Analysis of Binding Site Hot Spots on the Surface of Ras GTPase

We have recently discovered an allosteric switch in Ras, bringing an additional level of complexity to this GTPase whose mutants are involved in nearly 30% of cancers. Upon activation of the allosteric switch, there is a shift in helix 3/loop 7 associated with a disorder to order transition in the active site. Here, we use a combination of multiple solvent crystal structures and computational solvent mapping (FTMap) to determine binding site hot spots in the “off” and “on” allosteric states of the GTP-bound form of H-Ras. Thirteen sites are revealed, expanding possible target sites for ligand binding well beyond the active site. Comparison of FTMaps for the H and K isoforms reveals essentially identical hot spots. Furthermore, using NMR measurements of spin relaxation, we determined that K-Ras exhibits global conformational dynamics very similar to those we previously reported for H-Ras. We thus hypothesize that the global conformational rearrangement serves as a mechanism for allosteric coupling between the effector interface and remote hot spots in all Ras isoforms. At least with respect to the binding sites involving the G domain, H-Ras is an excellent model for K-Ras and probably N-Ras as well. Ras has so far been elusive as a target for drug design. The present work identifies various unexplored hot spots throughout the entire surface of Ras, extending the focus from the disordered active site to well-ordered locations that should be easier to target

Successful experience of treatment of a patient with generalized non-GCB- DLBCL using the R-mNHL-BFM-90 protocol with lenalidomide: case report and review of literature

Diffuse large B-cell lymphoma is categorized by gene expression profiling into germinal center (GCB) and activated B-cell (ABC) subtype, also referred to as non-germinal center B-cell (non-GCB) by immunohistochemistry. ABC DLBCL is characterized by NF-κB pathway activation and high expression of IRF4/MUM1, a key transcription factor in B cell differentiation. Patients with ABC DLBCL have a significantly worse outcome when treated with standard chemotherapy (R-CHOP). Lenalidomide have shown activity in the ABC-DLBCL in combination with R-CHOP. But about 40% of patients remain resistant. We present the experience of treatment of a patient with generalized non-GCB-DLBCL using the intensive protocol R-mNHL-BFM-90 with lenalidomide

Assessment of bone marrow biopsy in patients with masked polycythemia vera

Masked polycythemia vera (PV) is characterized by presence ot Jak2 mutation, specific morphological pattern in the bone marrow biopsy, and the lack demanding levels of Hb in accordance with criteria WHO, 2008 for PV. The purpose of this study was assessment of the pathomorphologic peculiarities of bone marrow biopsies in patients with masked PV. The group of 24 patients with masked PV was formed on the basis of morphological picture, clinical, laboratory and molecular data. Histological examination of bone marrow trephine biopsy in most cases showed hypercellular marrow 18/24 (75%) (age adujsted). Enlargement and rejuvenation of erythroid lineage was observed in 23/24 and 22/24 cases (95.9% and 91.7%). The histotopography of megakaryocytes in the majority of cases, 20/24 (83.3%) was characterized by discrete arrangement of megakaryocytes and forming intertrabecular loose clusters (3-16 cells). Typical for PV morphology of megakaryocytes was detected in the majority of cases, 19/24 (79.2%). There were 5/24 (20,8%) cases with characteristic features of essential thrombocythemia (ЕТ-like features). The grade of stroma fibrosis in all cases was MF-0. Morphological picture in bone marrow biopsy of patients with masked PV was characteristic for PV in most cases. However, in some cases of masked PV the morphology part of megakaryocytes was similar to essential thrombocythemia or pre-fibrotic/early stage of primary myelofibrosis.Маскированная истинная полицитемия (ИП) является клинической формой истинной полицитемии, для которой характерно наличие мутации JAK2, соответствующей морфологической картины в костном мозге, и недостаточный для установления диагноза по критериям ВОЗ 2008 уровень НЬ. Целью данного исследования была оценка морфологии костного мозга на материале трепанобиоптатов костного мозга у пациентов с маскированной формой ИП. Методы. На основании клинических данных при динамическом наблюдении, патоморфологического диагноза, данных молекулярного исследования была сформирована группа из 24 пациентов с маскированной ИП. С помощью разработанного гистологического кодификатора проводилось детальное гистологическое исследование первичных трепанобиоптатов костного мозга. При оценке степени ретикулинового фиброза срезы окрашивали по Гомори. Результаты: При гистологическом исследовании трепанобиоптатов костного мозга в большинстве случаев определялся гиперклеточный (относительно возрастной нормы) костный мозг 18/24 (75%). Во всех случаях выявлена пролиферация мегакариоцитов, полиморфных по размеру и морфологии, с наличием атипичных форм с гиперсегментированными ядрами, со зрелой морфологией. Расширение и омоложение эритроидного ростка наблюдалось соответственно в 23/24 и 22/24 случаях (95,9% и 91,7%). При оценке гистотопографии мегакариоцитов в большинстве случаев 20/24 (83,3%) определялось сочетание разрозненного расположения мегакариоцитов и формирование рыхлых кластеров (3-16 клеток). Характерная для истинной полицитемии морфология элементов мегакариоцитарного ростка наблюдалась в большинстве случаев 19/24 (79,2%). В 5/24 (20,8) случаев были выявлены признаки, характерные для эссенциальной тромбоцитемии («ЕТ-like» признаки). Степень фиброза стромы во всех случаях составляла MF-0. Выводы: Морфологическая картина костного мозга пациентов с маскированной формой ИП в большинстве проанализированных нами случаев была характерной для истинной полицитемии. Вместе с тем, в части наблюдений при маскированной ИП в морфологии и гистотопографии мегакариоцитарного ростка определялись признаки, характерные для эссенциальной тромбоцитемии или пре-фиброзной/ранней стадии первичного миелофиброза

Successful experience in treating primary cutaneous anaplastic large cell lymphoma occuring with common lesions of the skin and lung tissue

The aim of the study is to present a successful case in treating primary cutaneous anaplastic large cell lymphoma (PCALCL) occurring with common lesions of the skin and lung tissue.Materials and methods. For the verification of the diagnosis in a patient with three types of skin elements (spot, thin plaque with and without ulceration), differential diagnosis was performed between ulcerative pyoderma gangrenosum, PCALCL, large-cell transformation of mycosis fungoides, and secondary skin lesions under the nodal ALK-negtaive ALCL. A complex of studies, including histological, immunohisto - chemical, cytogenetic studies of skin tumor biopsy, allowed the verification of the PCALCL diagnosis. For the treatment of the patient, intensive induction chemotherapy was used followed by high-dose consolidation and autologous transplantation of hematopoietic stem cells.Results. The selected treatment tactics allowed a long-term complete remission of the disease to be achieved in a patient from the poor prognosis group.Conclusion. An algorithm for the differential diagnosis and tactics of treating is presented for a patient with primary anaplastic large cell lymphoma with a widespread skin lesion and extradermal foci

Difficulties in diagnosing intestinal T-cell lymphoma. Case report

The article describes a rare diagnosis of monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL), due to its veiled by a number of so-called masks of enteropathies. A detailed analysis of all clinical, morphological and immunohistochemical data made it possible to establish the correct diagnosis. The revealed pathology is extremely rare in practice, even among specialists in hematology. The article demonstrates the main stages of both a complex diagnosis and an attempt at therapy for this aggressive form of intestinal lymphoma

Синдром VEXAS: на рубеже смены представлений об известных заболеваниях

This article presents the first case of VEXAS syndrome identified in the Russian Federation as well as characteristics of currently known clinical manifestations and treatment approaches. The clinical observation described is an impressive example of how the identification of a new pathogenic mutation can change the understanding of the classification, diagnosis and treatment of previously known immunoinflammatory diseases. Thus, in refractory forms of relapsing polychondritis, neutrophilic dermatosis, atypical forms of vasculitis, inflammatory joint diseases or undifferentiated systemic inflammatory syndrome, especially when associated with macrocytic anemia and myelodysplastic syndrome, VEXAS syndrome should be suspected and genetic testing should be performed to exclude the autoinflammatory nature of the existing condition.В статье приведен первый случай синдрома VEXAS, выявленный в Российской Федерации, а также характеристика известных на настоящий момент клинических проявлений и подходов к его терапии. Описанное клиническое наблюдение является ярким примером того, как выявление новой патогенной мутации может изменить представление о классификации, диагностике и терапии ранее известных иммуновоспалительных заболеваний. Так, при рефрактерных формах рецидивирующего полихондрита, нейтрофильного дерматоза, нетипичных формах васкулита, воспалительных заболеваний суставов или недифференцированном системном воспалительном синдроме, особенно при ассоциации с макроцитарной анемией и миелодиспластическим синдромом, необходима настороженность в отношении синдрома VEXAS и проведение генетического исследования для исключения аутовоспалительной природы имеющегося состояния

Diagnosis of IgG4 - related ophthalmic disease in a group of patients with various lesions of the eye and orbits

Purpose of the study. To provide demographic, clinical, laboratory, ultrasound, radiological, morphological/ immunomorphological phenotype of IgG4-related ophthalmic diseases, which allowsmaking a differential diagnosis with granulomatous, autoimmune, inflammatory, endocrine and hematologic diseases affecting the eye and orbits. Materials and methods. From 2004 to 2016 108 (78.2%) of the 138 patients were diagnosed with non-tumoral lesions of eye and orbits. In 48 patients (35%) at admission and 5 patients in the follow were diagnosed IgG4-related ophthalmic disease. In the analysis of 82 (f-44, m-38) patients with IgG4-related disease, localization of lesions in orbit observed in 53 (f-36, m-17) and it was the most frequent involvement in patients with IgG4-related disease (64.5%). Only 7 patients had isolated IgG4-related ophthalmic disease, whereas 46 patients (87%) had involvement of 2-7 locations, as a manifestation of IgG4-related systemic disease.During the examination, the average age of patients with IgG4-related ophthalmic disease was 47.5 years (19-73 years). Median time to diagnosis was 52.8 months before 2004 and 36 months 2004-2016. Results. We noted the predominance of females in the ratio 2: 1 inthe group of patients with IgG4-related ophthalmic disease. Edema of the eyelids, nasal congestion (55-60%), tumor-like formations of the upper eyelids and increased lacrimation prevailed at the onset of the disease, whereas such functional impairment like limited mobility and pain in eyeballs, exophthalmos, ptosis and diplopia appeared later at 15-38% with a loss visual acuity in one case. Bilateral lesion (86%), mainly affecting the lacrimal glands (93.5%), infiltration of the extraocular muscles (83.5%) and retrobulbar tissue with a thickening of the optic nerve in one third of patients were the main localizations IgG4-related ophthalmic disease. Clinical symptoms were accompanied by the appearance of moderate inflammatory activity (38%), increased levels IgG (44%), IgG4(88%) and IgE (61%). Indicators of autoimmune disorders observed in 6-22% of patients, most often in patients with simultaneous involvement of the salivary glands. Significant lymphoplasmacytic infiltration (94%) with a ratio of plasma cells (IgG4/IgG) secreting IgG4> 40% (90%) with fibrosis formation (94%) and follicle formation (71%) with a moderate amount of eosinophils (34%) were the major morphological / immunomorphological manifestations of IgG4-related ophthalmic disease. Signs of vasculitis and obliterative phlebitis were found in a small amount of patients. Conclusion. Determination of elevated levels of IgG-4 / IgE in patients with edema, pseudotumor of the eyelid, sinusitis and increase of the palpebral lobe of the lacrimal gland suggests the presence of IgG4-related ophthalmic disease. Minimally invasive incisional biopsy of lacrimal glands and salivary glands followed by morphological / immunomorphological research is needed for the correct diagnosis. Diagnostic orbitotomy in ophthalmic hospitals in such cases is inexpedient, since it leads to the development of dry eye. Massive lymphoplasmacytic infiltration with IgG4 / IgG ratio more than 40%, advanced fibrosis in biopsiesof the orbits tissue or salivary glands when combined lesions are required for the making the diagnosis of IgG4-related ophthalmic disease

Function and Assembly of a Chromatin-Associated RNase P that Is Required for Efficient Transcription by RNA Polymerase I

Background: Human RNase P has been initially described as a tRNA processing enzyme, consisting of H1 RNA and at least ten distinct protein subunits. Recent findings, however, indicate that this catalytic ribonucleoprotein is also required for transcription of small noncoding RNA genes by RNA polymerase III (Pol III). Notably, subunits of human RNase P are localized in the nucleolus, thus raising the possibility that this ribonucleoprotein complex is implicated in transcription of rRNA genes by Pol I. Methodology/Principal Findings: By using biochemical and reverse genetic means we show here that human RNase P is required for efficient transcription of rDNA by Pol I. Thus, inactivation of RNase P by targeting its protein subunits for destruction by RNA interference or its H1 RNA moiety for specific cleavage causes marked reduction in transcription of rDNA by Pol I. However, RNase P restores Pol I transcription in a defined reconstitution system. Nuclear run on assays reveal that inactivation of RNase P reduces the level of nascent transcription by Pol I, and more considerably that of Pol III. Moreover, RNase P copurifies and associates with components of Pol I and its transcription factors and binds to chromatin of the promoter and coding region of rDNA. Strikingly, RNase P detaches from transcriptionally inactive rDNA in mitosis and reassociates with it at G1 phase through a dynamic and stepwise assembly process that is correlated with renewal of transcription

Function and Assembly of a Chromatin-Associated RNase P that Is Required for Efficient Transcription by RNA Polymerase I

Human RNase P has been initially described as a tRNA processing enzyme, consisting of H1 RNA and at least ten distinct protein subunits. Recent findings, however, indicate that this catalytic ribonucleoprotein is also required for transcription of small noncoding RNA genes by RNA polymerase III (Pol III). Notably, subunits of human RNase P are localized in the nucleolus, thus raising the possibility that this ribonucleoprotein complex is implicated in transcription of rRNA genes by Pol I.By using biochemical and reverse genetic means we show here that human RNase P is required for efficient transcription of rDNA by Pol I. Thus, inactivation of RNase P by targeting its protein subunits for destruction by RNA interference or its H1 RNA moiety for specific cleavage causes marked reduction in transcription of rDNA by Pol I. However, RNase P restores Pol I transcription in a defined reconstitution system. Nuclear run on assays reveal that inactivation of RNase P reduces the level of nascent transcription by Pol I, and more considerably that of Pol III. Moreover, RNase P copurifies and associates with components of Pol I and its transcription factors and binds to chromatin of the promoter and coding region of rDNA. Strikingly, RNase P detaches from transcriptionally inactive rDNA in mitosis and reassociates with it at G1 phase through a dynamic and stepwise assembly process that is correlated with renewal of transcription.Our findings reveal that RNase P activates transcription of rDNA by Pol I through a novel assembly process and that this catalytic ribonucleoprotein determines the transcription output of Pol I and Pol III, two functionally coordinated transcription machineries