Mapping differential interactomes by affinity purification coupled with data independent mass spectrometry acquisition

Characterizing changes in protein-protein interactions associated with sequence variants (e.g. disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies where cost and time are major considerations. To this end, we have coupled AP to data-independent mass spectrometric acquisition (SWATH), and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. Here, we use AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes, and propose a scalable pipeline for systems biology studies

piggybac- and PhiC31-Mediated Genetic Transformation of the Asian Tiger Mosquito, Aedes albopictus (Skuse)

The Asian tiger mosquito, Aedes albopictus, is a highly invasive mosquito and has spread from South East Asia to Europe, the United States and northern areas of Asia in the past 30 years. Aedes mosquitoes transmit a range of viral diseases, including dengue and chikungunya. Aedes albopictus is generally considered to be somewhat less of a concern in this regard than Aedes aegypti. However a recent mutation in the chikungunya virus dramatically increased its transmission by Aedes albopictus, causing an important outbreak in the Indian Ocean in 2006 that eventually reached Italy in 2007. This highlights the potential importance of this mosquito, which can thrive much further from the Equator than can Aedes aegypti. This paper describes the first genetic engineering of the Asian tiger mosquito. This is an essential step towards the development of genetics-based control methods against this mosquito, and also an invaluable tool for basic research. We describe both transposon-based and site-specific integration methods

Psychological well-being in Europe after the outbreak of war in Ukraine

The Russian invasion of Ukraine on February 24, 2022, has had devastating effects on the Ukrainian population and the global economy, environment, and political order. However, little is known about the psychological states surrounding the outbreak of war, particularly the mental well-being of individuals outside Ukraine. Here, we present a longitudinal experience-sampling study of a convenience sample from 17 European countries (total participants = 1,341, total assessments = 44,894, countries with >100 participants = 5) that allows us to track well-being levels across countries during the weeks surrounding the outbreak of war. Our data show a significant decline in well-being on the day of the Russian invasion. Recovery over the following weeks was associated with an individual’s personality but was not statistically significantly associated with their age, gender, subjective social status, and political orientation. In general, well-being was lower on days when the war was more salient on social media. Our results demonstrate the need to consider the psychological implications of the Russo-Ukrainian war next to its humanitarian, economic, and ecological consequences

Psychological well-being in Europe after the outbreak of war in Ukraine

The Russian invasion of Ukraine on February 24, 2022, has had devastating effects on the Ukrainian population and the global economy, environment, and political order. However, little is known about the psychological states surrounding the outbreak of war, particularly the mental well-being of individuals outside Ukraine. Here, we present a longitudinal experience-sampling study of a convenience sample from 17 European countries (total participants = 1,341, total assessments = 44,894, countries with >100 participants = 5) that allows us to track well-being levels across countries during the weeks surrounding the outbreak of war. Our data show a significant decline in well-being on the day of the Russian invasion. Recovery over the following weeks was associated with an individual’s personality but was not statistically significantly associated with their age, gender, subjective social status, and political orientation. In general, well-being was lower on days when the war was more salient on social media. Our results demonstrate the need to consider the psychological implications of the Russo-Ukrainian war next to its humanitarian, economic, and ecological consequences

The 5-Hydroxymethylcytosine Landscape of Prostate Cancer

Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE: In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.publishedVersionPeer reviewe

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Telephone conversation openings across languages, cultures and settings

The organization of telephone conversation has received much scholarly attention since Schegloff’s pioneering work in the 1960s and 1970s (Schegloff 1968, 1979). There are several reasons why researchers have been fascinated by telephone conversations in spite of their “apparently perfunctory character” (Schegloff 1986: 113). First, telephone calls are arguably the second most important site of speech interaction after face-to-face conversation. For tens of thousands of years face-to-face conversation was the only mode of speech interaction that humans had for communication. However, with the invention of the telephone in 1876 and its subsequent popularization, a new mode of communication was born. In today’s rapidly shrinking world of telecommunications, many people, particularly in the urban areas, are spending as much, if not more, time on telephone conversation than face-to-face interaction. Telephone conversation has thus gained a special status for students of language and social interaction. Second, for those interested in naturally occurring talk, the telephone offers a source of good quality data, unlike face-to-face conversations which often come with noise and other disturbances and complications. It is true that telephone calls are subject to a much more restrictive set of ‘ecological constraints’ than face-to-face conversations; for example, participants have no access to visual cues such as facial expressions and gestures. However, this turns out to be both a limitation and an advantage. From the analyst’s point of view, one of the attractions of telephone conversational data lies precisely in its absence of visual information. With telephone data, ‘what you hear is what you get’, which means that the same amount of speech information available to the participants is also available to the analyst. This contrasts significantly with recordings of face-to-face talk, where the analyst may not have access to visual cues, unless he also has a video recording. Yet another reason for the appeal of telephone conversations -- perhaps the most attractive one for many -- is the possibility of cross-linguistic and cross-cultural generalisations. As a type of speech event, telephone conversations the world over can in principle be defined and delimited by a set of organizational tasks, including such elements as making contact, establishing identity, exchanging preliminaries, presenting reason-for-call, managing topics, moving into closing, terminating calls, etc. With reference to these parameters researchers can chart variations in how these organizational tasks are handled in different linguistic, social and cultural settings. Thus, it has been suggested that “when it comes to making comparisons across linguistic and cultural settings, telephone conversations provide us with as close a situation as we could get to controlled experimental conditions.” (Luke and Pavlidou 2002: 6

Telephone conversation openings across languages, cultures and settings

The organization of telephone conversation has received much scholarly attention since Schegloff’s pioneering work in the 1960s and 1970s (Schegloff 1968, 1979). There are several reasons why researchers have been fascinated by telephone conversations in spite of their “apparently perfunctory character” (Schegloff 1986: 113). First, telephone calls are arguably the second most important site of speech interaction after face-to-face conversation. For tens of thousands of years face-to-face conversation was the only mode of speech interaction that humans had for communication. However, with the invention of the telephone in 1876 and its subsequent popularization, a new mode of communication was born. In today’s rapidly shrinking world of telecommunications, many people, particularly in the urban areas, are spending as much, if not more, time on telephone conversation than face-to-face interaction. Telephone conversation has thus gained a special status for students of language and social interaction. Second, for those interested in naturally occurring talk, the telephone offers a source of good quality data, unlike face-to-face conversations which often come with noise and other disturbances and complications. It is true that telephone calls are subject to a much more restrictive set of ‘ecological constraints’ than face-to-face conversations; for example, participants have no access to visual cues such as facial expressions and gestures. However, this turns out to be both a limitation and an advantage. From the analyst’s point of view, one of the attractions of telephone conversational data lies precisely in its absence of visual information. With telephone data, ‘what you hear is what you get’, which means that the same amount of speech information available to the participants is also available to the analyst. This contrasts significantly with recordings of face-to-face talk, where the analyst may not have access to visual cues, unless he also has a video recording. Yet another reason for the appeal of telephone conversations -- perhaps the most attractive one for many -- is the possibility of cross-linguistic and cross-cultural generalisations. As a type of speech event, telephone conversations the world over can in principle be defined and delimited by a set of organizational tasks, including such elements as making contact, establishing identity, exchanging preliminaries, presenting reason-for-call, managing topics, moving into closing, terminating calls, etc. With reference to these parameters researchers can chart variations in how these organizational tasks are handled in different linguistic, social and cultural settings. Thus, it has been suggested that “when it comes to making comparisons across linguistic and cultural settings, telephone conversations provide us with as close a situation as we could get to controlled experimental conditions.” (Luke and Pavlidou 2002: 6

Flight performance and teneral energy reserves of two genetically-modified and one wild-type strain of the yellow fever mosquito Aedes aegypti

The ability of sterile males to survive, disperse, find, and mate with wild females is key to the success of sterile insect technique (SIT). The Release of Insects carrying a Dominant Lethal (RIDL) system is a genetics-based SIT strategy for Aedes aegypti. We examine two aspects of insect performance, flight potential (dispersal ability) and teneral energy reserves, by comparing wild-type (WT) males with genetically-modified lines carrying the tetracycline-repressible constructs OX513A and OX3604C. Our results show significant differences in the flight capacity of the modified lines. OX513A males bred with tetracycline covered 38% less distance, while OX3604C males reared without tetracycline spent 21% less time in flight than their WT counterparts. Such differences in flight performance should be considered when designing release programs (e.g., by placing release sites sufficiently close together to achieve adequate coverage). All mosquito lines had similar teneral carbohydrate contents, though males of the OX3604C line contained more lipids. The addition of tetracycline to the larval diet did not influence the flight potential of the males; however, it did change the teneral sugar reserves of the WT and the lipid reserves of both the WT and the OX3604C lines