bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the West African forest island phenomenon: scientific insights gained, successes achieved and capacities strengthened
Authors: Logah Vincent , Azeez Jamiu O. , Compaore Halidou , Mesele Samuel Ayodele , Ocansey Caleb Melenya , Bougma Amelie B. , Tetteh Erasmus Narteh , Veenendaal Elmar , Lloyd Jon
Published: August 2024

Anthropogenic activities around local villages in mesic savanna landscapes of West Africa have resulted in soil improvement and forest establishment outside their climatic zones. Such unique ‘forest islands’ have been reported to provide ecosystem services including biodiversity conservation. However, the science underpinning their formations is limitedly studied. In 2015 and with funding support from the Royal Society-DFID (now FCDO), we set out to investigate the biogeochemistry of the forest islands in comparison with adjacent natural savanna and farmlands across 11 locations in Burkina Faso, Ghana and Nigeria. Our results showed that the forest islands do not differ significantly from the adjoining ecosystems in soil mineralogy implying that their formation was anthropogenically driven. We observed greater soil organic carbon and nutrient distributions in the forest islands, which also had more stable macro (>500 μm) and meso-aggregates (500–250 μm) than the adjoining agricultural lands. We found that soil micro-aggregate (250–53 μm) stability was climate (precipitation) driven in the West African ecosystems while meso- and macro-aggregate stability was land-use driven. In one of the unique forest islands we studied in the Mole National Park of Ghana, we found its mineral-associated organic carbon over 40% greater than the adjoining natural savanna with potential implications for the achievement of the global initiative of the ‘4p1000’ in West Africa. We conclude that the North–South–South research collaboration has established clearly, the science underlying the age-long West African forest island phenomenon and has, among many successes, led to capacity building of young scientists driving cutting-edge research in climate change adaptation and food systems transformation in the sub-region.
Chem4Energy: a consortium of the Royal Society Africa Capacity-Building Initiative
Authors: Ungerer Marietjie J. , Adei Evans , Amakali Theopolina , Botchway Cecil H. , Daniel Likius S. , Darkwa James , Dzade Nelson Y. , Mbaiwa Foster , Mensah Mary , Nyepetsi Maipelo , Makhubela Banothile , Mitchell Claire E. , Olaoye Oluwasegun Emmanuel , Oyetunji Olayinka A. , Sankar Meenakshisundaram , Sejie Fortunate P. , Sheehama Jacobina , Tia Richard , Uahengo Veikko , Živković Aleksandar , De Leeuw Nora H.
Published: August 2024

The Africa Capacity-Building Initiative is a Royal Society programme funded by the former UK Department for International Development to develop collaborative research between scientists in sub-Saharan Africa and the UK. Initially, four institutions were involved in the Chem4Energy consortium: Cardiff University in the UK and three African partners, the Kwame Nkrumah University of Science and Technology, Ghana, the University of Namibia and the University of Botswana, soon also including the Botswana International University of Science and Technology. The Chem4Energy research programme focused on ‘New materials for a sustainable energy future: linking computation with experiment’, aiming to deploy the synergy between state-of-the-art computational and experimental techniques to design and optimize new catalysts and semiconductor materials for renewable energy applications, based on materials that are abundant and readily available in African countries. The Chem4Energy consortium has achieved ambitious research goals, graduated seven PhD students and delivered a high-quality cross-disciplinary training programme in materials science and simulation techniques relevant to renewable energy applications. Since 2021, the extended consortium, including North-West University and the Centre for High-Performance Computing in South Africa, has remained active through an annual Chem4Energy conference series, with the sixth meeting taking place in Namibia in April 2025.
R21 malaria vaccine is protective against intradermal but not intravenousPlasmodium falciparumsporozoites in a randomized controlled human malaria infection study in Kenyan adults
Authors: Kapulu Melissa C , Orenge Francesca , Kimani Domtila , Kibwana Elizabeth , Kibet Hillary , Mutahi Mary , Datoo Mehreen S , Bellamy Duncan , Musembi Janet , Ngoto Omar , Rashid Hamisi , Akinyi Stellamaris , Mwatasa Mwaganyuma H , Nyamako Lydia , Keter Kelvias , Gatheru Rose , Mutiso Agnes , Musyoki Jennifer , Mwacharo Jedidah , Abebe Yonas , James Eric J , Billingsley Peter F , Ngetsa Caroline , Mosobo Moses , Makale Johnstone , Tawa Brian , Wamae Kevin , Ochola-Oyier Lynette I , Wambua Juliana , Lawrie Alison , Ramos-Lopez Fernando , Roberts Rachel , Richie Thomas L , Sim B. Kim Lee , Hoffman Stephen L , Ewer Katie J , Hill Adrian V S , Hamaluba Mainga , Bejon Philip
Published: August 2024

Falciparum malaria is a substantial public health problem. Vaccines and monoclonal antibodies targeting thePlasmodium falciparum(Pf) circumsporozoite protein (CSP) are promising control strategies. The protective mechanisms of anti-PfCSP antibodies are incompletely understood, and levels of anti-PfCSP antibodies are inconsistently predictive of protection. We undertook controlled human malaria infections in volunteers vaccinated with the PfCSP-based vaccine R21/Matrix-M, using either intradermal injection (ID) or direct venous inoculation (DVI) ofP. falciparumsporozoites (PfSPZ Challenge). R21/Matrix-M was highly protective against intradermal inoculation of PfSPZ Challenge (i.e. 100%, 12 out of 12) but not protective against PfSPZ Challenge by DVI (i.e. 0%, 0 out of 5). These findings imply that the variable delivery of Pf sporozoites into capillaries rather than the subdermal layers by infectious mosquito bites can account for the inconsistent protection provided by anti-PfCSP antibodies.
A Draft Pacific Ancestry Pangenome Reference
Authors: Littlefield Connor , Lazaro-Guevara Jose M. , Stucki Devorah , Lansford Michael , Pezzolesi Melissa H. , Taylor Emma J. , Wolfgramm Etoni-Ma’asi C. , Taloa Jacob , Lao Kime , Dumaguit C. Dave C. , Ridge Perry G. , Tavana Justina P. , Holland William L. , Raphael Kalani L. , Pezzolesi Marcus G.
Published: August 2024

Individuals of Pacific ancestry suffer some of the highest rates of health disparities yet remain vastly underrepresented in genomic research, including currently available linear and pangenome references. To begin addressing this, we developed the first Pacific ancestry pangenome reference using 23 individuals with diverse Pacific ancestry. We assembled 46 haploid genomes from these 23 individuals, resulting in highly accurate and contiguous genome assemblies with an average quality value of 55.0 and an average N50 of 40.7 Mb, marking the firstde novoassembly of highly accurate Pacific ancestry genomes. We combined these assemblies to create a pangenome reference, which added 30.6 Mb of novel sequence missing from the Human Pangenome Reference Consortium (HPRC) reference. Mapping short reads to this pangenome reduced variant call errors and yielded more true-positive variants compared to the HPRC and T2T-CHM13 references. This Pacific ancestry pangenome reference serves as a resource to enhance genetic analyses for this underserved population.
Structure and function of the human apoptotic scramblase Xkr4
Authors: Chakraborty Sayan , Feng Zhang , Lee Sangyun , Alvarenga Omar E. , Panda Aniruddha , Bruni Renato , Khelashvili George , Gupta Kallol , Accardi Alessio
Published: August 2024

Phosphatidylserine externalization on the surface of dying cells is a key signal for their recognition and clearance by macrophages and is mediated by members of the X-Kell related (Xkr) protein family. Defective Xkr-mediated scrambling impairs clearance, leading to inflammation. It was proposed that activation of the Xkr4 apoptotic scramblase requires caspase cleavage, followed by dimerization and ligand binding. Here, using a combination of biochemical approaches we show that purified monomeric, full-length human Xkr4 (hXkr4) scrambles lipids. CryoEM imaging shows that hXkr4 adopts a novel conformation, where three conserved acidic residues create an electronegative surface embedded in the membrane. Molecular dynamics simulations show this conformation induces membrane thinning, which could promote scrambling. Thinning is ablated or reduced in conditions where scrambling is abolished or reduced. Our work provides insights into the molecular mechanisms of hXkr4 scrambling and suggests the ability to thin membranes might be a general property of active scramblases.
Revealing unseen dynamical regimes of ecosystems from population time-series data
Authors: Medeiros Lucas P. , Sorenson Darian K. , Johnson Bethany J. , Palkovacs Eric P. , Munch Stephan B.
Published: August 2024

Many ecosystems can exist in alternative dynamical regimes for which small changes in an environmental driver can cause sudden jumps between regimes. However, predicting the dynamics of regimes that occur under unobserved levels of the environmental driver has remained an unsolved challenge in ecology with important implications for conservation and management. Here we show that integrating population time-series data and information on the putative driver into an empirical dynamic model allows us to predict new dynamical regimes without the need to specify a population dynamics model. As a proof of concept, we demonstrate that we can accurately predict fixed-point, cyclic, or chaotic dynamics under unseen driver levels for a range of simulated models. For a model with an abrupt population collapse, we show that our approach can anticipate the regime that follows the tipping point. We then apply our approach to data from an experimental microbial ecosystem and from a lake planktonic ecosystem. We find that we can reconstruct transitions away from chaos in the experimental ecosystem and anticipate the dynamics of the oligotrophic regime in the lake ecosystem. These results lay the groundwork for making rational decisions about preventing, or preparing for, regime shifts in natural ecosystems.
Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer
Authors: Marcarian Haley Q. , Sivakoses Anutr , Arias Anika M. , Ihedioha Olivia C. , Lee Benjamin R. , Bishop Maria C. , Bothwell Alfred L.M.
Published: August 2024

Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers.

SIGNIFICANCE STATEMENT

We have identified trogocytosis as a mechanism by which human clear cell renal carcinoma tumors acquire lymphocyte surface protein expression from tumor infiltrating immune cells. In addition to the transfer of membrane fragments, we have provided evidence to show that genomic DNA is transferred from a normal immune cell to a tumor cell during trogocytosis. This process alters the transcriptome of cancer cells such that they express significantly more mRNA for immune proteins such as the lymphocyte marker CD45 compared to tumor cells that have not undergone trogocytosis. This study provides an in-depth analysis of the interactions between cancer cells and tumor infiltrating lymphocytes, and how these interactions alter the development of human tumors.
Generating Multi-state Conformations of P-type ATPases with a Conditional Diffusion Model
Authors: Xu Jingtian , Wang Yong
Published: August 2024

Understanding and predicting the diverse conformational states of membrane proteins is essential for elucidating their biological functions. Despite advancements in computational methods, accurately capturing these complex structural changes remains a significant challenge. Here we introduce a computational approach to generate diverse and biologically relevant conformations of membrane proteins using a conditional diffusion model. Our approach integrates forward and backward diffusion processes, incorporating state classifiers and additional conditioners to control the generation gradient of conformational states. We specifically targeted the P-type ATPases, a critical family of membrane transporters, and constructed a comprehensive dataset through a combination of experimental structures and molecular dynamics simulations. Our model, incorporating a graph neural network with specialized membrane constraints, demonstrates exceptional accuracy in generating a wide range of P-type ATPase conformations associated with different functional states. This approach represents a meaningful step forward in the computational generation of membrane protein conformations using AI and holds promise for studying the dynamics of other membrane proteins.

TOC Graphic
Evaluation of anti-CENP reactivity in samples with centromere HEp-2 pattern and correlation with Systemic Sclerosis clinical features
Authors: Keppeke Gerson D. , Landoni Diana , Kayser Cristiane , Matos Pedro , Diogenes Larissa , Keppeke Jessica , Rodrigues Silvia Helena , Andrade Luis Eduardo C.
Published: August 2024

Background/Objectives

Anti-centromere antibodies are associated with limited cutaneous Systemic Sclerosis (lcSSc) and in general, with a more favorable prognosis for SSc. Centromere pattern (AC-3) observed in the immunofluorescence assay in HEp-2 cells (HEp-2-IFA) suggests the presence of antibodies against CENP antigens, mainly CENP-B/A. In this study, we evaluated the frequency of reactivity to CENP-B and CENP-A in samples with an AC-3 pattern in the HEp-2-IFA. We also correlated the demographic and clinical characteristics of SSc patients according to the presence of the AC-3 pattern.

Methods

Samples from 39 SSc patients with AC-3 pattern were included and evaluated for CENP-B/A reactivity by line-blot and indirect ELISA. As controls, 48 lcSSc without the AC-3 pattern (Non-AC-3 group) were included. Clinical characteristics were recovered for 69 patients, 21 with AC-3 and all those in the Non-AC-3 group.

Results

Out of 39 samples with AC-3, 33 (84.6%) were reactive against CENP-B and 32 (82.1%) were reactive against CENP-A using the line-blot assay. Using anti-CENP-B ELISA, 36 (92.3%) of the samples with AC-3 were positive for anti-CENP-B. There was 79.5% concordance for CENP-B reactivity between ELISA and line-blot. Using the immunoblot assay, 27 (69.2%) of the samples with AC-3 were reactive against CENP-B and CENP-A, and one sample was positive only for CENP-A. Altogether, 38 samples (97.4%) were reactive against CENP-B by at least one method and all 39 samples (100%) were positive for either CENP-B or CENP-A in at least one of the tests. Regarding the clinical features, interstitial lung disease was less frequent in patients with AC-3 pattern compared to Non-AC-3 (10%versus54.2%; p=0.001). Other organ involvement parameters had similar frequencies between the groups.

Conclusions

In conclusion, the HEp-2-IFA method was 100% sensitive in detecting antibodies to CENP-A and CENP-B. Anti-CENP-B is the predominant autoantibody in samples yielding the AC-3 pattern, but exclusive anti-CENP-A reactivity was observed less frequently. Among lcSSc patients, anti-centromere reactivity was associated with less frequent lung involvement.
Safety, Feasibility, and Utility of Digital Mobile Six-Minute Walk Testing in Pulmonary Arterial Hypertension: The DynAMITE Study
Authors: Schütz Narayan , Glinskii Vlad , Anderson Ryan , Del Rosario Patricia , Hedlin Haley , Lee Justin , Hess John , Van Wormer Steve , Lopez Alejandra , Hershman Steven G , De Jesus Perez Vinicio , Zamanian Roham T.
Published: August 2024

Rationale

Pulmonary arterial hypertension (PAH) is a life-threatening progressive cardiopulmonary disease associated with high morbidity and mortality. Changes in the six-minute walk test (6MWT) provide prognostic information and help guide treatment decisions for PAH. However, since 6MWT requires in-clinic visits, clinical interventions to address disease progression may be delayed. Wearable technologies could reduce this delay by allowing the performance of 6MWT in the community and delivering data to clinicians remotely.

Objectives

To perform a pilot study to determine the safety and feasibility of performing 6MWT in PAH outpatients using a wearable app-based tool.

Methods

PAH patients recruited at Stanford University were provided an Apple Watch with an app to perform daily, self-administered 6MWT over 12 weeks. Bland-Altman plots and correlations were used to assess the agreement and reliability of in-clinic vs. app-based 6MWT data at the beginning and end of the 12-week trial.

Measurements and Main Results

From 55 PAH participants, we collected 3,139 app-recorded walks during 979.7 patient-weeks of exposure. On average, participants performed 3±2.3 weekly walks. No serious adverse events were reported. App-derived walk distance was highly correlated (r≥ 0.9) to the baseline in-clinic 6MWD and showed excellent reliability (ICC=0.9). Correlation and agreement were significantly lower at the 12-week follow-up visit. App-derived metrics beyond 6MWD showed promising associations with disease status.

Conclusions

App-based outpatient 6MWT is feasible, safe, reasonably accurate, likely clinically relevant, and reliable in PAH patients but long-term measurement stability may be a concern. App-derived digital measures beyond distance show promise for future applications.
Medical termination of pregnancy from day 85 to day 153 of gestation: A randomized comparison between administration of the initial dose of misoprostol at home or in the clinic
Authors: Gemzell Danielsson Kristina , Rydelius Johanna
Published: August 2024

Study Protocol

Objectives

The objective of this study is to compare two groups of women requiring termination of pregnancy from the gestational age of 85 days. All women will receive Mifepristone during their first visit to the out-patient ward. One group of women will receive Misoprostol to administer the first dose (vaginally) at home and 2 hours later they will be admitted to the in-patient ward. They will be informed to present earlier if they start bleeding or experience pain corresponding to more than normal menstrual cramping.

The other group will receive the first dose of Misoprostol (vaginally) when admitted in the in-patient ward (usually in the morning) according to current practice.

Primary objective

To investigate the proportion of women who are successfully treated as day-care patients (day-care being defined as 9 hours from time of admission).

Design

The study will be a randomized, controlled, multi-centred open label trial with women recruited from four hospitals in Sweden.
Factors associated with breast lesions among women attending select teaching and referral health facilities in Kenya: a cross-sectional study
Authors: Rioki Josephine Nyabeta , Mweu Marshal , Rogena Emily , Songok Elijah M. , Mwangi Joseph , Muchiri Lucy
Published: August 2024

Background

Despite extensive research on the risk factors for breast cancer, little is known about the factors contributing to other breast lesions, of which some may indicate an increased risk for this disease. The objective of this study was to identify the risk factors for breast lesions among women with breast lumps seeking care at select teaching and referral hospitals in Kenya between December 2016 to December 2019.

Methods

An analytical cross-sectional study design was used to investigate the risk factors for breast lesions among 651 women with breast lumps. Data was collected using a semi-structured questionnaire. A multivariable logistic regression model was used to evaluate the impact of the predictors on the breast lesions. Ethical approval was granted by Kenyatta National Hospital (KNH) and the University of Nairobi Ethics and Research Committee (UoN-ERC) under study number P334/04/2016.

Results

The median age of participants was 30 years (range 16-87), with the majority having secondary education and belonging to the Kikuyu ethnic group. Parity, exercise, and contraceptive use were significant predictors of breast lesions identified. Nulliparous women had significantly lower odds of developing malignant (aOR: 0.11; 95% CI: 0.05-0.26), and suspicious (aOR: 0.23; 95% CI: 0.07-0.71) lesions. Regular exercise was associated with lower odds of both malignant and suspicious lesions. Conversely, contraceptive use increased the odds of developing atypical (aOR 0.92; 95% CI: 0.28-2.98) lesions, suspicious (aOR 0.33; 95% CI: 0.14-0.78), and malignant lesions (aOR of 0.31; 95% CI: 0.18-0.55).

Conclusion

Exercise, parity, and hormonal contraception were independently found to be significant predictors of breast lesions. These findings underscore the necessity for personalized risk reduction strategies and emphasize the importance of understanding the risk factors for both benign and malignant breast disease to inform public health policies.
Investigating the association between oral health behaviours and risk behaviours of university students – a quantitative study utilising online questionnaires
Authors: Azam Tanzeelah , Kitsaras George , Gomez Juliana , Goodwin Michaela
Published: August 2024

Background

Young adults are exposed to a variety of risk-related behaviours such as alcohol, smoking, and changes in dietary habits, which may result in unknown outcomes in their oral health. There is limited evidence on whether different risk behaviours are associated with oral health behaviours in the university student population. This study gathers data on the behaviours of students in their first year of university, which will inform the future development of oral health behaviour change interventions for this population.

Method

This longitudinal quantitative survey involved 205 first-year university students, aged 18-24. They completed questionnaires at baseline and a 6-month follow-up interval providing information regarding self-reported oral health status, hygiene routines, risk behaviours (e.g., diet, smoking, alcohol) and attitudes towards digital health.

Results

The findings show associations between oral health behaviours with risk behaviours including links with oral care routines, bleeding gums, brushing frequency, with exercise, vaping, and unhealthy food and drink intake. Significant changes over the two-time points were also observed, such as the worsening of the self-reported condition of the teeth (p<0.001), reduction in the self-reported condition of the gums (p=0.004), reduced brushing frequency (p=0.003), less regular dental visits (p=0.013), more students intending to visit their previous dentist rather than finding a new dentist at university (p=0.026), and increased consumption of unhealthy non-alcoholic drinks (p=0.003). Positive changes over time include reduced alcohol consumption frequency and units (p=0.030 and p=0.001), fewer instances of binge drinking (p=0.014), and less frequent consumption of unhealthy foods (p=0.034).

Conclusion

The findings highlight the complex relationship between oral heal and risk behaviours in this demographic. Poorer oral health behaviours are linked to engagement in risk behaviours. Therefore, oral health behaviours should be targeted alongside other risk behaviours. Tailored interventions should be developed to improve oral health and behaviour among university students.
Prospective Analysis of urINe LAM to Eliminate NTM Sputum Screening (PAINLESS) study: Rationale and trial design for testing urine lipoarabinomannan as a marker of NTM lung infection in cystic fibrosis
Authors: Calhoun Kara M. , Armantrout Emily , Poch Katie , Caceres Silvia , Lovell Valerie K. , Jones Marion , Malcolm Kenneth C. , Vestal Brian , Wheeler Emily , Rysavy Noel , Manzer Jordan , Aboellail Ibrahim , Chatterjee Delphi , Nick Jerry A.
Published: August 2024

Background

Routine screening for nontuberculous mycobacterial (NTM) lung disease is dependent on sputum cultures. This is particularly challenging in the cystic fibrosis (CF) population due to reduced sputum production and low culture sensitivity. Biomarkers of infection that do not rely on sputum may lead to earlier diagnosis, but validation trials require a unique prospective design.

Purpose

The rationale of this trial is to investigate the utility of urine lipoarabinomannan (LAM) as a test to identify people with CF with a new positive NTM culture. We hypothesize that urine LAM is a sensitive, non-invasive screening test with a high negative predictive value to identify individuals with a relatively low risk of having positive NTM sputum culture.

Study design

This is a prospective, single-center, non-randomized observational study in adults with CF, 3 years of negative NTM cultures, and no known history of NTM positive cultures. Patients are followed for two year-long observational periods with the primary endpoint being a positive NTM sputum culture within a year of a positive urine LAM result and a secondary endpoint of a positive NTM sputum culture within 3 years of a positive urine LAM result. Study implementation includes remote consent and sample collection to accommodate changes from the COVID-19 pandemic.

Conclusions

This report describes the study design of an observational study aimed at using a urine biomarker to assist in the diagnosis of NTM lung infection in pwCF. If successful, urine LAM could be used as an adjunct to traditional sputum cultures for routine NTM screening.
Adenomas from individuals with pathogenic biallelic variants in theMUTYHandNTHL1genes demonstrate base excision repair tumour mutational signature profiles similar to colorectal cancers, expanding potential diagnostic and variant classification applications
Authors: Walker Romy , Joo Jihoon E. , Mahmood Khalid , Clendenning Mark , Como Julia , Preston Susan G. , Joseland Sharelle , Pope Bernard J. , Medeiros Ana B. D. , Murillo Brenely V. , Pachter Nicholas , Sweet Kevin , Spigelman Allan D. , Groves Alexandra , Gleeson Margaret , Bernatowicz Krzysztof , Poplawski Nicola , Andrews Lesley , Healey Emma , Gallinger Steven , Grant Robert C. , Win Aung K. , Hopper John L. , Jenkins Mark A. , Torrezan Giovana T. , Rosty Christophe , Macrae Finlay A. , Winship Ingrid M. , Buchanan Daniel D. , Georgeson Peter
Published: August 2024

Background

Colorectal cancers (CRCs) from people with biallelic germline likely pathogenic/pathogenic variants inMUTYHorNTHL1exhibit specific single base substitution (SBS) mutational signatures, namely combined SBS18 and SBS36 (SBS18+SBS36), and SBS30, respectively. The aim was to determine if adenomas from biallelic cases demonstrated these mutational signatures at diagnostic levels.

Methods

Whole-exome sequencing of FFPE tissue and matched blood-derived DNA was performed on 9 adenomas and 15 CRCs from 13 biallelicMUTYHcases, on 7 adenomas and 2 CRCs from 5 biallelicNTHL1cases and on 27 adenomas and 26 CRCs from 46 non-hereditary (sporadic) participants. All samples were assessed for COSMIC v3.2 SBS mutational signatures.

Results

In biallelicMUTYHcases, SBS18+SBS36 signature proportions in adenomas (mean±standard deviation, 65.6%±29.6%) were not significantly different to those observed in CRCs (76.2%±20.5%,p-value=0.37), but were significantly higher compared with non-hereditary adenomas (7.6%±7.0%,p-value=3.4x10-4). Similarly, in biallelicNTHL1cases, SBS30 signature proportions in adenomas (74.5%±9.4%) were similar to those in CRCs (78.8%±2.4%) but significantly higher compared with non-hereditary adenomas (2.8%±3.6%,p-value=5.1x10-7). Additionally, a compound heterozygote with the c.1187G>A p.(Gly396Asp) pathogenic variant and the c.533G>C p.(Gly178Ala) variant of unknown significance (VUS) inMUTYHdemonstrated high levels of SBS18+SBS36 in four adenomas and one CRC, providing evidence for reclassification of the VUS to pathogenic.

Conclusions

SBS18+SBS36 and SBS30 were enriched in adenomas at comparable proportions observed in CRCs from biallelicMUTYHand biallelicNTHL1cases, respectively. Therefore, testing adenomas may improve the identification of biallelic cases and facilitate variant classification, ultimately enabling opportunities for CRC prevention.
Biallelic Loss of Molecular Chaperone Molecule AIP Results in a Novel Severe Multisystem Disease Defined by Defective Proteostasis
Authors: Korbonits Márta , Wang Xian , Barry Sayka , Lim Chung Thong , Suleyman Oniz , Tito Stefano De , Uddin Nazia , Vignola Maria Lillina , Hall Charlotte , Perna Laura , Chapple J. Paul , Czbik Gabor , Henson Sian M , Morales Valle , Bianchi Katiuscia , Eðvarðsson Viðar Örn , Ragnarsson Kristján Ari , Kristinsdóttir Viktoría Eir , Debeer Anne , Sleyp Yoeri , Zinchenko Rena , Anderson Glenn , Duchen Michael , Singh Kritarth , Chung Chih Yao , Yuan Yu , Patel Sandip , Aksoy Ezra , Borovikov Artem O. , Björnsson Hans Tómas , Esch Hilde Van , Tooze Sharon , Brennan Caroline , Haworth Oliver
Published: August 2024

Children born with deleterious biallelic variants of the chaperone aryl hydrocarbon receptor interacting protein (AIP) have a novel pediatric metabolic disease presenting a severe, complex clinical phenotype characterized by failure to develop following birth. Analysis ofAipknockout mouse embryonic fibroblasts and patient-derived dermal fibroblasts revealed that AIP was required to support proteostasis; including proteasome activity, induction of autophagy and lysosome function. aip knockout zebrafish, recapitulated the phenotype of the children; dying at an early stage of development when autophagy is required to adapt to periods of starvation. Our results demonstrate that AIP plays a crucial role in initiating autophagy and maintaining proteostasisin vitroandin vivo.

One Sentence Summary

Homozygous loss of the chaperone AIP results in a novel pediatric disease exhibiting multiple features of a lysosomal storage disease.
SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant tumor cells
Authors: Bernhardt Melissa , Rech Anne , Berthold Marion , Lappe Melina , Herbel Jan-Niklas , Erhard Florian , Paschen Anette , Schilling Bastian , Schlosser Andreas
Published: August 2024

The immunopeptidome is constantly monitored by T cells to detect foreign or aberrant HLA peptides. It is highly dynamic and reflects the current cellular state, enabling the immune system to recognize abnormal cellular conditions, such as those present in cancer cells. To precisely determine how changes in cellular processes, such as those induced by drug treatment, affect the immunopeptidome, quantitative immunopeptidomics approaches are essential. To meet this need, we developed a pulsed SILAC-based method for quantitative immunopeptidomics. Metabolic labeling with lysine, arginine, and leucine enabled isotopic labeling of nearly all HLA peptides across all allotypes (> 90% on average). We established a data analysis workflow that integrates thede novosequencing-based tool Peptide-PRISM for comprehensive HLA peptide identification with MaxQuant for accurate quantification. We employed this strategy to explore the modulation of the immunopeptidome upon MAPK pathway inhibition (MAPKi) and to investigate alterations associated with early cellular responses to inhibitor treatment and acquired resistance to MAPKi. Our analyses demonstrated significant changes in the immunopeptidome early during MAPKi treatment and in the resistant state. Moreover, we identified putative tumor-specific cryptic HLA peptides linked to these processes that might represent exploitable targets for cancer immunotherapy.

Synopsis

We have developed a mass spectrometric method that allowed us to investigate the effects of common MAPK inhibitors on the immunopeptidome of melanoma cells. This approach has led to the discovery of new potential targets for cancer immunotherapy.
Neurofibromin deficiency alters the patterning and prioritization of motor behaviors in a state-dependent manner
Authors: Suarez Genesis Omana , Kumar Divya S. , Brunner Hannah , Emel Jalen , Teel Jensen , Knauss Anneke , Botero Valentina , Broyles Connor N. , Stahl Aaron , Bidaye Salil S. , Tomchik Seth M.
Published: August 2024

Genetic disorders such as neurofibromatosis type 1 increase vulnerability to cognitive and behavioral disorders, such as autism spectrum disorder and attention-deficit/hyperactivity disorder. Neurofibromatosis type 1 results from loss-of-function mutations in the neurofibromin gene and subsequent reduction in the neurofibromin protein (Nf1). While the mechanisms have yet to be fully elucidated, loss of Nf1 may alter neuronal circuit activity leading to changes in behavior and susceptibility to cognitive and behavioral comorbidities. Here we show that mutations decreasing Nf1 expression alter motor behaviors, impacting the patterning, prioritization, and behavioral state dependence in aDrosophilamodel of neurofibromatosis type 1. Loss of Nf1 increases spontaneous grooming in a nonlinear spatial and temporal pattern, differentially increasing grooming of certain body parts, including the abdomen, head, and wings. This increase in grooming could be overridden by hunger in food-deprived foraging animals, demonstrating that the Nf1 effect is plastic and internal state-dependent. Stimulus-evoked grooming patterns were altered as well, withnf1mutants exhibiting reductions in wing grooming when coated with dust, suggesting that hierarchical recruitment of grooming command circuits was altered. Yet loss of Nf1 in sensory neurons and/or grooming command neurons did not alter grooming frequency, suggesting that Nf1 affects grooming via higher-order circuit alterations. Changes in grooming coincided with alterations in walking. Flies lacking Nf1 walked with increased forward velocity on a spherical treadmill, yet there was no detectable change in leg kinematics or gait. Thus, loss of Nf1 alters motor function without affecting overall motor coordination, in contrast to other genetic disorders that impair coordination. Overall, these results demonstrate that loss of Nf1 alters the patterning and prioritization of repetitive behaviors, in a state-dependent manner, without affecting motor coordination.
DMT1 knockout abolishes ferroptosis induced mitochondrial dysfunction inC. elegansamyloid β proteotoxicity
Authors: Peng Wilson , Chung Kaitlin B , Lawrence B Paige , O’Banion M Kerry , Dirksen Robert T , Wojtovich Andrew P , Onukwufor John O
Published: August 2024

Iron is critical for neuronal activity and metabolism, and iron dysregulation alters these functions in age-related neurodegenerative disorders, such as Alzheimer’s disease (AD). AD is a chronic neurodegenerative disease characterized by progressive neuronal dysfunction, memory loss and decreased cognitive function. AD patients exhibit elevated iron levels in the brain compared to age-matched non-AD individuals. However, the degree to which iron overload contributes to AD pathogenesis is unclear. Here, we evaluated the involvement of ferroptosis, an iron-dependent cell death process, in mediating AD-like pathologies inC. elegans. Results showed that iron accumulation occurred prior to the loss of neuronal function as worms age. In addition, energetic imbalance was an early event in iron-induced loss of neuronal function. Furthermore, the loss of neuronal function was, in part, due to increased mitochondrial reactive oxygen species mediated oxidative damage, ultimately resulting in ferroptotic cell death. The mitochondrial redox environment and ferroptosis were modulated by pharmacologic processes that exacerbate or abolish iron accumulation both in wild-type worms and worms with increased levels of neuronal amyloid beta (Aβ). However, neuronal Aβ worms were more sensitive to ferroptosis-mediated neuronal loss, and this increased toxicity was ameliorated by limiting the uptake of ferrous iron through knockout of divalent metal transporter 1 (DMT1). In addition, DMT1 knockout completely suppressed phenotypic measures of Aβ toxicity with age. Overall, our findings suggest that iron-induced ferroptosis alters the mitochondrial redox environment to drive oxidative damage when neuronal Aβ is overexpressed. DMT1 knockout abolishes neuronal Aβ−associated pathologies by reducing neuronal iron uptake.

Highlights

Energetic imbalance is an early event in iron-induced loss of neuronal function

Neuronal Aβ increases susceptibility to ferroptosis mediated oxidative damage

Divalent metal transporter 1 knockout protects against iron-induced oxidative damage and ferroptosis

Graphical Abstract
Efficient and effective identification of cancer neoantigens from tumor only RNA-seq
Authors: Tatoni Danilo , Dalsass Mattia , Brunelli Giulia , Grandi Guido , Chiariello Mario , D’Aurizio Romina
Published: August 2024

The growing accessibility of sequencing experiments has significantly accelerated the development of personalized immunotherapies based on the identification of cancer neoantigens. Still, the prediction of neoantigens involves lengthy and inefficient protocols, requiring simultaneous analysis of sequencing data from paired tumor/normal exomes and tumor transcriptome, often resulting in a low success rate. To date, the feasibility of adopting a more efficient strategy has not been fully evaluated. To this end, we developed ENEO, a computational approach to detect cancer neoantigens using solely the tumor RNA-seq data while addressing the lack of matched control through a Bayesian probabilistic model. ENEO was assessed on TESLA benchmark dataset, reporting efficient identification of DNA-alterations derived neoantigens and compelling results against state-of-art exome-based methods. We further validated the method on two independent cohorts, encompassing different tumor types and experimental procedures. Our work demonstrates that a tumor-only RNA-based approach, such as the one implemented in ENEO, maintains accuracy in identifying mutated peptides resulting from expressed genomic alterations, while also broadening the pool of potential pMHCs with RNAspecific mutations in a faster and cost-effective way. ENEO is freely available athttps://github.com/ctglab/ENEO
Reduced gene dosage of the psychiatric risk geneCacna1cis associated with impairments in hypothalamic-pituitary-adrenal axis activity in rats
Authors: Moon Anna L. , Mawson Elle , Gasalla Canto Patricia , Wilkinson Lawrence , Dwyer Dominic , Thomas Kerrie L. , Hall Jeremy
Published: August 2024

Common and rare variation inCACNA1Cgene expression has been consistently associated with neuropsychiatric disorders such as schizophrenia, bipolar disorder, and major depression, however the underlying biological pathways that cause this association have yet to be fully determined. In this study, we present evidence that rats with a reduced gene dosage ofCacna1chave increased basal corticosterone levels in the periphery and reducedNr3c1gene expression in the hippocampus and hypothalamus. These results are consistent with an effect ofCacna1cdosage on hypothalamus-pituitary-adrenal (HPA) axis function. We also show that the reduction ofNr3c1in the hippocampus may be caused by epigenetic modification of exon 17ofNr3c1, including the reduced interaction with the histone modifying markers H3K4me3 and H3K27ac. HeterozygousCacna1crats additionally show increased anxiety behaviours. These results support an association ofCacna1cheterozygosity with the altered activity of the HPA axis and function in the resting state and this may be a predisposing mechanism that contributes to the increased risk of psychiatric disorders with stress.
Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants
Authors: Komluski Jovan , Filatova Sofia , Schlütz Frank , Claaßen Benjamin , Rösch Manfred , Krause-Kyora Ben , Kirleis Wiebke , Stukenbrock Eva H.
Published: August 2024

In medieval central Europe, rye was one of the most important agricultural crops. It’s properties of frost resistance, general resilience and resistance to many pathogens made it invaluable for medieval farmers. Rye has a distinct domestication history compared to other cereal crops and was not domesticated directly from its wild ancestors, like barley and wheat. Rye is considered to be a “secondary domesticate”, i.e. a crop with domestication traits that initially evolved as an arable weed but eventually was intentionally sown and propagated as a crop. To study the history of rye domestication, genetic sequences of present-day plant populations as well as material from historical samples can provide insights into the temporal and spatial signatures of domestication. In this study we combined archaeobotanical methods and ancient DNA sequencing of well-preserved, historical rye material to study patterns of genetic diversity across four centuries. We first applied archaeobotanical methods to characterize rye material acquired from construction material ranging from the 14thto 18thcentury from different locations in Germany. Next, we extracted DNA to sequence complete chloroplast genomes of six individual samples. We compared the 115,000 bp chloroplast genomes of historical rye samples to chloroplast genomes of other cereal crops and identified 217 single nucleotide variants exclusive to historical samples. By comparing the aDNA chloroplast samples with modern rye chloroplasts, we show that the genetic variation in ancient rye populations was exceptionally high compared to samples from contemporary rye cultivars. This confirms that late domestication and selective breeding have reduced genetic variation in this important crop species only in the last few centuries.

Highlights

Historical plant material covering four centuries was obtained from half-timbered houses from five locations in Germany

Integrative archaeobotanical analyses and ancient DNA sequencing provided insights into genetic diversity of rye plants from historical farmland fields.

Sequence analyses of complete assembled chloroplast genomes reveal expectational diversity in rye populations.

Late domestication of rye preserved genetic diversity over centuries. The more recent intensification of rye breeding has however conferred a considerable loss of genetic diversity in this important crop.
Subcellular context-specific tuning of actomyosin ring contractility within a common cytoplasm
Authors: Linehan John B. , Zampetaki Alexandra , Werner Michael E. , Heck Bryan , Maddox Paul S. , Fürthauer Sebastian , Maddox Amy S.
Published: August 2024

The non-muscle actomyosin cytoskeleton generates contractile force through the dynamic rearrangement of its constituent parts. Actomyosin rings are a specialization of the non-muscle actomyosin cytoskeleton that drive cell shape changes during division, wound healing, and other events. Contractile rings throughout phylogeny and in a range of cellular contexts are built from conserved components including non-muscle myosin II (NMMII), actin filaments (F-actin), and crosslinking proteins. However, it is unknown whether diverse actomyosin rings close via a single unifying mechanism. To explore how contractile forces are generated by actomyosin rings, we studied three instances of ring closure within the common cytoplasm of theC. elegansoogenic germline: mitotic cytokinesis of germline stem cells (GSCs), apoptosis of meiotic compartments, and cellularization of oocytes. We found that each ring type closed with unique kinetics, protein density and abundance dynamics. These measurements suggested that the mechanism of contractile force generation varied across the subcellular contexts. Next, we formulated a physical model that related the forces generated by filament-filament interactions to the material properties of these rings that dictate the kinetics of their closure. Using this framework, we related the density of conserved cytoskeletal proteins anillin and NMMII to the kinematics of ring closure. We fitted model rings to in situ measurements to estimate parameters that are currently experimentally inaccessible, such as the asymmetric distribution of protein along the length of F-actin, which occurs naturally due to differences in the dimensions of the crosslinker and NMMII filaments. Our work predicted that the role of NMMII varies across these ring types, due in part to its distribution along F-actin and motoring. Our model also predicted that the degree of contractility and the impact of ring material properties on contractility differs among ring types.
Local Nearby Bifurcations Lead to Synergies in Critical Slowing Down: the Case of Mushroom Bifurcations
Authors: Fucho-Rius Mariona , Maretvadakethope Smitha , Pérez-Carrasco Rubén , Haro Àlex , Alarcón Tomás , Sardanyés Josep
Published: August 2024

The behavior of nonlinear systems close to critical transitions has relevant implications in assessing complex systems’ stability, transient properties, and resilience. Transient times become extremely long near phase transitions (or bifurcations) in a phenomenon generically known as critical slowing down, observed in electronic circuits, quantum electrodynamics, ferromagnetic materials, ecosystems, and gene regulatory networks. Typically, these transients follow well-defined universal laws of the formτ∼ |µ−µc|β, describing how their duration,τ, varies as the control parameter,µ, approaches its critical value,µc. For instance, transients’ delays right after a saddle-node (SN) bifurcation, influenced by so-called ghosts, followβ= −1/2. Despite intensive research on slowing down phenomena over the past decades for single bifurcations, both local and global, the behavior of transients when several bifurcations are close to each other remains unknown. Here, we study transients close to two SN bifurcations collapsing into a transcritical one. To do so, we analyze a simple nonlinear model of a self-activating gene regulated by an external signal that exhibits a mushroom bifurcation. We also propose and study a normal form for a system with two SN bifurcations merging into a transcritical one. For both systems, we show analytical and numerical evidence of a synergistic increase in transients due to the coupling of the two ghosts and the transcritical slowing down. We also explore the influence of noise on the transients in the gene-regulatory model. We show that intrinsic and extrinsic noise play opposite roles in the slowing down of the transition allowing us to control the timing of the transition without compromising the precision of the timing. This establishes novel molecular strategies to generate genetic timers with transients much larger than the typical timescales of the reactions involved.