CDKN2A Gene Mutations: Implications for Hereditary Cancer Syndromes

Malignant neoplasms, including pancreatic cancer and melanoma, are major global health challenges. This study investigates melanoma pancreatic syndrome, a rare hereditary tumor syndrome associated with CDKN2A gene mutations. CDKN2A mutations contribute to a lifetime risk of melanoma ranging from 28% to 67%. This study reports the clinical features of six individuals with CDKN2A mutations and identifies recurrent alterations such as c.307_308del, c.159G>C and c.71G>C. It highlights the need for CDKN2A mutation testing in suspected cases of familial atypical multiple mole melanoma. Clinically significant variants show associations with melanoma and pancreatic cancer. The challenges of treating individuals with CDKN2A mutations are discussed, and the lack of specific targeted therapies is highlighted. Preclinical studies suggest a potential benefit of CDK4/6 inhibitors, although clinical trials show mixed results. This study underscores the importance of continued research into improved diagnostic and therapeutic strategies to address the complexities of hereditary cancer syndromes.

Mass spectrometry-based autoimmune profiling reveals predictive autoantigens in idiopathic pulmonary fibrosis

Autoimmunity plays a role in certain types of lung fibrosis, notably connective tissue disease-associated interstitial lung disease (CTD-ILD). In idiopathic pulmonary fibrosis (IPF), an incurable and fatal lung disease, diagnosis typically requires clinical exclusion of autoimmunity. However, autoantibodies of unknown significance have been detected in IPF patients. We conducted computational analysis of B cell transcriptomes in published transcriptomics datasets and developed a proteomic Differential Antigen Capture (DAC) assay that captures plasma antibodies followed by affinity purification of lung proteins coupled to mass spectrometry. We analyzed antibody capture in two independent cohorts of IPF and CTL-ILD patients over two disease progression time points. Our findings revealed significant upregulation of specific immunoglobulins with V-segment bias in IPF across multiple cohorts. We identified a predictive autoimmune signature linked to reduced transplant-free survival in IPF, persisting over time. Notably, autoantibodies against thrombospondin-1 were associated with decreased survival, suggesting their potential as predictive biomarkers.

Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome

Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion of the method to complex tissues would greatly enhance biological insights. Here we describe single-cell Deep Visual Proteomics (scDVP), a technology that integrates high-content imaging, laser microdissection and multiplexed mass spectrometry. scDVP resolves the context-dependent, spatial proteome of murine hepatocytes at a current depth of 1,700 proteins from a cell slice. Half of the proteome was differentially regulated in a spatial manner, with protein levels changing dramatically in proximity to the central vein. We applied machine learning to proteome classes and images, which subsequently inferred the spatial proteome from imaging data alone. scDVP is applicable to healthy and diseased tissues and complements other spatial proteomics and spatial omics technologies.

Deposition of Nanostructured Tungsten Oxide Layers by a New Method: Periodic Modulation of the Deposition Angle

Periodic modulation of the deposition angle (PMDA) is a new method to deposit nanostructured and continuous layers with controllable periodic density fluctuation. The method is used for the magnetron sputtering of a WO3 layer for an electrochromic device (ECD). An experimental study indicates that the electrochromic coloration-bleaching rate nearly doubles and the electrochromic efficiency grows by about 25% in comparison with the traditional method. The ECD efficiency rises with the increasing degree of nanostructure ordering, surface roughness, and homogeneity of the WO3 layer. The method is promising for coating deposition techniques needed to produce versatile devices with specific requirements for ion transport in surface layers, coatings, and interfaces, such as fuel cells, batteries, and supercapacitors.

The CFTR Gene Germline Heterozygous Pathogenic Variants in Russian Patients with Malignant Neoplasms and Healthy Carriers: 11,800 WGS Results

More than 275 million people in the world are carriers of a heterozygous mutation of the CFTR gene, associated with cystic fibrosis, the most common autosomal recessive disease among Caucasians. Some recent studies assessed the association between carriers of CFTR variants and some pathologies, including cancer risk. The aim of this study is to analyze the landscape of germline pathogenic heterozygous CFTR variants in patients with diagnosed malignant neoplasms. For the first time in Russia, we evaluated the frequency of CFTR pathogenic variants by whole-genome sequencing in 1800 patients with cancer and compared this with frequencies of CFTR variants in the control group (1825 people) adjusted for age and 10,000 healthy individuals. In the issue, 47 out of 1800 patients (2.6%) were carriers of CFTR pathogenic genetic variants: 0.028 (42/1525) (2.8%) among breast cancer patients, 0.017 (3/181) (1.7%) among colorectal cancer patients and 0.021 (2/94) (2.1%) among ovarian cancer patients. Pathogenic CFTR variants were found in 52/1825 cases (2.85%) in the control group and 221 (2.21%) in 10,000 healthy individuals. Based on the results of the comparison, there was no significant difference in the frequency and distribution of pathogenic variants of the CFTR gene, which is probably due to the study limitations. Obviously, additional studies are needed to assess the clinical significance of the heterozygous carriage of CFTR pathogenic variants in the development of various pathologies in the future, particularly cancer.

Mutual Interactions between Brain States and Alzheimer's Disease Pathology: A Focus on Gamma and Slow Oscillations

Brain state varies from moment to moment. While brain state can be defined by ongoing neuronal population activity, such as neuronal oscillations, this is tightly coupled with certain behavioural or vigilant states. In recent decades, abnormalities in brain state have been recognised as biomarkers of various brain diseases and disorders. Intriguingly, accumulating evidence also demonstrates mutual interactions between brain states and disease pathologies: while abnormalities in brain state arise during disease progression, manipulations of brain state can modify disease pathology, suggesting a therapeutic potential. In this review, by focusing on Alzheimer's disease (AD), the most common form of dementia, we provide an overview of how brain states change in AD patients and mouse models, and how controlling brain states can modify AD pathology. Specifically, we summarise the relationship between AD and changes in gamma and slow oscillations. As pathological changes in these oscillations correlate with AD pathology, manipulations of either gamma or slow oscillations can modify AD pathology in mouse models. We argue that neuromodulation approaches to target brain states are a promising non-pharmacological intervention for neurodegenerative diseases.

Impact of the azoximer bromide concomitant therapy on patient outcomes in patients with melanoma

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Background: Immunomodulators are used in the treatment of patients with melanoma. However, their role as anticancer therapeutic agents requires further investigation. Azoximer bromide (AB) is a well-tolerated immunomodulator that has been used in cases of melanoma. We investigated the impact of AB when used concomitantly with other melanoma treatment modalities on the overall survival (OS) and time to progression (TTP). Methods: We reviewed per protocol, a single-center real practice database that included 1,391 patients. Forty-two patients had received AB as a concomitant therapeutic agent. Concomitant medications included immune checkpoint inhibitors, cytokines, vaccines, targeted therapy and surgery alone in the adjuvant or metastatic setting. We built Cox proportional-hazards models for OS and TTP stratified by stage in SPSS v19. All known prognostic factors (LDH, TNM stage and sub-stage, mutations, sex, age, therapy by type, and by immunologic action) were included in the model along with AB therapy. Known factors were separated from unknown (AB therapy) by different variable blocks. A step forward method was used for model construction. Results: Significant (p < 0.05) factors to emerge in the OS model were LDH (Hazards ration [HR]: 1.458 for high LDH), sub-stage (HR: 1.718 for M1b-d sub-stage), BRAF mutation (HR: 0.698 if present), current therapy type (HR: 0.501 for immune checkpoint inhibitors (ICI), HR: 0.656 for targeted therapy (TT), HR: 1.275 for systemic immunotherapy, HR: 0.825 per added method for complex treatment, HR: 0.605 for surgery), previous treatment (HR: 0.778 for ICI, HR: 1.207 for single-agent chemotherapy, HR 1.176 for targeted or local treatment, HR: 1.315 for combination chemotherapy, HR: 2.039 for immunosuppressive factors reduction methods), male sex (HR: 1.204) and AB therapy (HR: 0.475). Significant factors in the TTP model were LDH (HR: 1.348 for high LDH), sub-stage (HR: 1.434 for B-D sub-stage), current therapy type (HR: 0.432 for (ICI), HR: 0.541 for TT, HR: 0.692 per added method for complex therapy HR: 0.705 for surgery), previous therapy (HR: 0.789 for ICI), male sex (HR: 1.167) and AB therapy (HR: 0.478). Conclusions: The addition of AB to standard therapy in melanoma appears to be an independent favorable prognostic factor. Prospective, randomized, clinical trials are needed to investigate these findings further.

Progression prediction model for solid tumors with clinical and immunological parameters

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Background: The immune system has well-known relation to tumor progression. Numerous immune-related parameters exist, but only a minor part could be used as biomarkers, especially dynamic ones. We trained a progression prediction model based on clinical features and peripheral immune system assessments. Methods: Patients with immunogenic (melanoma, 295, kidney cancer, 81), non-immunogenic (soft tissue sarcoma, 47, colorectal cancer, 26) and multiple primary tumors (29) with immunologic assessments before treatment (23.5%), on therapy (58.3), and in follow-up after the treatment (18.2%) were randomly divided in 7:3 ratio to the training and test groups. Counts of lymphocytes, T-, B, NK cells, cytotoxic lymphocytes, T-helpers were used as immunologic parameters. Age, sex, disease, stage, therapy, mutational status, last response on treatment, disease and therapy duration, previous treatments were used as clinical ones. The model was trained to predict disease progression in the next three months using “Catboost” gradient boosting. We used ROC AUC to test model performance and Yoden’s index for optimal cutoff calculation. We also studied the influence of model prediction on overall survival (OS) and time to progression (TTP) on the test dataset using the Kaplan-Meyer method and Cox regression. Results: We used 1682 assessments of immune parameters (immune status, IS) done in 354 patients (average 5 per patient) to train the model and 616 IS in 124 patients for validation. All IS of one patient were in the same group. The ROC AUC value of the model was 0.801. The model prediction of progression increased the probability of progressive disease from 37.5 to 62% and decreased the response rate from 37,5% to 8.4% (p = 0.016). The model prediction did not add information over known prognostic factors for OS in the multifactorial model but was an independent prognostic factor for TTP (HR 2.204, p = 0.011). False-positive results separate the group of patients with poor prognosis (OS 16 months, TTP 6 months) among patients with clinical benefit from patients with favorable prognosis (OS 61 months, TTP 18 months, p < 0.001), who had a truly negative model prediction. The possibility of prognosis improvement with therapy change was an essential factor for OS and TTP prediction (р < 0.001). The model was useful in predicting higher OS in patients with disease progression (p = 0.033) and shorter response duration in patients with clinical benefit (р = 0.03). Conclusions: Our progression prediction model provides clinically useful information and can be used for decision making in several clinical situations. Its utility should be tested in a prospective trial.

Impact of the azoximer bromide concomitant therapy on outcomes in patients with soft tissue sarcoma

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Background: Immunomodulators are used in the management of patients with soft tissue sarcoma, (STS). However, the precise mechanism behind their benefits in anticancer therapy effects have yet to be determined. We assessed the impact of the immunomodulator azoximer bromide (AB) as a prognostic factor for survival when used concomitant with standard therapy in patients with STS. Methods: We reviewed medical history and disease outcomes in STS patients attending the Petrov National Medical Research Centre of Oncology (St Petersburg, Russia). Data were collected per protocol on treatments and patient outcomes. A Cox proportional-hazards model for time-to-progression (TTP) was constructed in SPSS v19. Known prognostic factors (TNM stage and substage, sex, age, therapy by type, and by immunologic action, as well as treatment modality), setting and AB therapy extracted from patient records were included in the model. The model employed a ‘step-forward’ method with AB therapy identified as the ‘unknown’ variable. Results: Complete patient records were available on 243 clinic attendees (from 2010 to 2020), 25 had received treatment with AB. The median follow-up was 20.9 months. Patients received single- and multi-agent chemotherapy, vaccines, cytokines, radiation therapy and/or surgery in the adjuvant or metastatic setting. Significant factors in the TTP model were current therapy type (Hazards ratios: 0.59 for surgery, 0.533 per added method for complex therapy and HR 1.689 for single-agent chemotherapy), previous systemic chemotherapy (HR: 1.451) and AB therapy (HR 0.547). Conclusions: Use of AB with standard therapy in STS emerged as an independent favorable prognostic factor. Appropriately controlled, well-designed prospective trials are needed to investigate this finding further. [Table: see text]

Perovskite Puzzle for Revolutionary Functional Materials

Widely spread crystal lattices of perovskites represent a natural flexible platform for chemical design of various advanced functional materials with unique features. An interplay between chemical bonding, defects and crystallochemical peculiarities makes the perovskite structure a "LEGO designer" utilizing natural features of chemical elements of the renowned Mendeleev's Periodic Table (PTE) celebrating its 150-year anniversary. In this mini-review, crystal chemistry and bonding features, physical and functional properties, preparation methods and tuning functional properties with periodicity "tools" of the PTE will be exemplified for legendary families of high-temperature superconductive cuprates, colossal magnetoresistive manganites and hybrid lead halides for a new generation of solar cells.

Functional shifts in estuarine zooplankton in response to climate variability

Functional traits are becoming more common in the analysis of marine zooplankton community dynamics associated with environmental change. We used zooplankton groups with common functional properties to assess long-term trends in the zooplankton caused by certain environmental conditions in a highly eutrophicated gulf.Time series of zooplankton traits have been collected since the 1960s in the Gulf of Riga, Baltic Sea, and were analyzed using a combination of multivariate methods (principal coordinate analysis) and generalized additive models.One of the most significant changes was the considerable increase in the amount of the zooplankton functional groups (FGR) in coastal springtime communities, and dominance shifts from more complex to simpler organism groups-cladocerans and rotifers.The results also show that functional trait organism complexity (body size) decreased considerably due to cladoceran and rotifer increase following elevated water temperature. Salinity and oxygen had negligible effects on the zooplankton community.

Abstract A1: Clinical outcomes in patients with chronic hepatitis C and metastatic renal cell carcinoma (mRCC) after treatment with nivolumab

Clinical trials of immune checkpoint inhibitors have historically excluded patients with chronic hepatitis C (HCV) infection. The safety and efficacy profile of nivolumab is unknown in this under-represented population. Data were collected in a retrospective fashion on 36 patients with metastatic clear-cell mRCC. Patients were required to have a chronic HCV infection, no evidence of other malignancy or cirrhosis, and to have received nivolumab (3 mg/kg every 2 weeks) as second- or third-line therapy. Clinical outcomes included overall survival (OS), progression-free survival (PFS), and objective response rate (ORR). Safety was evaluated. Median follow-up was 17.5 months. Nivolumab was well tolerated in all HCV-infected patients (grade 3-4 toxicity was found in 6 of 36 cases [17%]). No unexpected toxicity was observed. Exposure to nivolumab was not associated with increased risk for hepatocellular carcinoma and cirrhosis (N=0). Medians OS and PFS were 23.9 (95% CI 20.7-26.5) and 6.8 (95% CI 4.9-8.7) months, respectively. 23% of patients had partial responses. The efficacy and safety profile observed in this study supports the administration of nivolumab in mRCC patients infected with HCV and warrants further investigation.

Citation Format: Ilya Tsimafeyeu, Rustem Gafanov, Anna Semenova, Ani Oganesyan, Anastasia Bondarenko, Sufia Safina, Kristina Zakurdaeva, Svetlana Protsenko. Clinical outcomes in patients with chronic hepatitis C and metastatic renal cell carcinoma (mRCC) after treatment with nivolumab [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A1.

Long-term survival in patients (pts) with locally advanced or disseminated malignant melanoma (MM) or renal cell carcinoma (RCC), treated with tag-7 gene-modified (GMV) tumor cells: A phase II trial

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Background: Immunotherapy may produce long lasting effects on survival.Magnitude of efficacy may be depended from immune factors. We evaluated the overall survival (OS) in pts treated with GMV with biomarker analysis of immunosuppressive factors (ISF) production by their tumor cells. Methods: Since 2001 to 2014 80 pts received GMV: 68 with MM and 12 pts with RCC. Treatment was given in the metastatic setting in 61 pts (MM-51, RCC – 10) and in the adjuvant (after complete cytoreduction) setting in 19 pts (MM-17, RCC-2). Stage 3 was in 26 (33%) pts, stage 4 in 54 (67%). Pt’s tumor samples were transferred to culture, transfected with TAG7and inactivated by radiation. Produced product was injected SC every 3 weeks until progression or 2y of therapy. ISF (MICA, TGF-β1, IL-10 and VEGF) were measured in the supernatants of the tumor cell cultures and used as predictive factors. Results: The 5-yr OS in intention to treat population was 25.1%. There was no differences in MM and RCC OS (Log-rank p = 0.44). Median OS in metastatic setting was 0,7 y, in adjuvant – 3,1 y. Classification trees were built on the basis of ISF production. The median OS was 6.6 y in favorable prognosis (FP) group (MICA level ≤582 pg/ml, n = 15), 4.6 mo in unfavorable (UF) group (MICA level > 582 pg/ml, n = 12) (p < 0.0001). No significant differences were found between classification trees based on the other ISF (TGF-β1, IL-10 and VEGF). In stage 3-4 MM pts with FP median OS was 2,3 y with 31% pts alive in 10y, in UF group – 0,4 y; log-rank p = 1,94E-5. No FP pts received modern immunotherapy. Conclusions: GMV shows high results in carefully selected pts with low ISF production. Method should be further investigated in pts with FP. [Table: see text]

eDNA and specific primers for early detection of invasive species--A case study on the bivalve Rangia cuneata, currently spreading in Europe

Intense human activities facilitate the successful spread and establishment of non-indigenous aquatic organisms in marine and freshwater ecosystems. In some cases such intrusions result in noticeable and adverse changes in the recipient environments. In the Baltic Sea, the discovery and rapid initial spread of the North American wedge clam Rangia cuneata represents a new wave of invasion which may trigger unpredictable changes of the local benthic communities. In this study we present a species-specific DNA-based marker developed in silico and experimentally tested on environmental samples. Marker specificity and sensitivity were assessed in vitro from water samples containing different mixtures of the target species and other five bivalves currently present in the region: the native Cerastoderma glaucum, Macoma balthica and Mytilus trossulus, the invasive Dreissena polymorpha and the cryptogenic Mya arenaria. Cross-species amplification was not found in any case. The method allows to detecting at least 0.4 ng of R. cuneata DNA per μl, and 0.1 g of tissue per liter of water. Finally, the marker performance was assessed in water samples from the Baltic Sea and Vistula Lagoon. The coincidence between independent visual observations of R. cuneata and positive PCR amplification of the marker from the water samples confirmed the efficiency of this highly reproducible, fast, and technically easy method. R. cuneata traces can be detected from environmental DNA even when the population is sparse and small, enabling rapid management responses and allowing to track the invasion dynamics.

[The Influence of the Functional State of Brain Regulatory Structures on the Programming, Selective Regulation and Control of Cognitive Activity in Children. Report I: Neuropsychological and EEG Analysis of Age-Related Changes in Brain Regulatory Functions in Children Aged 9-12 Years]

Age-related changes in brain regulatory functions in children aged from 9 to 12 years with typical development were studied by means of neuropsychological and EEG analysis. The participants of the study were 107 children without learning difficulties and behavior deviations; they were devided into three groups (9-10, 10-11 and 11-12 years). The neuropsychological tests revealed nonlinear age-related changes in different executive brain functions. The group of 10-11-year-old children showed better results in programming, in- hibition of impulsive reactions and in the perception of socially relevant information than the group of 9-10- year-old children. At the same time, these children had more difficulties with selective activity regulation as compared with the younger group. The difficulties were mainly caused by switching from one element of the program to another and by retention of learned sequence of actions. These children also showed a lower level of motivation for task performance. The children aged 11-12 years had less difficulties with selective activity regulation; however, impulsive behavior was more frequent; these children also had a higher level of task performance motivation than in children aged 10-11 years. The analysis of resting state EEG revealed age-related differences in deviated EEG patterns associated with non-optimal functioning of fronto-thalamic system and hypothalamic structures. The incidence of these two types of EEG patterns was significantly higher in children aged 10-11 years as compared with children aged 9-10 years. The EEG of the groups of 10-11 and 11-12-years-old children did not show any significant differences.