bluuebunny/crossref_metadata_2025 huggingface dataset:
Cytoplasmic Cyclin E Expression Predicts for Response to Neoadjuvant Chemotherapy in Breast Cancer
Authors: Karakas Cansu , Francis Ashleigh M. , Ha Min Jin , Wingate Hannah F. , Meena Richard A. , Yi Min , Rasaputra Komal S. , Barrera Angelica M. Gutierrez , Arun Banu , Do Kim-Anh , Sahin Aysegul , Keyomarsi Khandan , Hunt Kelly K.
Published: August 2019

Background:

Pathologic complete response (pCR) has been shown to be associated with favorable outcomes in breast cancer. Predictors of pCR could be useful in guiding treatment decisions regarding neoadjuvant therapy. The objective of this study was to evaluate cyclin E as a predictor of response to neoadjuvant chemotherapy in breast cancer.

Methods:

Patients (n = 285) with stage II–III breast cancer were enrolled in a prospective study and received neoadjuvant chemotherapy with anthracyclines, taxanes, or combination of the two. Pretreatment biopsies from 190 patients and surgical specimens following chemotherapy from 192 patients were available for immunohistochemical analysis. Clinical and pathologic responses were recorded and associated with presence of tumor infiltrating lymphocytes, cyclin E, adipophilin, programmed cell death-ligand 1, and elastase staining and other patient, tumor and treatment characteristics.

Results:

The pCR rate was significantly lower in patients with cytoplasmic cyclin E staining compared with those who had no cyclin E expression (16.1% vs 38.9%, P = 0.0005). In multivariable logistic regression analysis, the odds of pCR for patients who had cytoplasmic negative tumors was 9.35 times (P value < 0.0001) that compared with patients with cytoplasmic positive tumors after adjusting for ER, PR, and HER2 status. Cytoplasmic cyclin E expression also predicts long-term outcome and is associated with reduced disease free, recurrence free, and overall survival rates, independent of increased pretreatment tumor infiltrating lymphocytes.

Conclusions:

Cyclin E independently predicted response to neoadjuvant chemotherapy. Hence, its routine immunohistochemical analysis could be used clinically to identify those breast cancer patients expected to have a poor response to anthracycline/taxane-based chemotherapy.
Laparoscopic to Open Cholecystectomy: The Risk Factors and the Reasons; A Retrospective Analysis of 1950 Cases of a Single Tertiary Center
Authors: Kara Yasin , Kalayci Mustafa U.
Published: August 2019

Purpose:

We investigated the reasons, rates, and risk factors for the conversion to open cholecystectomies (CTOC) by statistical analysis with the demographic properties.

Materials and Methods:

Demographic properties (age and sex), abdominal operations, and intraoperative and postoperative reasons for cholecystectomies were analyzed in 1950 patients.

Results:

The patients included 1540 (79%) women and 410 (21%) men (F/M=3.8); of these 115 (5.9%) had CTOC in early or late period. The rate of CTOC in men was significantly high (P= 0.009). There was no mortality. The reasons for CTOC were: significant inflammation (n=53, 46%), inadequate dissection of Calot triangle due to fibrotic adhesions (n=31, 27%), adhesions of previous surgery (n=9, 7.8%), uncontrollable bleeding (n=5, 4.3%), technical insufficiency (n=5, 4.3%), bile duct injury (n=5, 4.3%), anatomical variations (n=3, 2.6%), iatrogenic visceral injury (n=2, 1.7%), isolated right posterior bile duct injury (strasberg type-C) (n=1, 0.9%), and common hepatic duct partial injury (n=1, 0.9%).

Conclusions:

Significant inflammation, inadequate dissection of Calot triangle due to fibrotic adhesions, and adhesions due to previous surgery were the 3 main reasons for conversion. Men and elderly patients were associated with significantly high rate of conversion.
The impact of reactive mass vaccination campaigns on measles outbreaks in the Katanga region, Democratic Republic of Congo
Authors: Funk Sebastian , Takahashi Saki , Hellewell Joel , Gadroen Kartini , Carrion-Martin Isidro , van Lenthe Marit , Rivette Katiana , Dietrich Sebastian , Edmunds W. John , Siddiqui Ruby , Rao V. Bhargavi
Published: August 2019

The Katanga region in the Democratic Republic of Congo (DRC) has been struck by repeated epidemics of measles, with large outbreaks occurring in 2010–13 and 2015. In many of the affected health zones, reactive mass vaccination campaigns were conducted in response to the outbreaks. Here, we attempted to determine how effective the vaccination campaigns in 2015 were in curtailing the ongoing outbreak. We further sought to establish whether the risk of large measles outbreaks in different health zones could have been determined in advance to help prioritise areas for vaccination campaign and speed up the response. In doing so, we first attempted to identify factors that could have been used in 2015 to predict in which health zones the greatest outbreaks would occur. Administrative vaccination coverage was not a good predictor of the size of outbreaks in different health zones. Vaccination coverage derived from surveys, on the other hand, appeared to give more reliable estimates of health zones of low vaccination coverage and, consequently, large outbreaks. On a coarser geographical scale, the provinces most affected in 2015 could be predicted from the outbreak sizes in 2010–13. This, combined with the fact that the vast majority of reported cases were in under-5 year olds, would suggest that there are systematic issues of undervaccination. If this was to continue, outbreaks would be expected to continue to occur in the affected health zones at regular intervals, mostly concentrated in under-5 year olds. We further used a model of measles transmission to estimate the impact of the vaccination campaigns, by first fitting a model to the data including the campaigns and then re-running this without vaccination. We estimated the reactive campaigns to have reduced the size of the overall outbreak by approximately 21,000 (IQR: 16,000–27,000; 95% CI: 8300–38,000) cases. There was considerable heterogeneity in the impact of campaigns, with campaigns started earlier after the start of an outbreak being more impactful. Taken together, these findings suggest that while a strong routine vaccination regime remains the most effective means of measles control, it might be possible to improve the effectiveness of reactive campaigns by considering predictive factors to trigger a more targeted vaccination response.
Evaluation of a rapid lateral flow calprotectin test for the diagnosis of prosthetic joint infection
Authors: Trotter Alexander J. , Dean Rachael , Whitehouse Celia E. , Mikalsen Jarle , Hill Claire , Brunton-Sim Roxanne , Kay Gemma L. , Shakokhani Majeed , Durst Alexander , Wain John , McNamara Iain , O’Grady Justin
Published: August 2019

Background

Microbiological diagnosis of prosthetic joint infection (PJI) relies on culture techniques that are slow and insensitive. Rapid tests are urgently required to improve patient management. Calprotectin is a neutrophil biomarker of inflammation that has been demonstrated to be effective for the diagnosis of PJI. A calprotectin based lateral flow test has been developed for the rapid detection of PJI using synovial fluid samples.

Methods

A convenience series of 69 synovial fluid samples from patients at the Norfolk and Norwich University Hospitals (NNUH) were collected intraoperatively from 52 hip and 17 knee revision operations. Calprotectin levels were measured using a new commercially available lateral flow assay for PJI diagnosis (Lyfstone). For all samples, synovial fluid was pipetted onto the lateral flow device and the signal was read using a mobile phone app after 15 minutes incubation at room temperature.

Results

According to the Musculoskeletal Infection Society (MSIS) criteria, 24 patients were defined as PJI positive and the remaining 45 were negative. The overall accuracy of the lateral flow test against the MSIS criteria was 75%. The test had a sensitivity and specificity of 75% and 76% respectively with a positive predictive value (PPV) of 62% and a negative predictive value (NPV) of 85%. Discordant results were then reviewed by the clinical team using available patient data to develop an alternative gold standard for defining presence/absence of infection (MSIS+). Compared to MSIS+, the test showed an overall accuracy of 83%, sensitivity and specificity of 95% and 78% respectively, a PPV of 62% and an NPV of 98%. Test accuracy for hip revisions was 77% and for knee revisions was 100%.

Conclusions

This study demonstrates that the calprotectin lateral flow assay is an effective diagnostic test for PJI. Our data suggests that the test is likely to generate false positive results in patients with metallosis and gross osteolysis.
Challenges in Building and Maintaining Rare Disease Patient Registries: Results of a Questionnaire Survey in Japan at 2012
Authors: Morita Mizuki , Ogishima Soichi
Published: August 2019

Background

Research infrastructure such as patient registries and biobanks is expected to play important roles by aggregating information and biospecimens to promote research and development for rare diseases. However, both building and maintaining them can be costly. This paper presents results of a survey of patient registries for rare diseases in Japan conducted at the end of 2012, with emphasis on clarifying costs and efforts related to building and maintaining them.

Results

Of 31 patient registries in Japan found by searching a database of research grant reports and by searching the internet, 11 returned valid responses to this survey. Results show that labor and IT system costs are major expenses for developing and maintaining patient registries. Half of the respondent patient registries had no prospect of securing a budget to maintain them. Responders required the following support for patient registries: financial support, motivation of registrants (medical doctors or patients), and improved communication with and visibility to potential data users. These results resemble those reported from another survey conducted almost simultaneously in Europe (EPIRARE survey).

Conclusions

Survey results imply that costs and efforts to build and maintain patient registries for many rare diseases make them unrealistic. Some alternative strategy is necessary to reduce burdens, such as offering a platform that supplies IT infrastructure and basic secretariat functions that can be used commonly among many patient registries.
Multidrug therapy with terbinafine plus daily fluconazole is more effective than terbinafine alone or terbinafine plus weekly fluconazole in current epidemic of altered dermatophytosis in India: Results of a randomized pragmatic trial
Authors: Singh Sanjay , Jha Bandana , Shukla Prakriti , Anchan Vinayak N
Published: August 2019

Background

Treatment responsiveness of tinea has decreased considerably in recent past in India. We tested effectiveness of oral terbinafine daily plus fluconazole weekly (TFw) and terbinafine daily plus fluconazole daily (TFd) versus oral terbinafine daily (T) in tinea corporis, tinea cruris and tinea faciei in a pragmatic randomized open trial.

Methods

One hundred and seventeen microscopy confirmed patients were allocated to T (6 mg/kg/day), TFw (terbinafine 6 mg/kg/day+fluconazole 12 mg/kg once weekly), or TFd (terbinafine 6 mg/kg/day+fluconazole 6 mg/kg/day) groups by concealed randomization and treated for 8 weeks or cure. Each group included 39 patients.

Results

At 4 weeks, 9 (23.1%), 8 (20.5%) and 14 (35.9%) patients were cured in T, TFw and TFd groups, respectively (P=0.279). At 8 weeks, number of patients cured was as follows: T 13 (33.3%), TFw 18 (46.2%) and TFd 25 (64.1%). TFd was more effective than T (P=0.012), other comparisons were not significantly different. However, effect size as calculated by number needed to treat (NNT) (versus terbinafine) was 8 for TFw and 4 for TFd. Relapse rates one month after cure were similar in all groups (P=0.664).

Conclusions

In view of cure rates and NNT, terbinafine plus daily fluconazole is more effective than terbinafine alone or terbinafine plus weekly fluconazole in current epidemic of altered dermatophytosis in India.

One Sentence Summary

Terbinafine plus daily fluconazole is more effective than terbinafine alone or terbinafine plus weekly fluconazole in current epidemic of altered dermatophytosis in India.
Characterization of the gut microbiota in the Anjak (Schizocypris altidorsalis), a native fish species of Iran
Authors: Ghanbari Mahdi , Jami Mansooreh , Shahraki Hadi , Domig Konrad J.
Published: August 2019

The antiquity, diversity and dietary variations among fish species present an exceptional opportunity for understanding the variety and nature of symbioses in vertebrate gut microbial communities. In this study for the first time the composition of the gut bacterial communities in the anjak was surveyed by 16S rRNA gene 454-pyrosequencing. Anjak (Schizocypris altidorsalis), is a native benthopelagic and commercially important fish species in Hamun Lake and Hirmand River system in Sistan basin, Iran. Thirteen 16S rRNA PCR libraries were generated, representing 13 samples of Anjak gut microbiota. After quality filtering, a total of 137 978 read pairs remained from the V3–V6 16S rRNA gene regions, each measuring 680 bp, and were assigned to bacterial OTU’s at a minimum sequence homology of 97%, resulted in total 608 OTUs. The results provided evidence of the presence of a very diverse microbial community present in this fish. The majority of sequences belonged to members of the Firmicutes; however, members of the Proteobacteria, Tenericutes, Bacteroidetes and Cyanobacteria were also well represented in the anjak gut microbiota. The most abundant classes recorded in the samples were uncultured CK-1C4-19 class of Tenericutes, Flavobacteriia, α-Proteobacteria, Erysipelotrichi, Synechococcophycideae, γ-Proteobacteria, and Clostridia. The presence of many different types of bacteria in the anjak is not unexpected since it has been shown that eukaryotes with a detritivorous and planktivorous diet have a higher microbial diversity compared to omnivorous and herbivorous fish species. Many of these microbes might be of high physiological relevance for snow trout and may play key roles in the functioning of a healthy gut in this fish.
Exploring the microbial diversity in oil-contaminated mangrove sediments using 16S rRNA metagenomics
Authors: Ghanbari Mahdi , Jami Mansooreh , Moghadam Mohsen Shahriari , Domig Konrad J.
Published: August 2019

With an area of 390 hectares, the mangrove forests of Nayband Bay are the widest mangrove communities above 27 degrees latitude in the Persian Gulf. They are the last dense, extensive structures of these ecosystems found in the north-west Indian Ocean. Growing industrial activities near the Nayband Bay and the consequent marine pollution has resulted in damage and threatened different marine habitats in recent years. To date, a comprehensive description of the microbial life in the mangrove ecosystem that has been exposed to oil contamination is lacking. This information could significantly contribute to a better overview of the function and resilience of the ecosystem. This work represents a first effort to better understand the Nayband Bay mangrove microbiology by applying 16S rRNA metagenomics. A total of 65,408 readings from the V3–V4 16S rRNA gene regions were obtained from 24 sediment samples, each measuring 440 bp. Most sequences belonged to members of the Proteobacteria phylum (mainly γ-Proteobacteria); however, members of the Bacteroidetes phylum (mainly Flavobacteriia) were also well represented in the samples. We discovered that the community of this ecosystem strongly exhibit typical structures of oil-contaminated marine environments. This is likely due to the growing industrial activity in the area and its consequent marine polluting effects. The use of practicable and applicable bioremediation protocols for habitat restoration in this valuable area is needed.
Does meiotic drive alter male mate preference?
Authors: Finnegan Sam Ronan , Nitsche Leslie , Mondani Matteo , Camus M. Florencia , Fowler Kevin , Pomiankowski Andrew
Published: August 2019

Male mate preferences have been demonstrated across a range of species, including the Malaysian stalk-eyed fly,Teleopsis dalmanni. This species is subject to SR, an X-linked male meiotic driver, that causes the dysfunction of Y-sperm and the production all female broods. SR is associated with a low frequency inversion spanning most of the X chromosome that causes reduced organismal fitness. While there has been work considering female avoidance of meiotic drive males, the mating decisions of drive-bearing males have not been considered previously. As drive males are of lower genetic quality they may be less able to bear the cost of choice or may experience weaker selection for its maintenance if they are avoided by females. We investigated preference of drive males using binary choice trials. We confirmed that males prefer to mate with large females (indicative of greater fecundity) but found no evidence that the strength of male mate preference differs between drive and standard males. This suggests that the cost of choice does not restrict male reference among drive males. In a further experiment, we found that large eyespan males showed strong preference whereas small eyespan males showed no preference. This is likely to weaken mate preference in drive males, as on average they have reduced eyespan compared to standard males. In this respect, drive males are subject to and exert weak sexual selection.

Lay summary

We studied male mate preference in stalk-eyed flies. This species suffers from meiotic drive, a selfish genetic element that causes a reduction in sperm production and organismal fitness. We predicted that males with meiotic drive would show weak mate preference. Males preferred to mate with large females, but there was no difference in the strength of preference between drive and non-drive males. Males with larger eyespan showed stronger mate preference. Meiotic drive males usually have reduced eyespan so on average they exert weaker sexual selection on females, but this is mediated by eyespan, not genotypeper se.
Base-resolution models of transcription factor binding reveal soft motif syntax
Authors: Avsec Žiga , Weilert Melanie , Shrikumar Avanti , Krueger Sabrina , Alexandari Amr , Dalal Khyati , Fropf Robin , McAnany Charles , Gagneur Julien , Kundaje Anshul , Zeitlinger Julia
Published: August 2019

The arrangement of transcription factor (TF) binding motifs (syntax) is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution ChIP-nexus binding profiles of pluripotency TFs. We develop interpretation tools to learn predictive motif representations and identify soft syntax rules for cooperative TF binding interactions. Strikingly, Nanog preferentially binds with helical periodicity, and TFs often cooperate in a directional manner, which we validate using CRISPR-induced point mutations. Our model represents a powerful general approach to uncover the motifs and syntax of cis-regulatory sequences in genomics data.

Highlights

The neural network BPNet accurately predicts TF binding data at base-resolution.

Model interpretation discovers TF motifs and TF interactions dependent on soft syntax.

Motifs for Nanog and partners are preferentially spaced at ∼10.5 bp periodicity.

Directional cooperativity is validated: Sox2 enhances Nanog binding, but not vice versa.
Ancestral hybridisation facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation
Authors: Svardal Hannes , Quah Fu Xiang , Malinsky Milan , Ngatunga Benjamin P , Miska Eric A , Salzburger Walter , Genner Martin J , Turner George F , Durbin Richard
Published: August 2019

The adaptive radiation of cichlid fishes in East Afrian Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800 thousand years from a common founder population. It has been proposed that hybridisation between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria Region cichlid superflock. Here we report that Lake Malawi cichlid genomes also show evidence of hybridisation between two lineages that split 3-4 million years ago, today represented by Lake Victoria cichlids and the riverine Astatotilapia sp. ‘ruaha blue’. The two ancestries in Malawi cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridisation are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridisation in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.
Pod and seed trait QTL identification to assist breeding for peanut market preferences
Authors: Chavarro Carolina , Chu Ye , Holbrook Corley , Isleib Thomas , Bertioli David , Hovav Ran , Butts Christopher , Lamb Marshall , Sorensen Ronald , Jackson Scott A. , Ozias-Akins Peggy
Published: August 2019

Although seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explorethe distribution of recombination and potential chromosomal rearrangements. These traits were phenotyped over three consecutive years for the purpose of developing trait-associated markers for breeding. Forty-nine QTL were identified in 14 LG for seed size index, kernel percentage, seed weight, pod weight, single-kernel, double-kernel, pod area and pod density. Twenty QTL demonstrated phenotypic variance explained (PVE) greater than 10% and eight more than 20%. Of note, seven of the eight major QTL for pod area, pod weight and seed weight (PVE >20% variance) were attributed to NC 3033 and located in a single linkage group, LG B06_1. In contrast, the most consistent QTL for kernel percentage were located on A07/B07 and derived from Tifrunner.
Heart Rate n-Variability (HRnV) and Its Application to Risk Stratification of Chest Pain Patients in the Emergency Department
Authors: Liu Nan , Guo Dagang , Koh Zhi Xiong , Ho Andrew Fu Wah , Xie Feng , Tagami Takashi , Sakamoto Jeffrey Tadashi , Pek Pin Pin , Chakraborty Bibhas , Lim Swee Han , Tan Jack Wei Chieh , Ong Marcus Eng Hock
Published: August 2019

Background

Chest pain is one of the most common complaints among patients presenting to the emergency department (ED). Causes of chest pain can be benign or life threatening, making accurate risk stratification a critical issue in the ED. In addition to the use of established clinical scores, prior studies have attempted to create predictive models with heart rate variability (HRV). In this study, we proposed heart rate n-variability (HRnV), an alternative representation of beat-to-beat variation in electrocardiogram (ECG) and investigated its association with major adverse cardiac events (MACE) for ED patients with chest pain.

Methods

We conducted a retrospective analysis of data collected from the ED of a tertiary hospital in Singapore between September 2010 and July 2015. Patients >20 years old who presented to the ED with chief complaint of chest pain were conveniently recruited. Five to six-minute single-lead ECGs, demographics, medical history, troponin, and other required variables were collected. We developed the HRnV-Calc software to calculate HRnV parameters. The primary outcome was 30-day MACE, which included all-cause death, acute myocardial infarction, and revascularization. Univariable and multivariable logistic regression analyses were conducted to investigate the association between individual risk factors and the outcome. Receiver operating characteristic (ROC) analysis was performed to compare the HRnV model (based on leave-one-out cross-validation) against other clinical scores in predicting 30-day MACE.

Results

A total of 795 patients were included in the analysis, of which 247 (31%) had MACE within 30 days. The MACE group was older and had a higher proportion of male patients. Twenty-one conventional HRV and 115 HRnV parameters were calculated. In univariable analysis, eleven HRV parameters and 48 HRnV parameters were significantly associated with 30-day MACE. The multivariable stepwise logistic regression identified 16 predictors that were strongly associated with the MACE outcome; these predictors consisted of one HRV, seven HRnV parameters, troponin, ST segment changes, and several other factors. The HRnV model outperformed several clinical scores in the ROC analysis.

Conclusions

The novel HRnV representation demonstrated its value of augmenting HRV and traditional risk factors in designing a robust risk stratification tool for patients with chest pain at the ED.
Two forms of Opa1 cooperate to complete fusion of the mitochondrial inner-membrane
Authors: Ge Yifan , Shi Xiaojun , Boopathy Sivakumar , McDonald Julie , Smith Adam W. , Chao Luke H.
Published: August 2019

Mitochondrial membrane dynamics is a cellular rheostat that relates metabolic function and organelle morphology. Using an in vitro reconstitution system, we describe a mechanism for how mitochondrial inner-membrane fusion is regulated by the ratio of two forms of Opa1. We found that the long-form of Opa1 (l-Opa1) is sufficient for membrane docking, hemifusion and low levels of content release. However, stoichiometric levels of the processed, short form of Opa1 (s-Opa1) work together with l-Opa1 to mediate efficient and fast membrane pore opening. Additionally, we found that excess levels of s-Opa1 inhibit fusion activity, as seen under conditions of altered proteostasis. These observations describe a mechanism for gating membrane fusion.
Mitochondrial protein interaction landscape of SS-31
Authors: Chavez Juan D. , Tang Xiaoting , Campbell Matthew D. , Reyes Gustavo , Kramer Philip A. , Stuppard Rudy , Keller Andrew , Marcinek David J. , Bruce James E.
Published: August 2019

Mitochondrial dysfunction underlies the etiology of a broad spectrum of diseases including heart disease, cancer, neurodegenerative diseases, and the general aging process. Therapeutics that restore healthy mitochondrial function hold promise for treatment of these conditions. The synthetic tetrapeptide, elamipretide (SS-31), improves mitochondrial function, but mechanistic details of its pharmacological effects are unknown. Reportedly, SS-31 primarily interacts with the phospholipid cardiolipin in the inner mitochondrial membrane. Here we utilize chemical cross-linking with mass spectrometry to identify protein interactors of SS-31 in mitochondria. The SS-31-interacting proteins, all known cardiolipin binders, fall into two groups, those involved in ATP production through the oxidative phosphorylation pathway and those involved in 2-oxoglutarate metabolic processes. Residues cross-linked with SS-31 reveal binding regions that in many cases, are proximal to cardiolipin-protein interacting regions. These results offer the first glimpse of the protein interaction landscape of SS-31 and provide new mechanistic insight relevant to SS-31 mitochondrial therapy.

Significance Statement

SS-31 is a synthetic peptide that improves mitochondrial function and is currently undergoing clinical trials for treatments of heart failure, primary mitochondrial myopathy, and other mitochondrial diseases. SS-31 interacts with cardiolipin which is abundant in the inner mitochondrial membrane, but mechanistic details of its pharmacological effects are unknown. Here we apply a novel chemical cross-linking/mass spectrometry method to provide the first direct evidence for specific interactions between SS-31 and mitochondrial proteins. The identified SS-31 interactors are functional components in ATP production and 2-oxoglutarate metabolism and signaling, consistent with improved mitochondrial function resultant from SS-31 treatment. These results offer the first glimpse of the protein interaction landscape of SS-31 and provide new mechanistic insight relevant to SS-31 mitochondrial therapy.
Sirolimus plus nintedanib treats vascular pathology in HHT mouse models
Authors: Ruiz Santiago , Zhao Haitian , Chandakkar Pallavi , Papoin Julien , Choi Hyunwoo , Nomura-Kitabayashi Aya , Patel Radhika , Gillen Matthew , Diao Li , Chatterjee Prodyot K. , He Mingzhu , Al-Abed Yousef , Wang Ping , Metz Christine N. , Oh S. Paul , Blanc Lionel , Campagne Fabien , Marambaud Philippe
Published: August 2019

Hereditary hemorrhagic telangiectasia (HHT), a genetic bleeding disorder leading to systemic arteriovenous malformations (AVMs), is caused by loss-of-function mutations in the ALK1-ENG-Smad1/5/8 pathway. Evidence suggests that HHT pathogenesis strongly relies on overactivated PI3K-Akt-mTOR and VEGFR2 pathways in endothelial cells (ECs). In the BMP9/10-immunoblocked (BMP9/10ib) neonatal mouse model of HHT, we report here that the mTOR inhibitor, sirolimus, and the receptor tyrosine-kinase inhibitor, nintedanib, could synergistically fully block, but also reversed, retinal AVMs to avert retinal bleeding and anemia. Sirolimus plus nintedanib prevented vascular pathology in the oral mucosa, lungs, and liver of the BMP9/10ib mice, as well as significantly reduced gastrointestinal bleeding and anemia in inducible ALK1-deficient adult mice. Mechanistically, in vivo in BMP9/10ib mouse ECs, sirolimus and nintedanib blocked the overactivation of mTOR and VEGFR2, respectively. Furthermore, we found that sirolimus activated ALK2-mediated Smad1/5/8 signaling in primary ECs—including in HHT patient blood outgrowth ECs—and partially rescued Smad1/5/8 activity in vivo in BMP9/10ib mouse ECs. These data demonstrate that the combined correction of endothelial Smad1/5/8, mTOR, and VEGFR2 pathways opposes HHT pathogenesis. Repurposing of sirolimus plus nintedanib might provide therapeutic benefit in HHT patients.
Leptin promotes expression of EMT-related transcription factors and invasion in a Src and FAK-dependent pathway in MCF10A mammary epithelial cells
Authors: Olea-Flores Monserrat , Zuñiga-Eulogio Miriam , Tacuba-Saavedra Arvey , Bueno-Salgado Magdalena , Sánchez-Carvajal Andrea , Vargas-Santiago Yovani , Mendoza-Catalán Miguel A. , Salazar Eduardo Pérez , García-Hernández Alejandra , Padilla-Benavides Teresita , Navarro-Tito Napoleón
Published: August 2019

Leptin is one of the main adipokines secreted in breast tissue, and has been associated with epithelial-mesenchymal transition (EMT) and tumor progression in breast cancer. Leptin promotes EMT, cell migration and invasion in epithelial breast cells, leading to tumor progression. However, the molecular mechanism that underlies these events is not fully understood; however, the activation of different signaling pathways appears to be essential. In this sense, the effect of leptin on the activation of kinases like Src and FAK, which regulate signaling pathways that activate the EMT program, has not been completely described. Therefore, we investigated the involvement of these kinases using anin vitromodel for leptin-induced EMT process in the non-tumorigenic MCF10A cell line. To this end, MCF10A cells were stimulated with leptin, and Src and FAK activation was assessed. Specific events occurring during EMT were also evaluated in the presence or absence of the kinases’s chemical inhibitors PP2 and PF-573228. For instance, we tested the expression and subcellular localization of the EMT-related transcription factors Twist and □-catenin, by western blot and immunofluorescence. We also evaluated the secretion and activation of matrix metalloproteases (MMP-2 and MMP-9) by gelatin zymography. Invasiveness properties of leptin-stimulated cells were determined by invadopodia formation assays, and by the transwell chamber method. Our results showed that leptin promotes EMT through Src and FAK activation, which leads to the secretion and activation of MMP-2 and MMP-9, invadopodia formation and cell invasion in MCF10A cells. In conclusion, our data suggest that leptin promotes an increase in the expression levels of Twist and □-catenin, the secretion of MMP-2, MMP-9, the invadopodia formation and invasion in MCF10A cells in a Src and FAK-dependent manner.
Optogenetic control of protein binding using light-switchable nanobodies
Authors: Gil Agnieszka A. , Zhao Evan M. , Wilson Maxwell Z. , Goglia Alexander G. , Carrasco-Lopez Cesar , Avalos José L. , Toettcher Jared E.
Published: August 2019

A growing number of optogenetic tools have been developed to control binding between two engineered protein domains. In contrast, relatively few tools confer light-switchable binding to a generic target protein of interest. Such a capability would offer substantial advantages, enabling photoswitchable binding to endogenous target proteins in vivo or light-based protein purification in vitro. Here, we report the development of opto-nanobodies (OptoNBs), a versatile class of chimeric photoswitchable proteins whose binding to proteins of interest can be enhanced or inhibited upon blue light illumination. We find that OptoNBs are suitable for a range of applications: modulating intracellular protein localization and signaling pathway activity and controlling target protein binding to surfaces and in protein separation columns. This work represents a first step towards programmable photoswitchable regulation of untagged, endogenous target proteins.

Highlights

Opto-Nanobodies (OptoNBs) enable light-regulated binding to a wide range of protein targets.

We identify an optimized LOV domain and two loop insertion sites for light-regulated binding.

OptoNBs function in vivo: when expressed in cells and fused to signaling domains, OptoNBs enable light-activated and light-inhibited Ras/Erk signaling.

OptoNBs function in vitro: Target proteins can be reversibly bound to OptoNB-coated beads and separated through size-exclusion chromatography.
Prolonged tonic pain in healthy humans disrupts intrinsic brain networks implicated in pain modulation
Authors: Meeker Timothy J. , Schmid Anne-Christine , Keaser Michael L. , Khan Shariq A. , Gullapalli Rao P. , Dorsey Susan G. , Greenspan Joel D. , Seminowicz David A.
Published: August 2019

Neural mechanisms of ongoing nociceptive processing in the human brain remain largely obscured by the dual challenge of accessing neural dynamics and safely applying sustained painful stimuli. Recently, pain-related neural processing has been measured using fMRI resting state functional connectivity (FC) in chronic pain patients. However, ongoing pain-related processing in normally pain-free humans remains incompletely understood. Therefore, differences between chronic pain patients and controls may be due to comorbidities with chronic pain. Decreased FC among regions of the descending pain modulation network (DPMN) are associated with presence and severity of chronic pain disorders. We aimed to determine if the presence of prolonged tonic pain would lead to disruption of the DPMN. High (10%) concentration topical capsaicin was combined with a warm thermode applied to the leg to create a flexible, prolonged tonic pain model to study the FC of brain networks in otherwise healthy, pain-free subjects in two separate cohorts (n=18; n=32). We contrasted seed-based FC during prolonged tonic pain with a pain-free passive task. In seed-based FC analysis prolonged tonic pain led to enhanced FC between the anterior middle cingulate cortex (aMCC) and the somatosensory leg representation. Additionally, FC was enhanced between the pregenual anterior cingulate cortex (pACC), right mediodorsal thalamus and the posterior parietal cortex bilaterally. Further, in the seed-driven PAG network, positive FC with the left DLPFC became negative FC during prolonged tonic pain. These data suggest that some altered DPMN FC findings in chronic pain could partially be explained by the presence of ongoing pain.
Modeling vaccine-induced immunotherapy: treatment scheduling and robustness with virtual mice cohorts
Authors: Bhatt Priya , Kambara Manoj , Pilon-Thomas Shari , Rejniak Katarzyna A. , Chamseddine Ibrahim M.
Published: August 2019

Therapeutic vaccines are used to boost patients’ immune system activity by imposing signals that increase T cell proliferation or infiltration. A large population of cytotoxic T cells may then be able to reduce tumor growth. We developed here a mathematical model of vaccine-induced immunotherapy and used it to test the vaccine frequency and doses that can reduce tumor burden. Since tumors are heterogeneous, we examined if the proposed treatments are robust; i.e, are successful for a wide range of tumors. This was assessed by constructing virtual mice cohorts. Together, the optimal and most robust treatment protocol was determined through mathematical modeling.
Optimising network modelling methods for fMRI
Authors: Pervaiz Usama , Vidaurre Diego , Woolrich Mark W. , Smith Stephen M.
Published: August 2019

A major goal of neuroimaging studies is to develop predictive models to analyse the relationship between whole brain functional connectivity patterns and behavioural traits. However, there is no single widely-accepted standard pipeline for analyzing functional connectivity. The common procedure for designing functional connectivity based predictive models entails three main steps: parcellating the brain, estimating the interaction between defined parcels, and lastly, using these integrated associations between brain parcels as features fed to a classifier for predicting non-imaging variables e.g., behavioural traits, demographics, emotional measures, etc. There are also additional considerations when using correlation-based measures of functional connectivity, resulting in three supplementary steps: utilising Riemannian geometry tangent space parameterization to preserve the geometry of functional connectivity; penalizing the connectivity estimates with shrinkage approaches to handle challenges related to short time-series (and noisy) data; and removing confounding variables from brain-behaviour data. These six steps are contingent on each-other, and to optimise a general framework one should ideally examine these various methods simultaneously. In this paper, we investigated strengths and short-comings, both independently and jointly, of the following measures: parcellation techniques of four kinds (categorized further depending upon number of parcels), five measures of functional connectivity, the decision of staying in the ambient space of connectivity matrices or in tangent space, the choice of applying shrinkage estimators, six alternative techniques for handling confounds and finally four novel classifiers/predictors. For performance evaluation, we have selected two of the largest datasets, UK Biobank and the Human Connectome Project resting state fMRI data, and have run more than 9000 different pipeline variants on a total of ∼14000 individuals to determine the optimum pipeline. For independent performance validation, we have run some best-performing pipeline variants on ABIDE and ACPI datasets (∼1000 subjects) to evaluate the generalisability of proposed network modelling methods.
Evolution of Ty1 copy number control in yeast by horizontal transfer of agaggene
Authors: Czaja Wioletta , Bensasson Douda , Ahn Hyo Won , Garfinkel David J. , Bergman Casey M.
Published: August 2019

Insertion of mobile DNA sequences typically has deleterious effects on host fitness, and thus diverse mechanisms have evolved to control mobile element proliferation across the tree of life. Mobility of the Ty1 retrotransposon inSaccharomycesyeasts is regulated by a novel form of copy number control (CNC) mediated by a self-encoded restriction factor derived from the Ty1gagcapsid gene that inhibits virus-like particle function. Here, we survey a panel of wild and human-associated strains ofS. cerevisiaeandS. paradoxusto investigate how genomic Ty1 content influences variation in Ty1 mobility. We observe high levels of mobility for a canonical Ty1 tester element in permissive strains that either lack full-length Ty1 elements or only contain full-length copies of the Ty1’ subfamily that have a divergentgagsequence. In contrast, low levels of canonical Ty1 mobility are observed in restrictive strains carrying full-length Ty1 elements containing canonicalgag. Phylogenomic analysis of full-length Ty1 elements revealed that Ty1’ is the ancestral subfamily present in wild strains ofS. cerevisiae, and that canonical Ty1 inS. cerevisiaeis a derived subfamily that acquiredgagfromS. paradoxusby horizontal transfer and recombination. Our results provide evidence that variation in the ability ofS. cerevisiaeandS. paradoxusstrains to repress canonical Ty1 transpositionviaCNC is encoded by the genomic content of different Ty1 subfamilies, and that self-encoded forms of transposon control can spread across species boundaries by horizontal transfer.
Genome sequencing of the nine-spined stickleback (Pungitius pungitius) provides insights into chromosome evolution
Authors: Varadharajan Srinidhi , Rastas Pasi , Löytynoja Ari , Matschiner Michael , Calboli Federico C. F. , Guo Baocheng , Nederbragt Alexander J. , Jakobsen Kjetill S. , Merilä Juha
Published: August 2019

The Gasterostidae fish family hosts several species that are important models for eco-evolutionary, genetic and genomic research. In particular, a wealth of genetic and genomic data have been generated for the three-spined stickleback (Gasterosteus aculeatus), the ‘ecology’s supermodel’, while the genomic resources for the nine-spined stickleback(Pungitius pungitius)have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly ofP. pungitiusconsisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and ca. 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromeric-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years (MYA) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 MYA. Compared to the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
GapMind: Automated annotation of amino acid biosynthesis
Authors: Price Morgan , Deutschbauer Adam M. , Arkin Adam P.
Published: August 2019

GapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl/gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 seconds. To avoid error-prone “transitive” annotations, GapMind relies primarily on a database of experimentally-characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for “best hit” approaches. To improve GapMind’s coverage, we examined genetic data from 35 bacteria that grow in minimal media and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates inBacteroides thetaiotaomicronand we propose thatDyella japonicasynthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. If a potential gap in the genome of interest is also a gap in a related microbe that can grow in minimal media, GapMind marks the gap as “known.”
A Toxic RNA Catalyzes the Cellular Synthesis of Its Own Inhibitor, Shunting It to Endogenous Decay Pathways
Authors: Benhamou Raphael I. , Angelbello Alicia J. , Wang Eric T. , Disney Matthew D.
Published: August 2019

Myotonic dystrophy type 2 (DM2) is a genetically defined muscular dystrophy caused by a toxic expanded repeat of r(CCUG) [heretofore (CCUG)exp], harbored in intron 1 of CHC-Type Zinc Finger Nucleic Acid Binding Protein (CNBP) pre-mRNA. This r(CCUG)exp causes DM2 via a gain-of-function mechanism that results in three hallmarks of its pathology: (i) binding to RNA-binding proteins (RBPs) that aggregate into nuclear foci; (ii) sequestration of muscleblind-like-1 (MBNL1) protein, a regulator of alternative pre-mRNA splicing, leading to splicing defects; and (iii) retention of intron 1 in the CNBP mRNA. Here, we find that CNBP intron retention is caused by the r(CCUG)exp-MBNL1 complex and can be rescued by small molecules. We studied two types of small molecules with different modes of action, ones that simply bind and ones that can be synthesized by a r(CCUG)exp-templated reaction in cells, that is the RNA synthesizes its own drug. Indeed, our studies completed in DM2 patient-derived fibroblasts show that the compounds disrupt the r(CCUG)exp-MBNL1 complex, reduce intron retention, subjecting the liberated intronic r(CCUG)exp to native decay pathways, and rescue other DM2-associated cellular defects. Collectively, this study shows that small molecules can affect RNA biology by shunting toxic transcripts towards native decay pathways.

HIGHLIGHTS

Intron retention in RNA repeat expansions can be due to repeats binding to proteins

Small molecules that bind RNA repeats and inhibit protein binding can trigger decay

A toxic RNA repeat can catalyze the synthesis of its own inhibitor on-site

On-site drug synthesis most potently affects disease biology

eTOC BLURB

The most common way to target RNA is to use antisense oligonucleotides to target unstructured RNAs for destruction. Here, we show for the first time that small molecules targeting structured, disease-causing RNAs can shunt them towards native decay pathways by affecting their processing.