Assinatura da infecção severa com SARS-COV-2 em biópsias pulmonares e o seu uso para o reposicionamento de fármacos : estudo comparativo de dados de amostras clínicas e de modelos pré-clínicos

COVID-19 é uma doença viral aguda causada pelo novo coronavírus SARS-CoV-2. Com milhões de casos de COVID-19 em todo o mundo, opções terapêuticas são urgentemente necessárias para mitigar a sua morbidade e mortalidade, mas atualmente permanecem limitadas. Uma estratégia promissora para obter informações relevantes sobre sua fisiopatologia que possam ter aplicações terapêuticas é investigar os mecanismos regulatórios envolvidos na progressão para COVID-19 severa. Este trabalho tem como objetivo reconstruir a rede regulatória de COVID-19 severa e encontrar seus Reguladores Mestres (chamados de assinatura da doença). Usamos séries de conjuntos de dados de expressão gênica, disponíveis publicamente, derivados de autópsias pulmonares de pacientes para inferir a rede regulatória associada a COVID-19 severa. Identificamos um conjunto de seis fatores de transcrição (TAL1, TEAD4, EPAS1, ATOH8, ERG e ARNTL2) como potenciais Reguladores Mestres da doença. Após, pela abordagem de Mapa de Conectividade para o reposicionamento de drogas, encontramos 52 drogas diferentes (anti-inflamatórios, anti-infecções, psicotrópicos, reguladores da pressão arterial e do ritmo cardíaco) que potencialmente revertem a assinatura COVID-19 severa, e podem representar novas alternativas terapêuticas para a doença. Além disso, usando o índice de Jaccard, avaliamos a sobreposição entre a assinatura clínica severa de COVID-19 inferida e os medicamentos com os resultados obtidos da análise de amostras de esfregaço (swab) nasofaríngeo de pacientes infectados e células Vero, A549 e NHBE infectadas com diferentes MOI (multiplicity of infection) de SARS-CoV-2, modelos pré-clínicos celulares amplamente usados para pesquisar novas opções terapêuticas potenciais. Nossos dados demonstram uma semelhança significativa de células NHBE com assinatura COVID-19 clínica severa, enquanto as células A549 e Vero foram mais semelhantes às amostras de swabs nasofaríngeos. Usando uma abordagem de transcritômica integrada, identificamos candidatos a reguladores mestres envolvidos com COVID-19 severa, bem como várias drogas que potencialmente revertem esse padrão de expressão e também fornecem novas perspectivas sobre alvos moleculares e reposicionamento de drogas para futura investigação e validação na doença. Ademais, nosso estudo demonstra a limitada sobreposição entre os dados clínicos e pré-clínicos na pesquisa COVID-19 e destaca ainda a necessidade crítica de escolher o melhor modelo pré-clínico disponível para orientar a pesquisa sobre a fisiopatologia e o reposicionamento de drogas em potencial.COVID-19 is an acute viral illness caused by the novel SARS-CoV-2 coronavirus. With millions of COVID-19 cases worldwide, therapeutic options are urgently needed to mitigate morbidity and mortality, but currently remain limited. A promising strategy to gain relevant information regarding its pathophysiology that could have therapeutic applications is to investigate the regulatory mechanisms involved in severe COVID-19 progression. This work aims to reconstruct the severe COVID-19 regulatory network and find its transcriptional master regulators (so called disease signature). We use a series of gene expression datasets, publicly available, from patient lung biopsies to infer the co-expression network associated with severe COVID-19. We identified a set of six transcription factors as potential master regulators (TAL1, TEAD4, EPAS1, ATOH8, ERG, and ARNTL2). After, by Connectivity Map drug repositioning approach, we found 52 different drugs (anti-inflammatories, anti-infections, psychotropics, blood pressure, and heart rhythm regulators) that potentially revert severe COVID-19 signature, and could be a new therapeutic venue for the disease. In addition, using Jaccard index, we evaluated the overlap between the inferred clinical severe COVID-19 signature and drugs with the ones obtained from infected patients nasopharyngeal swab samples of, and Vero, A549 and NHBE cells infected with different MOI (multiplicity of infection) of SARS-CoV-2, preclinical cell models widely used to research for new potential therapeutic options. Our data demonstrate a significant similarity of NHBE cells with clinical severe COVID-19 signature, whereas A549 and Vero cells were more similar to nasopharyngeal swabs samples. Using an integrated transcriptomics approach, we identified master regulators candidates involved with severe COVID-19, as well as several drugs that potentially reverse these expression patterns, and provides new perspectives on molecular targets and drug repositioning for future investigation and validation in severe COVID-19 management. Moreover, our study demonstrates how limited is the overlap between clinical and preclinical data in COVID-19 research and further highlights the critical need to choose the best preclinical model available to guide research into the pathophysiology and potential drugs repositioning

A RACIALIZED SETTLER WOMAN'S TRANSFORMATIVE JOURNEY IN CANADA: BUILDING RELATIONAL ACCOUNTABILITIES

This dissertation tells the story of my racialized settler woman’s transformative journey toward reconciliation and mutual empowerment through community in Canada. The dissertation discusses how Indigenous Land-based learning became healing and empowering for me as a newly arrived settler woman of a colour, learning about my positioning on the stolen Indigenous Lands of treaty six territory. It recounts the journey of migrating from one colonial Land to another, building a family and new community networks, and learning about Indigenous histories, cultures, Land-based learning, and about diverse newcomer settler communities in Saskatoon, Canada. The dissertation discusses how collaborative learning has supported taking responsibility for understanding the meaning of Land in solidarity with Indigenous and newcomer communities, through involvement in a community garden project, community radio show, and various cultural community activities. Using decolonial feminist relational autoethnography as my research methodology, this dissertation discusses my quest to challenge everyday racisms and colonial practices ingrained in the daily lives of newcomer Canadians. Following 12 years of community activities in Treaty 6 and 7 territories, this research emphasizes a key lesson from this life journey: the need to be responsible for understanding the Indigenous meaning of Land in order to create belongingness with the Land and its original peoples, while resisting the assimilationist forces impacting Indigenous and newcomer communities through their unique histories, despite the orchestrated biases operating through colonialist structures. The author concludes with the hope that the analysis of decolonial, collaborative learning stories and connections with the Land may help other non-Indigenous communities build meaningful relationships with the Land and Indigenous communities

Resiliency in Disaster: The Relevance of Indigenous Land-based Practice

The COVID-19 pandemic, as a Natural Disaster, has significantly affected the vulnerable portion of society, particularly Indigenous and visible minority immigrants in Canada. As a color settler immigrant family in Indigenous land in Treaty 6 territory, we explore Indigenous Land-based Education (ILBE) from Indigenous Elders and Knowledge-keeper’s land-based stories, traditional knowledge, resiliency, and practice. As a family, we have been learning and practicing ILBE to develop resiliency during natural disasters like the COVID-19 pandemic. This paper used land-based decolonizing autoethnography to understand health and wellness from an ILBE perspective. We discussed why ILBE matters for building resiliency, resistance, and self-determination within a family and community; how can it help others? We have seen how COVID-19 has severely impacted our mental and physical health. During the high climate change era, many pandemics are yet to come, and the ILBE can build resiliency for both humans and non-humans

A comparative study of COVID-19 transcriptional signatures between clinical samples and preclinical cell models in the search for disease master regulators and drug repositioning candidates

Coronavirus disease 2019 (COVID-19) is an acute viral disease with millions of cases worldwide. Although the number of daily new cases and deaths has been dropping, there is still a need for therapeutic alternatives to deal with severe cases. A promising strategy to prospect new therapeutic candidates is to investigate the regulatory mechanisms involved in COVID-19 progression using integrated transcriptomics approaches. In this work, we aimed to identify COVID-19 Master Regulators (MRs) using a series of publicly available gene expression datasets of lung tissue from patients which developed the severe form of the disease. We were able to identify a set of six potential COVID-19 MRs related to its severe form, namely TAL1, TEAD4, EPAS1, ATOH8, ERG, and ARNTL2. In addition, using the Connectivity Map drug repositioning approach, we identified 52 different drugs which could be used to revert the disease signature, thus being candidates for the design of novel clinical treatments. Furthermore, we compared the identified signature and drugs with the ones obtained from the analysis of nasopharyngeal swab samples from infected patients and preclinical cell models. This comparison showed sig- nificant similarities between them, although also revealing some limitations on the overlap between clinical and preclinical data in COVID-19, highlighting the need for careful selection of the best model for each disease stage

Understanding Sustainability Education: A Community-Based Experience

Sustainability education policies are widely focused on modern technologies, green profits, and development projects in many Indigenous communities. However, there has been minimal attention given to critical areas such as: Indigenous world views, spiritual and relational practices, culture, lands, and revitalization. This imbalance, combined with the destruction and lack of recognition to Indigenous knowledge (systems), suggests that Indigenous environmental education policies are still in a state of adolescence as a field of academic inquiry. The present study examines how an Indigenous community understands sustainability and analyzes these understandings in relation to the literature on the politics of nature as well as Indigenous and postcolonial studies. This research followed a relational Participatory Action Research (PAR) research approach with a focus on the researchers’ relational accountabilities and obligations to study participants and site

Characterising HIV acquisition risk, treatment gaps and populations reached through venue-based outreach and clinical services in Blantyre, Malawi: findings from a district-wide CLOVE Study.

BACKGROUND: In 2017, Blantyre district had the highest adult HIV prevalence in Malawi (17.7%) and lowest viral suppression (60%). In response, the Ministry of Health expanded prevention and treatment services. We assessed whether outreach to social venues could identify individuals with increased HIV acquisition risk or with unsuppressed HIV not currently reached by clinic-based services. METHODS: We conducted a cross-sectional bio-behavioral survey in Blantyre, Malawi, from January to March 2022. We visited social venues where people meet new sexual partners and government clinics providing HIV testing or STI screening. Participants aged > 15 years were interviewed, and tested for HIV infection if not on ART. HIV recency tests were performed on those testing positive, and dried blood spots (DBS) was collected to quantify viral load and also to identify acute infection in those with HIV- results. RESULTS: HIV prevalence (18.5% vs 8.3%) and unsuppressed HIV infection (3.9% vs 1.7%) were higher among venue-recruited (n=1802) compared with clinic-recruited participants(n=2313). Among PLHIV at both clinics (n=199) and venues (n=289), 79% were virally suppressed. Few had acute(n=1) or recent infection(n=8). Among women, HIV prevalence was four times higher (38.9% venue vs 8.9% clinic). At clinics, PLHIV reporting visiting venues were less likely to be suppressed (54.6 vs 82.6%). More men at venues than at clinics reported paying for sex (49% vs 30%) or having multiple sex partners in the past 4 weeks (32% vs 16%). CONCLUSIONS: Enhanced venue-based prevention and testing for men and women could reduce treatment lapses, HIV treatment outcomes and reduce onward transmission

Perceptions of cervical cancer and motivation for screening among women in Rural Lilongwe, Malawi: A qualitative study

Introduction Cervical cancer is the leading cause of cancer death among women in Malawi. Low awareness of cervical cancer and negative perceptions of screening can prevent women from participating in preventative strategies. We sought to explore perceptions and motivations for screening among women who participated in a cervical cancer screen-and-treat pilot study in rural Malawi. Materials and methods We conducted a qualitative sub-study of a community-based cervical cancer screen-and-treat pilot study in rural Lilongwe between July-August 2017. From October 2017-February 2018, 17 women who underwent screening using visual inspection with acetic acid (VIA) and same-day thermal ablation treatment were recruited at their 12-week follow-up visit post treatment to participate in this qualitative sub-study. Semi-structured interview guides that explored baseline knowledge of cervical cancer, perceptions, and motivation for screening were used for in-depth interviews (IDIs). IDIs were conducted in the local language, Chichewa, translated and transcribed to English. Data was analyzed using NVivo® V12.0. Results Findings included fatalistic views on cancer, but limited knowledge specific to cervical cancer. Misconceptions of cervical cancer screening were common; however, there was a unique understanding of screening as prevention (i.e., finding and treating early disease to prevent progression to worsening disease). This understanding appeared to stem from HIV prevention concepts known to the community. Motivations for screening included desire to know one’s health status, convenience of community-based screening, and peer encouragement. Conclusion Despite limited knowledge of cervical cancer and misconceptions of screening, the concept of screening for prevention, desire to know one’s health status, convenient access, and peers’ influence were motivators for participation in screening. Cervical cancer screen-and-treat programs in high HIV prevalence areas should consider utilizing language that parallels HIV prevention language to communicate the need for cervical cancer screening and treatment and utilize prevention concepts that may already be familiar to women living there

Experiences of women participating in a human papillomavirus-based screen-triage-and treat strategy for cervical cancer prevention in Malawi

Objective To explore the experiences of Malawian women who underwent a human papillomavirus (HPV)-based screen-triage-treat algorithm for cervical cancer (CxCa) prevention. This algorithm included GeneXpert® HPV testing of self-collected vaginal samples, visual inspection with acetic acid (VIA) and colposcopy for HPV-positive women, and thermal ablation of ablation-eligible women. Method In-depth interviews were conducted with participants of a trial that evaluated the feasibility of a HPV-based screen-triage-treat algorithm among women living with HIV and HIV negative women in Lilongwe, Malawi. Participants were recruited from 3 groups: 1) HPV-negative; 2) HPV-positive/VIA-negative; 3) HPV-positive/VIA-positive and received thermal ablation. Interviews explored baseline knowledge of CxCa and screening, attitudes towards self-collection, and understanding of test results. Content analysis was conducted using NVIVO v12. Results Thematic saturation was reached at 25 interviews. Advantages of HPV self-collection to participants were convenience of sampling, same-day HPV results and availability of same-day treatment. There was confusion surrounding HPV-positive/VIA-negative results, as some participants still felt treatment was needed. Counseling, and in particular anticipatory guidance, was key in helping participants understand complex screening procedures and results. Overall, participants expressed confidence in the HPV screen-triage-treat strategy. Discussion HPV testing through self-collected samples is a promising tool to increase CxCa screening coverage. A multi-step screening algorithm utilizing HPV self-testing, VIA triage and thermal ablation treatment requires proper counseling and anticipatory guidance to improve patient understanding. Incorporating thorough counseling in CxCa screening programs can change women’s perspectives about screening, build trust in healthcare systems, and influence healthcare seeking behavior towards routine screening and prevention