Effect of Conformational Variability on the Drug Resistance of Candida auris ERG11p and FKS1.

Candida auris infection has been recognized as an urgent threat to antifungal drug resistance, and the Eagle effect of C. auris FKS1 (1,3-ß-d-glucan synthase) wild-type isolates has also been noted. The Eagle effect, namely, where higher concentrations of antifungals reduce fungicidal activity relative to lower concentrations, is a confounding factor of apparent antifungal resistance, but the detailed mechanism remains unclear. Here, we present the conformational variability of mutation sites for ERG11p (lanosterol 14α-demethylase) and FKS1 from deep neural network-based prediction along with the reported X-ray crystallographic and cryo-electron microscopy (cryo-EM) structures of antifungals. The sequence variability maps provide valuable insights into the inconsistent correlation between azole resistance and the mysterious Eagle effect with the dispersion of minimal inhibitory concentration (MIC) for echinocandin resistance. The conformational variability prediction supports the hypothesis that mutations K143R of clade I, VF125AL of clade III, and Y132F of clade IV for C. auris ERG11p make the corresponding site variable and that an increased population of invisible variable conformations potentially contributes to triazole resistance. In contrast, the predicted rigid conformation by the S639F mutation of hot spot region 1 (HS1) for FKS1 suggests that caspofungin (CAS) is involved in an uncompetitive inhibition, and a decreased population of the CAS-bound state of FKS1 with Rho1 leads to drug resistance. The predicted variable HS1 region for FKS1 WT isolates and the rigid one for FKS1 S639F mutants support the in vivo drug response and the in vitro MIC dispersion. A plausible mechanism of the Eagle effect is hereby proposed, namely, that a high concentration of CAS with a high membrane affinity reduces the population of the CAS-bound state of FKS1 with Rho1, as well as accompanying events such as aggregation or association depending on the conformational variability of HS1.

Effect of Conformational Variability on Seasonable Thermal Stability and Cell Entry of Omicron Variants.

The Omicron BA.1 variant of SARS-CoV-2 preferentially infects through the cathepsin-mediated endocytic pathway, but the mechanism of cell entry has not been solved yet because BA.4/5 is more fusogenic and more efficiently spread in human lung cells than BA.2. It has been unclear why the Omicron spike is inefficiently cleaved in virions compared with Delta, and how the relatively effective reproduction proceeds without the cell entry through plasma membrane fusion. Conformational variability from deep neural network-based prediction correlates well with the thermodynamic stability of variants. The difference of seasonable pandemic variants in summer and those in winter is distinguishable by this conformational stability, and the geographical optimization of variants is also traceable. Further, the predicted conformational variability maps rationalize the less efficient S1/S2 cleavage of Omicron variants and provide a valuable insight into the cell entry through the endocytic pathway. It is concluded that conformational variability prediction is able to complement transformation information on motifs in protein structures for drug discovery.

Spinal endodermal cyst undergoing malignant transformation and marked elevation of serum carbohydrate 19-9 level.

Endodermal cyst (EC) is a benign tumor that can arise along the craniospinal axis. Infrequently, ECs undergo malignant transformation. A 43-year-old man presented with numbness in the right arm, leg and occipitalgia. MRI revealed a multicystic, intradural extramedullary tumor at C2 with enhancement along the ventral surface of the spinal cord. Blood test showed an abnormal increase in serum carbohydrate antigen 19-9 (CA 19-9) level. Systemic positron emission tomography-computed tomography was normal. He underwent total tumor resection and was diagnosed with EC. He developed double vision, hearing loss, and swallowing difficulty on postoperative day 70. Cerebral MRI revealed marked extensions of leptomeningeal dissemination. The serum CA 19-9 level increased continuously and finally reached 1515.0 U/ml. He died of respiratory failure on day 108. An autopsy did not reveal abnormalities in the abdominal and chest organs. On microscopic examination, the post-mortem specimen revealed adenocarcinoma. Immunohistochemically, both the surgical and autopsy specimens were positive for CA 19-9. Spinal ECs may lead to malignant transformation with leptomeningeal dissemination that causes abnormal elevation of serum CA 19-9 levels.

Hodgkinoid histiocytosis: an atypical nodal CD30 and S100-positive histiocytosis with eosinophilia.

Histiocytes and dendritic cells may display cytological atypia and an aberrant immunophenotype even in reactive processes. Herein, we describe two cases of "Hodgkinoid histiocytosis" that show distinctive clinicopathological features, mimicking morphologically classic Hodgkin lymphoma (CHL), but suggesting reactive histiocytic/dendritic cell proliferation in lymph nodes. Both the patients presented with peripheral lymphadenopathy and blood eosinophilia with skin manifestations. Lymph node biopsy revealed scattered large histiocytes resembling Hodgkin cells with a round or stellate shape, abundant cytoplasm, and distinct nucleoli admixed in a predominant inflammatory background. The Hodgkinoid histiocytes occasionally showed emperipolesis. They expressed CD30, S100, and PD-L1 proteins but lacked PAX5 and CD1a expressions, Epstein-Barr association, BRAF V600E mutation, and PD-L1 gene amplification. Neither of the patients showed overt progression to malignant haematopoietic neoplasms during the disease course. An identical case series of four patients has been reported to date. Both these series highlight the potential of being interpreted as CHL due to the presence of Hodgkinoid histiocytes with CD30 positivity.

Isolated idiopathic myositis of the inferior oblique muscle biopsied through lateral orbitotomy.

Background: Isolated orbital myositis of the inferior oblique muscle (IObM) is rare, with few reported cases. Case Description: A 65-year-old woman was aware of double vision and left dacryorrhea for 2 months. At presentation, the patient showed mild restriction on the downward gaze. In addition, a subcutaneous mass was palpated on the left eyelid. The blood examination showed normal findings. Cranial computed tomography revealed an isodense mass in the left orbit, located in the inferior, inferolateral, and posterior aspects of the bulb. On magnetic resonance imaging, the mass was well-demarcated, appeared isointense on both T1- and T2-weighted imaging, and was intensely enhanced after intravenous infusion of gadolinium. The patient underwent biopsy through lateral orbitotomy. Microscopically, the resected specimen showed sheet-like proliferation of small round nonneoplastic cells. These cells were positively immunostained for both B- and T-lymphocyte markers. Therefore, we diagnosed the patient with isolated idiopathic myositis of the IObM. The patient was managed with steroids, which resulted in a remarkable resolution of her orbital symptoms. Conclusion: Biopsy findings should be considered when the presentation of orbital myositis is atypical. Lateral orbitotomy may provide a useful surgical window when approaching the posterior belly of the IObM.

A large cystic meningioma incidentally detected during general examination for breast cancer.

A 57-year-old woman who underwent needle biopsy for a subcutaneous mass in the breast was diagnosed with invasive ductal carcinoma. General examination incidentally revealed an intracranial tumor. At presentation, the patient showed memory disturbance but no focal neurological deficits. Cranial computed tomography (CT) revealed a large, hypodense cyst in the left frontotemporal region, involving a tumor with extensive hyperostotic changes in the left sphenoid and frontal bones. Magnetic resonance imaging showed that the tumor was attached to the dura mater of the pterional region and extensively enhanced, with involvement of the frontal and sphenoid bones. The less vascular tumor was removed en bloc by drilling the affected sphenoid and frontal bones as much as possible. The microscopic findings of the tumor were consistent with meningothelial meningioma with invasion into the dura mater and bone. Cystic meningioma should be considered when encountered with a dural-based cystic tumor, even in patients with cancer. In such circumstances, prompt and preferential resection may be indicated for intracranial tumors for timely initiation of the long-term treatment of cancer.

Mucoepidermoid carcinoma of the lacrimal gland in a patient with the CRTC1-MAML2 fusion gene.

Mucoepidermoid carcinoma (MEC) of the lacrimal gland (LG) is a rare entity. A 47-year-old woman was aware of periorbital swelling for 3 months. At presentation, the patient showed periorbital swelling in the right eye. CT scan showed an isodense mass in the anterior superolateral part of the orbit. MRI delineated the mass as enhancing, extra-conal tumor appearing isointense on T1-weighted sequences, and to be of mixed intensity on T2-weighted sequences. The tumor was totally resected. Microscopically, the tumor tissue was comprised of squamous, epithelioid cells, and cells with plump and clear cytoplasm. Necrosis, neural invasion, or mitotic figures were not observed. Immunohistochemical examination revealed intense staining for cytokeratin 7. A subset of the cells was positively stained with periodic acid-Schiff and mucicarmine stains. Genetic analysis revealed the presence of the CRTC1-MAML2 fusion. The CRTC1-MAML2 fusion may be a useful indicator for the prognosis and planning of adjuvant therapy.

Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds.

Identifying the fundamental cause of transmissibility of multiple mutation strains and vaccine nullification is difficult in general and is a source of significant concern. The conformational variability of the mutation sites for B.1.617.2 (Δ), B.1.617.1 (κ), B.1.427/429 (ε), P.1 (γ), B.1.351 (ß), B.1.1.7 (α), S477N, and the wild-type strain has been assessed using a deep neural-network-based prediction program of conformational flexibility or rigidity in proteins (SSSCPreds). We find that although the conformation of G614 is rigid, which is assigned as a left-handed (LH) α-helix-type one, that of D614 is flexible without the hydrogen bonding latch to T859. The rigidity of glycine, which stabilizes the local conformation more effectively than that of aspartic acid with the latch, thereby contributes to the reduction of S1 shedding, high expression, and increase in infectivity. The finding that the sequence flexibility/rigidity map pattern of B.1.1.7 is similar to that of the wild-type strain but is largely different from those of B.1.351 and P.1 correlates with the minor escape ability of B.1.1.7. The increased rigidity of the amino acid sequence YRYRLFR from the SSSCPreds data of B.1.427/429 near the L452R mutation site contributes to the 2-fold increased B.1.427/B.1.429 viral shedding in vivo and the increase in transmissibility relative to wild-type circulating strains in a similar manner to D614G. The concordance and rigidity ratios of multiple mutation strains such as B.1.617.2 against the wild-type one at the receptor-binding domain (RBD) and receptor-binding motif (RBM) regions provide a good indication of the transmissibility and neutralization escape ability except for binding affinity of mutation sites such as N501Y.

Use of Ibrutinib in 10 Patients with Treatment-Naïve or Relapsed/Refractory Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma in Real-World Clinical Practice -A Report from a Single Medical Institution.

In Japan, ibrutinib has been approved as both a front-line and later-line treatment for chronic leukemia/small lymphocytic lymphoma(CLL/SLL). However, little is known about the actual outcomes and adverse events(AEs)associated with the use of ibrutinib in Japanese patients. OBJECTIVE: The outcomes and AEs of patients treated with ibrutinib in a real-world setting were investigated. METHODS: A retrospective cohort study of all patients with CLL/SLL who were treated with ibrutinib at a single institution was conducted. RESULT: In total, 10 patients, including 5 treatment-naïve patients(50%), were enrolled. The median follow-up period was 9.8 months(range, 0.2-21.6 months), and the estimated overall response rate (ORR: complete remission plus partial remission)was 60%. The median overall survival and progression-free survival outcomes were not reached. During the follow-up period, 4 patients(40%)had at least one AE and 1 patient(10%)had at least one grade≥3 AE. Ibrutinib was discontinued in 4 patients(40%)because of AEs in 2 patients(20%), the progression of CLL in 1 patient(10%), and financial reasons in 1 patient(10%). Richter's transformation did not occur in any of the cases. CONCLUSION: The ORR was lower(60%)than that observed in clinical trials. The frequency and severity of AEs were both relatively low, although the discontinuation rate was high(40%). Patient education and medication adherence were considered important.

Low‒Risk Essential Thrombocythemia Who Presented with Recurrent Episodes of Cerebral Hemorrhage during Pregnancy and Developed Cerebral Infarction during Puerperium.

A 42‒year‒old woman. At week 27 of pregnancy, she developed subcortical hemorrhage and underwent open cranial surgery for hematoma evacuation. The platelet(Plt)count was 297,000/µL. At week 34 of pregnancy, she developed subcortical hemorrhage again. The Plt count was 429,000/µL. At week 35 of pregnancy, the ventricular rupture and she underwent drainage and emergency cesarean section. The Plt count was 687,000/µL. Two days after delivery, hemorrhage was detected. The Plt count was 815,000/µL. Six days after delivery, she developed infarction. The Plt count was 915,000/µL. MRI revealed no evidence of aneurysm, arteriovenous malformations or tumor. Ten days after delivery, the Plt count was 1,173,000/µL. Bone marrow examination led to the diagnosis of essential thrombocythemia(ET). JAK2, CARL and MPL was negative. She was rated as"low‒risk"by IPSET‒thrombosis, and as"ultralow"risk by revised IPSET‒thrombosis. von Willebrand factor(VWF)activity was as high as 247%. The bleeding time and platelet aggregation activity were normal. There was no evidence of disseminated intravascular coagulation(DIC)or hypertensive disorders of pregnancy(HDP). She died of cerebral hemorrhage and infarction, 26 days after delivery.

The Current Status of Screening for Essential Thrombocythemia and Polycythemia Vera in Clinical Practice-Report from a Single Institution.

OBJECTIVE: We investigate the current status of screening for essential thrombocythemia(ET)and polycythemia vera(PV), at our hospital. METHODS: According to the World Health Organization(WHO)diagnostic criteria. PATIENTS: All patients who visited Juntendo University Urayasu Hospital between May 1984(when the hospital opened)and January 2019. RESULT: More than 90% of patients with elevated platelet counts(PLT)(n=25,062)and more than 90% of patients with elevated hemoglobin( Hb)or hematocrit(Ht)levels(n=16,422)did not visit the department of hematology, suggesting that there could be a high percentage of patients with potentially latent ET and PV visiting the hospital. In addition, a large number of patients fulfilling the laboratory criteria for ET/PV visited various departments of the hospital other than the department of hematology. CONCLUSION: Because ET/PV manifests with diverse symptoms, including non-specific symptoms and symptoms pertaining to other organ systems. Based on the findings, we consider that it is essential to disseminate information about the WHO diagnostic criteria/clinical symptoms and possibility of latent ET/PV to all departments of the hospital, and to establish cooperation between the department of hematology and other departments.

SSSCPreds: Deep Neural Network-Based Software for the Prediction of Conformational Variability and Application to SARS-CoV-2.

Amino acid mutations that improve protein stability and rigidity can accompany increases in binding affinity. Therefore, conserved amino acids located on a protein surface may be successfully targeted by antibodies. The quantitative deep mutational scanning approach is an excellent technique to understand viral evolution, and the obtained data can be utilized to develop a vaccine. However, the application of the approach to all of the proteins in general is difficult in terms of cost. To address this need, we report the construction of a deep neural network-based program for sequence-based prediction of supersecondary structure codes (SSSCs), called SSSCPrediction (SSSCPred). Further, to predict conformational flexibility or rigidity in proteins, a comparison program called SSSCPreds that consists of three deep neural network-based prediction systems (SSSCPred, SSSCPred100, and SSSCPred200) has also been developed. Using our algorithms we calculated here shows the degree of flexibility for the receptor-binding motif of SARS-CoV-2 spike protein and the rigidity of the unique motif (SSSC: SSSHSSHHHH) at the S2 subunit and has a value independent of the X-ray and Cryo-EM structures. The fact that the sequence flexibility/rigidity map of SARS-CoV-2 RBD resembles the sequence-to-phenotype maps of ACE2-binding affinity and expression, which were experimentally obtained by deep mutational scanning, suggests that the identical SSSC sequences among the ones predicted by three deep neural network-based systems correlate well with the sequences with both lower ACE2-binding affinity and lower expression. The combined analysis of predicted and observed SSSCs with keyword-tagged datasets would be helpful in understanding the structural correlation to the examined system.

Atypical meningeal hemangiopericytoma presenting with punched-out calvarial erosion.

Meningeal hemangiopericytoma (HPC) is an infrequent but distinct entity affecting the craniospinal axis. A previously healthy 48-year-old man sustained a gradually progressing motor weakness in the left lower extremity. CT showed a hyperdense mass in the right frontal lobe. On MRI, it was 29 × 30 × 36 mm in dimension, appeared isointense on T1 and hyperintense on T2, and was intensely enhanced with erosive changes in the inner table adjacent to the tumor. The patient underwent tumor resection. Reflection of the bone flap revealed a punched-out erosion in the inner table with a defect of the dura over the upper part of the tumor. Microscopic findings were consistent with grade III HPC with dural invasion. A punched-out calvarial erosion and dural defect caused by an extra-axial tumor may be a high-grade HPC that requires extensive surgical resection.

Significant role of magnetic resonance imaging for the diagnosis and evaluation of cardiac amyloidosis in primary light chain amyloidosis.

A 47-year-old male with macroglossia presented with dyspnea on effort and chest pain at rest. Cardiac MRI revealed diffuse global subendocardial late gadolinium enhancement below the left ventricular endocardium and a dark blood pool of intracardiac contrast medium. Tongue biopsy revealed amyloid deposition, which was limited in the myocardium. He was diagnosed with primary light chain amyloidosis. His condition was stage I according to the Mayo Clinic staging system. He underwent autologous peripheral blood stem cell transplantation. On Day 10, he developed chest pain and died suddenly on Day 11. Postmortem examination revealed amyloid deposition throughout the heart.

Methotrexate-associated Hodgkin Lymphoma in a Patient with Rheumatoid Arthritis Successfully Treated with Brentuximab Vedotin in Combination with Doxorubicin, Vinblastine, and Dacarbazine (BV+AVD).

A 53-year-old woman had been diagnosed with rheumatoid arthritis (RA) in X-6. She was started on methotrexate (MTX) in X-1. She developed a cough, and chest computed tomography showed abnormalities. In X, MTX was discontinued, but the cough persisted. A lung biopsy revealed a diagnosis of nodular sclerosis classic Hodgkin lymphoma (CHL-NS). She was considered to have "other iatrogenic immunodeficiency-associated lymphoproliferative disorders" (OIIA-LPD), MTX-associated Hodgkin lymphoma (MTX-HL). She received six courses of brentuximab vedotin (BV) in addition to AVD (BV+AVD). A complete metabolic response was obtained, and the RA went into remission. This is the fourth reported case of BV+AVD for MTX-HL.

A Case of Primary Myelofibrosis in Which Ruxolitinib Therapy Ameliorated the Fibrosis, but Resulted in Fatty Marrow.

A 63-year-old woman was referred to our department in 2015 because of anemia and thrombocytosis. MPL W515/K was positive, JAK-2V617F and CALR exon 9 were negative. Bone marrow(BM)biopsy led to a diagnosis of primary myelofibrosis (PMF)in the prefibrotic/early stage(Grade 1). BMbiopsy performed in 2016 showed overt fibrotic stage(Grade 2). She was classified according to the Dynamic International Prognostic Scoring System(DIPSS)as intermediate(Int)-Ⅱrisk. Ruxolitinib 10 mg daily was initiated. Ruxolitinib was suspended for hepatic dysfunction after the dose was increased to 15 mg. Subsequently, ruxolitinib was resumed at 10 mg. BM biopsy performed in 2017 showed progression of myelofibrosis(MF)to Grade 3. BM biopsy performed in 2018 showed improved to Grade 0-1, however, BM was fatty. Currently in 2019, she continues to be on ruxolitinib. Results of immunohistochemical staining of BM biopsy specimens for cytokines and CD34 suggested the role of cytokines in the pathogenesis of the PMF. It was speculated that ruxolitinib blocked the production of cytokines to ameliorate the MF and restore the hematopoietic function of the BM. Although the pathogenesis of the fatty marrow remained unclear, the possibility of involvement of ruxolitinib cannot be denied.

Multiple cerebral infarction diagnosed as Eosinophilic Granulomatosis with Polyangiitis by autopsy.

BACKGROUND: Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare systemic vasculitis of unknown cause involving the brain and accompanied by prominent eosinophilia. Intracardiac thrombosis is a major cardiac complication of EGPA that may cause thromboembolism. CASE PRESENTATION: A 53-year-old man presenting with abulia (consciousness disturbance) and left upper limb paralysis was admitted to our hospital. His case was complicated by penetrating branches, small vessel infarcts, and endocardial thrombosis in the right and left ventricle. Cardiomyopathy was also observed. Sixteen days after admission, the patient died from intracranial hemorrhage. Brain autopsy revealed two major findings: 1) large hemorrhagic infarction caused by cardiac embolism; and 2) granuloma and eosinophil infiltration. Vasculitis was accompanied by eosinophil infiltration in the cortical blood vessels and granuloma. CONCLUSIONS: In this case study, we report autopsy findings of brain infarction in a patient with EGPA and endocardial thrombosis. The brain infarction was caused by the cardiac embolisms and vasculitis.

Retrospective Analysis of 20 Patients with DLBCL Who Received MCVAC Followed by Autologous Peripheral Blood Stem Cell Transplantation.

Autologous peripheral blood stem cell transplantation(auto-PBSCT)combined with high-dose chemotherapy has been considered as the standard therapy for relapsed or induction therapy-refractory aggressive lymphomas sensitive to chemotherapy. While various regimens have been applied as the conditioning,none has yet been established as the standard. We have begun to employ high-dose ranimustine,cytarabine,etoposide and cyclophosphamide(MCVAC)regimen. The present study was undertaken to review the efficacy and safety of MCVAC. Regimen: We carried out a retrospective analysis of 20 patients diagnosed as diffuse large B-cell lymphoma. The median follow-up duration of 20 patients was 13.05 months(range, 0.57-49.5 months). The 4-year OS and PFS were 57.8% and 30.2%,respectively. Relapse was the most frequent cause of treatment failure(n=7). The major toxicities were anorexia/nausea(95%),diarrhea (75%),hypokalemia (70%). One patient died of hepatic veno-occlusive disease(VOD). The serious adverse events included hypokalemia,arrhythmia,cerebral hemorrhage,and heart failure(1 case[5%]each). There was 1 case of a late-onset adverse event: therapy-related myelo- dysplastic syndrome/acute myeloblastic leukemia(MDS/AML). MCVAC regimen was concluded as effective and well-toler- ated. However,we should carefully monitored for the possible development of VOD and MDS/AML. Further follow-up is needed to evaluate the long-term efficacy and safety.