi in AML.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-22874-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8110775PMC
May 2021

Aurora B switches relative strength of kinetochore-microtubule attachment modes for error correction.

J Cell Biol 2021 Jun;220(6)

Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.

To establish chromosome biorientation, aberrant kinetochore-microtubule interaction must be resolved (error correction) by Aurora B kinase. Aurora B differentially regulates kinetochore attachment to the microtubule plus end and its lateral side (end-on and lateral attachment, respectively). However, it is still unclear how kinetochore-microtubule interactions are exchanged during error correction. Here, we reconstituted the budding yeast kinetochore-microtubule interface in vitro by attaching the Ndc80 complexes to nanobeads. These Ndc80C nanobeads recapitulated in vitro the lateral and end-on attachments of authentic kinetochores on dynamic microtubules loaded with the Dam1 complex. This in vitro assay enabled the direct comparison of lateral and end-on attachment strength and showed that Dam1 phosphorylation by Aurora B makes the end-on attachment weaker than the lateral attachment. Similar reconstitutions with purified kinetochore particles were used for comparison. We suggest the Dam1 phosphorylation weakens interaction with the Ndc80 complex, disrupts the end-on attachment, and promotes the exchange to a new lateral attachment, leading to error correction.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1083/jcb.202011117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8050843PMC
June 2021

High-resolution crystal structures of transient intermediates in the phytochrome photocycle.

Structure 2021 Mar 20. Epub 2021 Mar 20.

Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA. Electronic address:

Phytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting Pr state and the light-activated Pfr state. Light signals are transduced as structural change through the entire protein to modulate its activity. It is unknown how the Pr-to-Pfr interconversion occurs, as the structure of intermediates remains notoriously elusive. Here, we present short-lived crystal structures of the photosensory core modules of the bacteriophytochrome from myxobacterium Stigmatella aurantiaca captured by an X-ray free electron laser 5 ns and 33 ms after light illumination of the Pr state. We observe large structural displacements of the covalently bound bilin chromophore, which trigger a bifurcated signaling pathway that extends through the entire protein. The snapshots show with atomic precision how the signal progresses from the chromophore, explaining how plants, bacteria, and fungi sense red light.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.str.2021.03.004DOI Listing
March 2021

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.

Elife 2021 03 23;10. Epub 2021 Mar 23.

RIKEN SPring-8 Center, Hyogo, Japan.

Channelrhodopsins (ChRs) are microbial light-gated ion channels utilized in optogenetics to control neural activity with light . Light absorption causes retinal chromophore isomerization and subsequent protein conformational changes visualized as optically distinguished intermediates, coupled with channel opening and closing. However, the detailed molecular events underlying channel gating remain unknown. We performed time-resolved serial femtosecond crystallographic analyses of ChR by using an X-ray free electron laser, which revealed conformational changes following photoactivation. The isomerized retinal adopts a twisted conformation and shifts toward the putative internal proton donor residues, consequently inducing an outward shift of TM3, as well as a local deformation in TM7. These early conformational changes in the pore-forming helices should be the triggers that lead to opening of the ion conducting pore.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.62389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987342PMC
March 2021

Flow cytometric immunophenotypic alterations of persistent clonal haematopoiesis in remission bone marrows of patients with NPM1-mutated acute myeloid leukaemia.

Br J Haematol 2021 Mar 22;192(6):1054-1063. Epub 2021 Feb 22.

The Department of Hematopathology, MD Anderson Cancer Center, Houston, TX, USA.

Clonal haematopoiesis (CH) in patients with acute myeloid leukaemia (AML) may persist beyond attaining complete remission. From a consecutive cohort of 67 patients with nucleophosmin 1-mutated (NPM1 ) AML, we identified 50 who achieved NPM1 clearance and had parallel multicolour flow cytometry (MFC) and next generation sequencing (NGS). In total, 13 (26%) cleared all mutations, 37 (74%) had persistent CH frequently involving DNA methyltransferase 3α (DNMT3A,70%), tet methylcytosine dioxygenase 2 (TET2, 27%), isocitrate dehydrogenase 2 (IDH2, 19%) and IDH1 (11%). A small number (<1%) of aberrant CD34 myeloblasts, but immunophenotypically different from original AML blasts [herein referred to as a pre-leukaemic (PL) phenotype], was detected in 17 (49%) patients with CH, but not in any patients with complete clearance of all mutations (P = 0·0037). A PL phenotype was associated with higher mutation burden (P = 0·005). Persistent IDH2 and serine and arginine-rich splicing factor 2 (SRSF2) mutations were exclusively observed in PL CH cases (P = 0·016). Persistent dysplasia was seen exclusively in cases with a PL phenotype (29% vs. none; P = 0·04). The PL phenotype did not correlate with age, intensity of induction therapy or relapse-free survival. Post-remission CH in the setting of NPM1 clearance is common and may result in immunophenotypic changes in myeloid progenitors. It is important to not misinterpret these cells as AML measurable residual disease (MRD).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/bjh.17347DOI Listing
March 2021

Distinct effects of chondroitin sulfate on hematopoietic cells and the stromal microenvironment in bone marrow hematopoiesis.

Exp Hematol 2021 Apr 12;96:52-62.e5. Epub 2021 Feb 12.

Department of Stem Cell Transplantation, Niigata University Medical and Dental Hospital, Niigata, Japan. Electronic address:

The bone marrow (BM) microenvironment, known as the BM niche, regulates hematopoiesis but is also affected by interactions with hematopoietic cells. Recent evidence indicates that extracellular matrix components are involved in these interactions. Chondroitin sulfate (CS), a glycosaminoglycan, is a major component of the extracellular matrix; however, it is not known whether CS has a physiological role in hematopoiesis. Here, we analyzed the functions of CS in hematopoietic and niche cells. CSGalNAcT1, which encodes CS N-acetylgalactosaminyltransferase-1 (T1), a key enzyme in CS biosynthesis, was highly expressed in hematopoietic stem and progenitor cells (HSPCs) and endothelial cells (ECs), but not in mesenchymal stromal cells (MSCs) in BM. In T1 knockout (T1KO) mice, a greater number of HSPCs existed compared with the wild-type (WT), but HSPCs from T1KO mice showed significantly impaired repopulation in WT recipient mice on serial transplantation. RNA sequence analysis revealed the activation of IFN-α/β signaling and endoplasmic reticulum stress in T1KO HSPCs. In contrast, the number of WT HSPCs repopulated in T1KO recipient mice was larger than that in WT recipient mice after serial transplantation, indicating that the T1KO niche supports repopulation of HSPCs better than the WT niche. There was no obvious difference in the distribution of vasculature and MSCs between WT and T1KO BM, suggesting that CS loss alters vascular niche functions without affecting its structure. Our results revealed distinct roles of CS in hematopoietic cells and BM niche, indicating that crosstalk between these components is important to maintain homeostasis in BM.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.exphem.2021.02.003DOI Listing
April 2021

Pan RAS-binding compounds selected from a chemical library by inhibiting interaction between RAS and a reduced affinity intracellular antibody.

Sci Rep 2021 Jan 18;11(1):1712. Epub 2021 Jan 18.

Leeds Institute of Medical Research, St James Hospital, Brenner Building, Beckett St., Leeds, LS9 7TF, UK.

Intracellular antibodies are valuable tools for target validation studies for clinical situations such as cancer. Recently we have shown that antibodies can be used for drug discovery in screening for chemical compounds surrogates by showing that compounds could be developed to the so-called undruggable RAS protein family. This method, called Antibody-derived compound (Abd) technology, employed intracellular antibodies binding to RAS in a competitive surface plasmon resonance chemical library screen. Success with this method requires a high affinity interaction between the antibody and the target. We now show that reduction in the affinity (dematuration) of the anti-active RAS antibody facilitates the screening of a chemical library using an in vitro AlphaScreen method. This identified active RAS specific-binding Abd compounds that inhibit the RAS-antibody interaction. One compound is shown to be a pan-RAS binder to KRAS, HRAS and NRAS-GTP proteins with a Kd of average 37 mM, offering the possibility of a new chemical series that interacts with RAS in the switch region where the intracellular antibody binds. This simple approach shows the druggability of RAS and is generally applicable to antibody-derived chemical library screening by affording flexibility through simple antibody affinity variation. This approach can be applied to find Abd compounds as surrogates of antibody-combining sites for novel drug development in a range of human diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-81262-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7814043PMC
January 2021

Structure of the dopamine D receptor in complex with the antipsychotic drug spiperone.

Nat Commun 2020 12 22;11(1):6442. Epub 2020 Dec 22.

Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

In addition to the serotonin 5-HT receptor (5-HTR), the dopamine D receptor (DR) is a key therapeutic target of antipsychotics for the treatment of schizophrenia. The inactive state structures of DR have been described in complex with the inverse agonists risperidone (DR) and haloperidol (DR). Here we describe the structure of human DR in complex with spiperone (DR). In DR, the conformation of the extracellular loop (ECL) 2, which composes the ligand-binding pocket, was substantially different from those in DR and DR, demonstrating that ECL2 in DR is highly dynamic. Moreover, DR exhibited an extended binding pocket to accommodate spiperone's phenyl ring, which probably contributes to the selectivity of spiperone to DR and 5-HTR. Together with DR and DR, the structural information of DR should be of value for designing novel antipsychotics with improved safety and efficacy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-20221-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755896PMC
December 2020

Isoprenoid-chained lipid EROCOC: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.

Sci Rep 2020 11 9;10(1):19305. Epub 2020 Nov 9.

RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

In meso crystallization of membrane proteins relies on the use of lipids capable of forming a lipidic cubic phase (LCP). However, almost all previous crystallization trials have used monoacylglycerols, with 1-(cis-9-octadecanoyl)-rac-glycerol (MO) being the most widely used lipid. We now report that EROCOC mixed with 10% (w/w) cholesterol (Fig. 1) serves as a new matrix for crystallization and a crystal delivery medium in the serial femtosecond crystallography of Adenosine A receptor (AR). The structures of EROCOC-matrix grown AR crystals were determined at 2.0 Å resolution by serial synchrotron rotation crystallography at a cryogenic temperature, and at 1.8 Å by LCP-serial femtosecond crystallography, using an X-ray free-electron laser at 4 and 20 °C sample temperatures, and are comparable to the structure of the MO-matrix grown AR crystal (PDB ID: 4EIY). Moreover, X-ray scattering measurements indicated that the EROCOC/water system did not form the crystalline L phase at least down to - 20 °C, in marked contrast to the equilibrium MO/water system, which transforms into the crystalline L phase below about 17 °C. As the L phase formation within the LCP-matrix causes difficulties in protein crystallography experiments in meso, this feature of EROCOC will expand the utility of the in meso method.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-76277-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652841PMC
November 2020

Cyclin-Dependent Kinase 1 Is Essential for Muscle Regeneration and Overload Muscle Fiber Hypertrophy.

Front Cell Dev Biol 2020 14;8:564581. Epub 2020 Oct 14.

Department of Orthopedic and Trauma Research, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.

Satellite cell proliferation is an essential step in proper skeletal muscle development and muscle regeneration. However, the mechanisms regulating satellite cell proliferation are relatively unknown compared to the knowledge associated with the differentiation of satellite cells. Moreover, it is still unclear whether overload muscle fiber hypertrophy is dependent on satellite cell proliferation. In general, cell proliferation is regulated by the activity of cell cycle regulators, such as cyclins and cyclin-dependent kinases (CDKs). Despite recent reports on the function of CDKs and CDK inhibitors in satellite cells, the physiological role of Cdk1 in satellite cell proliferation remains unknown. Herein, we demonstrate that Cdk1 regulates satellite cell proliferation, muscle regeneration, and muscle fiber hypertrophy. Cdk1 is highly expressed in myoblasts and is downregulated upon myoblast differentiation. Inhibition of CDK1 activity inhibits myoblast proliferation. Deletion of in satellite cells leads to inhibition of muscle recovery after muscle injury due to reduced satellite cell proliferation . Finally, we provide direct evidence that Cdk1 expression in satellite cells is essential for overload muscle fiber hypertrophy . Collectively, our results demonstrate that Cdk1 is essential for myoblast proliferation, muscle regeneration, and muscle fiber hypertrophy. These findings could help to develop treatments for refractory muscle injuries and muscle atrophy, such as sarcopenia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcell.2020.564581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591635PMC
October 2020

Immunogenicity and Safety of a Two-Dose Series of a Meningococcal (Groups A, C, W, and Y) Polysaccharide Diphtheria Toxoid Conjugate Vaccine (Men-ACWY-D) in Healthy Japanese Adults.

Jpn J Infect Dis 2021 May 30;74(3):193-199. Epub 2020 Oct 30.

Sanofi Pasteur, France.

The quadrivalent meningococcal polysaccharide diphtheria toxoid conjugate vaccine (Men-ACWY-D) has been licensed for use in Japan since 2014. An earlier registration study demonstrated the immunogenicity of a single dose in Japanese adults, wherein the immunogenicity against serogroup C was the lowest. The determination of the potential to increase the serogroup C response with a second dose was, therefore, of interest. This study (NCT02591290) evaluated the safety and immunogenicity of two doses administered 8 weeks apart to 60 healthy Japanese adults aged 20-55 years. Blood samples were collected at 28-35 days after vaccination. Immunogenicity endpoints included seroprotection and seroconversion rates. Safety assessments included systemic adverse events (AEs), non-serious AEs, and serious AEs. Fifty-eight participants (96.7%) completed the study. The seroprotection rates for serogroups A, C, W, and Y before vaccination were 76.8%, 26.8%, 26.8%, and 50.0%, respectively, increasing to 100%, 83.9%, 91.1%, and 96.4% and 100%, 92.9%, 94.6%, and 94.6%, respectively, after two doses. The seroconversion rates for the four serogroups were 100%, 93.8%, 97.1%, and 94.1%, respectively, after the first dose, and 100%, 96.9%, 100%, and 100%, respectively, after the second. The increase between the doses was insignificant, and there were no safety concerns. The two-dose series was well tolerated; however, the clinical benefits of a second dose within 8 weeks seemed to be low.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7883/yoken.JJID.2020.411DOI Listing
May 2021

Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics.

Nat Commun 2020 10 21;11(1):5327. Epub 2020 Oct 21.

Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Clonal diversity is a consequence of cancer cell evolution driven by Darwinian selection. Precise characterization of clonal architecture is essential to understand the evolutionary history of tumor development and its association with treatment resistance. Here, using a single-cell DNA sequencing, we report the clonal architecture and mutational histories of 123 acute myeloid leukemia (AML) patients. The single-cell data reveals cell-level mutation co-occurrence and enables reconstruction of mutational histories characterized by linear and branching patterns of clonal evolution, with the latter including convergent evolution. Through xenotransplantion, we show leukemia initiating capabilities of individual subclones evolving in parallel. Also, by simultaneous single-cell DNA and cell surface protein analysis, we illustrate both genetic and phenotypic evolution in AML. Lastly, single-cell analysis of longitudinal samples reveals underlying evolutionary process of therapeutic resistance. Together, these data unravel clonal diversity and evolution patterns of AML, and highlight their clinical relevance in the era of precision medicine.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-19119-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7577981PMC
October 2020

Effective Method Using a Stool in Cardiopulmonary Resuscitation (CPR) on Dialysis Chair.

Emerg Med Int 2020 27;2020:5691607. Epub 2020 Jul 27.

Department of Dental Anesthesiology, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.

Background: Heart failure is the leading cause of death in dialysis patients. Cardiac arrest due to hypotension may also occur during dialysis therapy. If cardiac arrest is elicited, manual chest compressions (MCCs) should be started as soon as possible. However, all types of dialysis chairs are not stable for MCC, because there is no steady support between the backboard of the dialysis chair and the floor. These conditions may alter the effectiveness of MCC.

Methods: We investigated whether a round chair is effective in supporting the dialysis chair for MCC. Four adult males performed MCC on a mannequin placed on three dialysis chairs. MCC was performed in sets of 2 (each set was 100 times per minute) per person, with and without a round chair. A total of 4,800 compressions were performed by four executors.

Results: When the chair was not used as a stabilizer, the mean values of the fluctuation range were 20.8 ± 8.1 mm, 18.7 ± 5.5 mm, and 12.8 ± 1.8 mm, respectively. When the chair was used, the mean values of the fluctuation range were 6.1 ± 1.1 mm, 7.5 ± 2.1 mm, and 1.0 ± 0 mm, decreasing by 70%, 59%, and 92%.

Conclusion: MCC performed with the stool under the backrest as a stabilizer was effective in supporting the dialysis chair.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1155/2020/5691607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7403903PMC
July 2020

Marker chromosome is a strong poor prognosis factor after allogeneic HSCT for adverse-risk AML patients.

Eur J Haematol 2020 Nov 11;105(5):616-625. Epub 2020 Aug 11.

Department of Hematopoietic Cell Transplantation, Niigata University Medical and Dental Hospital, Niigata, Japan.

Introduction: Chromosome analysis is necessary for the risk classification of acute myeloid leukemia (AML). Marker chromosome (MC) is a fragmented chromosome whose origin cannot be identified from other chromosomes and originates from marked genomic instability. Although AML with MC (MC+) has a poor prognosis even after intensive chemotherapy, its influence on the outcome after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is unclear.

Objective And Methods: We retrospectively analyzed 162 AML patients after allo-HSCT. To evaluate the significance of MC, we compared it with other chromosomal abnormalities.

Result: Marker chromosome was detected in 14 (8.6%, MC+) patients (vs MC-, n = 158). The 2-year overall survival (OS) in MC+ vs MC- was 26.8% vs 62.2% (P = .0098). The 2-year cumulative incidence of relapse (CIR) in MC+ vs MC- was 80.4% vs 35.5% (P = .0004). Among adverse-risk AML (AD-AML, n = 36), AD-AML/MC+ (n = 11) demonstrated a poorer 2-year OS (9.1%, vs AD-AML/MC- n = 25, 58.3%, P = .0031) and higher 2-year CIR (89.6%, vs AD-AML/MC- 44.7%, P = .002). In multivariate analysis, MC (HR 3.08, 95% CI; 1.02-9.29, P = .046) and HCT-CI (HR 3.23, 95% CI; 1.00-10.4, P = .049) were independent risk factors for CIR among AD-AML.

Conclusion: Our study suggests MC as a new independent factor for chromosome risk classification to further classify AD-AML.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/ejh.13495DOI Listing
November 2020

Invasive liver abscess syndrome accompanied by spondylodiscitis: a case report and review of the literature.

Clin J Gastroenterol 2020 Oct 7;13(5):927-934. Epub 2020 Jul 7.

Department of Internal Medicine, Nagano Prefectural Kiso Hospital, Kiso, Japan.

A 65-year-old man who had diabetes mellitus was referred to our hospital due to fever and back pain. Laboratory findings showed liver dysfunction and C-reactive protein (CRP) elevation. Enhanced computed tomography (CT) showed multiple liver abscesses, hepatic vein and inferior vena cava thrombosis, and spondylodiscitis in the fourth lumbar vertebrae. Based on several detections of Klebsiella pneumoniae (K. pneumoniae) in blood culture, he was diagnosed as having invasive liver abscess syndrome (ILAS), which is characterized by liver abscess and metastatic infection caused by K. pneumoniae. Despite the prompt improvement of liver abscess and thrombosis, after administering antibiotics and anticoagulant, spondylodiscitis worsened. Additionally, iliopsoas abscess emerged on repeated CT imaging. Lumbar laminectomy was needed as a radical treatment. We reviewed 12 cases of ILAS representing spondylodiscitis, and surgical treatments for spondylodiscitis were required in 7 of these cases (58%). When encountering patients with liver abscess and spondylodiscitis, we should consider the possibility of invasive disseminated K. pneumoniae infection, which is hard to treat with antibiotics alone and sometimes requires surgical treatments for spondylodiscitis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12328-020-01161-0DOI Listing
October 2020

Zooming in on chromosome dynamics.

Cell Cycle 2020 06 13;19(12):1422-1432. Epub 2020 May 13.

Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK.

Until recently, our understanding of chromosome organization in higher eukaryotic cells has been based on analyses of large-scale, low-resolution changes in chromosomes structure. More recently, CRISPR-Cas9 technologies have allowed us to "zoom in" and visualize specific chromosome regions in live cells so that we can begin to examine in detail the dynamics of chromosome organization in individual cells. In this review, we discuss traditional methods of chromosome locus visualization and look at how CRISPR-Cas9 gene-targeting methodologies have helped improve their application. We also describe recent developments of the CRISPR-Cas9 technology that enable visualization of specific chromosome regions without the requirement for complex genetic manipulation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/15384101.2020.1757242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480819PMC
June 2020

Hypereosinophilia-related liver pseudotumor with elevated interleukin-5 levels preceding T-cell lymphoma.

JGH Open 2020 Apr 6;4(2):312-314. Epub 2019 Sep 6.

Division of Gastroenterology and Hepatology, Graduate School of Medical and Dental Sciences Niigata University Niigata Japan.

A 61-year-old woman with hypereosinophilia and elevated interleukin (IL)-5 level was admitted to our hospital after detection of multiple liver tumors. Liver biopsy demonstrated that the tumor consisted of scar tissue with remnants of eosinophilic infiltration, suggesting that it had formed by massive eosinophilic infiltration. The hypereosinophilia was treated mainly by prednisolone, and thereafter, the liver tumors disappeared. However, 10 months postadmission, CD4+ T-cell lymphoma, which can produce IL-5, was detected in the nasopharynx and oropharynx. Therefore, we believe that this is a rare case of hypereosinophilia-related liver pseudotumor induced by presumed by IL-5 elevation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jgh3.12253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144778PMC
April 2020

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser.

Elife 2020 03 31;9. Epub 2020 Mar 31.

Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.

Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.53514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164956PMC
March 2020

A Heterodimeric Antibody Fragment for Passive Immunotherapy Against Norovirus Infection.

J Infect Dis 2020 07;222(3):470-478

Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, Tokyo, Japan.

Human noroviruses cause an estimated 685 million infections and 200 000 deaths annually worldwide. Although vaccines against GII.4 and GI.1 genotypes are under development, no information is available regarding vaccines or monoclonal antibodies to other noroviral genotypes. Here, we developed 2 variable-domain llama heavy-chain antibody fragment (VHHs) clones, 7C6 and 1E4, against GII.4 and GII.17 human noroviruses, respectively. Although 7C6 cross-reacted with virus-like particles (VLPs) of GII.17, GII.6, GII.3, and GII.4, it neutralized only GII.4 norovirus. In contrast, 1E4 reacted with and neutralized only GII.17 VLPs. Both VHHs blocked VLP binding to human induced pluripotent stem cell-derived intestinal epithelial cells and carbohydrate attachment factors. Using these 2 VHHs, we produced a heterodimeric VHH fragment that neutralized both GII.4 and GII.17 noroviruses. Because VHH fragments are heat- and acid-stable recombinant monoclonal antibodies, the heterodimer likely will be useful for oral immunotherapy and prophylaxis against GII.4 and GII.17 noroviruses in young, elderly, or immunocompromised persons.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/infdis/jiaa115DOI Listing
July 2020

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.

IUCrJ 2020 Mar 26;7(Pt 2):306-323. Epub 2020 Feb 26.

Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan.

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1107/S205225252000072XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055375PMC
March 2020

Comparison of virological and serological methods for laboratory confirmation of rubella.

J Clin Virol 2020 02 31;123:104257. Epub 2019 Dec 31.

Sakai City Institute of Public Health, 3-2-8 Kaicho-Higashi, Sakai, Osaka, 590-0953, Japan. Electronic address:

Background: Work toward rubella elimination has accelerated globally. A reliable laboratory confirmation of rubella-suspected cases is required for effective surveillance in the rubella-elimination phase. The use of adequate specimens is a key to improving the quality of this surveillance.

Study Design: We conducted rubella virus (RUBV) isolation and RUBV genome or anti-RUBV IgM detection on 1023 specimens from 372 rubella- or measles-suspected cases collected through the national surveillance program in Sakai city of Osaka prefecture, Japan between 2011 and 2013. The resulting data were analyzed by specimen type, collection date, and immunological status.

Results: Among the three specimen types (throat swab, serum or plasma, and urine) collected through 10 days post-rash onset, the highest success rates for RUBV genome detection and RUBV isolation were obtained using throat swabs. In agreement with previous work, RUBV-specific IgM were undetectable in 50% of the rubella-confirmed cases until 3 days after rash onset. The success rates of RUBV genome detection and RUBV isolation declined in association with the appearance of RUBV-specific antibodies in blood, especially in serum, plasma, or urine samples.

Conclusion: Throat swabs are the most optimal specimen types for both RUBV genome detection and RUBV isolation; serum/plasma samples may be suboptimal, especially for RUBV isolation. The findings from this study will provide useful information for improving laboratory surveillance for rubella in the elimination phase.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jcv.2019.104257DOI Listing
February 2020

High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure.

J Appl Crystallogr 2019 Dec 17;52(Pt 6):1280-1288. Epub 2019 Oct 17.

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.

A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump-probe techniques.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1107/S1600576719012846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6878880PMC
December 2019

High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures.

Struct Dyn 2019 Sep 17;6(5):054701. Epub 2019 Sep 17.

Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, Illinois 60625, USA.

Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the mechanisms by which these natural photoswitches can control single cell development, although the role of BphPs remains largely unknown. BphPs are dimeric proteins that consist of a photosensory core module (PCM) and an enzymatic domain, often a histidine kinase. The PCM is composed of three domains (PAS, GAF, and PHY). It holds a covalently bound open-chain tetrapyrrole (biliverdin, BV) chromophore. Upon absorption of light, the double bond between BV rings C and D isomerizes and reversibly switches the protein between Pr and Pfr states. We report crystal structures of the wild-type and mutant (His275Thr) forms of the canonical BphP from the nonphotosynthetic myxobacterium (BphP2) in the Pr state. Structures were determined at 1.65 Å and 2.2 Å (respectively), the highest resolution of any PCM construct to date. We also report the room temperature wild-type structure of the same protein determined at 2.1 Å at the SPring-8 Angstrom Compact free electron LAser (SACLA), Japan. Our results not only highlight and confirm important amino acids near the chromophore that play a role in Pr-Pfr photoconversion but also describe the signal transduction into the PHY domain which moves across tens of angstroms after the light stimulus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1063/1.5120527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748860PMC
September 2019

Patient-based prediction algorithm of relapse after allo-HSCT for acute Leukemia and its usefulness in the decision-making process using a machine learning approach.

Cancer Med 2019 Sep 15;8(11):5058-5067. Epub 2019 Jul 15.

Department of Hematopoietic Cell Transplantation, Niigata University Medical and Dental Hospital, Niigata, Japan.

Although allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative therapy for high-risk acute leukemia (AL), some patients still relapse. Since patients simultaneously have many prognostic factors, difficulties are associated with the construction of a patient-based prediction algorithm of relapse. The alternating decision tree (ADTree) is a successful classification method that combines decision trees with the predictive accuracy of boosting. It is a component of machine learning (ML) and has the capacity to simultaneously analyze multiple factors. Using ADTree, we attempted to construct a prediction model of leukemia relapse within 1 year of transplantation. With the model of training data (n = 148), prediction accuracy, the AUC of ROC, and the κ-statistic value were 78.4%, 0.746, and 0.508, respectively. The false positive rate (FPR) of the relapse prediction was as low as 0.134. In an evaluation of the model with validation data (n = 69), prediction accuracy, AUC, and FPR of the relapse prediction were similar at 71.0%, 0.667, and 0.216, respectively. These results suggest that the model is generalized and highly accurate. Furthermore, the output of ADTree may visualize the branch point of treatment. For example, the selection of donor types resulted in different relapse predictions. Therefore, clinicians may change treatment options by referring to the model, thereby improving outcomes. The present results indicate that ML, such as ADTree, will contribute to the decision-making process in the diversified allo-HSCT field and be useful for preventing the relapse of leukemia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/cam4.2401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718546PMC
September 2019

Contractile acto-myosin network on nuclear envelope remnants positions human chromosomes for mitosis.

Elife 2019 07 3;8. Epub 2019 Jul 3.

Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom.

To ensure proper segregation during mitosis, chromosomes must be efficiently captured by spindle microtubules and subsequently aligned on the mitotic spindle. The efficacy of chromosome interaction with the spindle can be influenced by how widely chromosomes are scattered in space. Here, we quantify chromosome-scattering volume (CSV) and find that it is reduced soon after nuclear envelope breakdown (NEBD) in human cells. The CSV reduction occurs primarily independently of microtubules and is therefore not an outcome of interactions between chromosomes and the spindle. We find that, prior to NEBD, an acto-myosin network is assembled in a LINC complex-dependent manner on the cytoplasmic surface of the nuclear envelope. This acto-myosin network remains on nuclear envelope remnants soon after NEBD, and its myosin-II-mediated contraction reduces CSV and facilitates timely chromosome congression and correct segregation. Thus, we find a novel mechanism that positions chromosomes in early mitosis to ensure efficient and correct chromosome-spindle interactions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.46902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6634967PMC
July 2019