bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunophenotype Drift of Residual Plasma Cells Indicates Therapeutic Response and Prognosis in Multiple Myeloma
Authors: Du Chenxing , Gang An , Xu Yan , Mao Xuehan , Yan Yuting , Liu Jiahui , Fan Huishou , Sui Weiwei , Deng Shuhui , Zengjun Li , Zhao Jiawei , Yi Shuhua , Zou Dehui , Qiu Lugui
Published: November 2019

Background

Chemotherapy resistance remains a significant hurdle in the treatment of multiple myeloma (MM). However, it is difficult to discriminate the potential refractory patients from the very early stage. Flow cytometry is a convenient tool to detect the residual myeloma cell tiding, indicating therapeutic response sensitively.

Methods

From June, 2014 to December, 2016, 172 sequential patients with newly diagnosed multiple myeloma were enrolled in the BDH2008/02 clinical trial. Patient informed consent was obtained in accordance with the Declaration of Helsinki. 144 patients with at least two flow cytometry detections were analyzed. Bone marrow samples were detected by an eight-color EuroFlow panel. CD20 negative and CD81 positive is defined as normal phenotype.

Results

We conducted a median of 3-time (2-8) flow cytometry detection on each patient. When newly diagnosed and achieved best response, CD20, CD81 expression rates were 29.9%, 9.7% and 14.9%, 64.4% (P=0.0091, P<0.0001), respectively. According to the status variation of CD20 and CD81, all patients were divided into three groups: both markers were always normal (Group A), either CD20 or CD81 was abnormal at diagnosed and turned normal during therapy (Group B) and markers stayed abnormal (Group C). Patients with undetectable residual tumor cells were also classified as Group A. The overall response rate of the patients in Group C was inferior to Group B (>PR rate: 54.3% vs. 71.4%, P=0.021). And the OS of Group C was significantly worse than Group A and B (47.9 months vs. not reached vs. not reached, P=0.036).

Conclusion

CD20/CD81 switching to normal phenotype during therapy indicates therapeutic response and an improved outcome than that staying abnormal. The expression tiding of CD20 and CD81 may be a reasonable combination to dynamically stratify MM patients, directing the choice of maintenance therapy.

Figure

Disclosures

No relevant conflicts of interest to declare.
Cost per Progression Free Survival (PFS) of Daratumumab, Elotuzumab, Carfilzomib and Ixazomib Combinations with Lenalidomide/Dexamethasone (DRd, ERd, KRd, IRd) in Patients with Relapsed/Refractory Multiple Myeloma (RRMM)
Authors: Santana Pamela , Saad Ricardo , Kolanian Adrielle , Fioratti Cyntia , Junqueira Marcela , Decimoni Tassia
Published: November 2019

OBJECTIVES: Multiple myeloma (MM) is the second most common hematological malignancy with several available therapies and an extensive pipeline. A metanalysis comparing pivotal relapsed/refractory (RRMM) studies that assessed DRd, ERd, KRd and IRd showed that DRd had the best PFS results. The goal of this analysis was to compare the cost per progression-free survival (PFS) for each of the comparators from the perspective of the Brazilian private healthcare system.

METHODS: We calculated the cost per PFS individually using the most recent available data from follow-up (FUP) studies of the therapies assessed. PFS values were based on POLLUX 3-year FUP (DRd), ENDEAVOR 4-year FUP (ERd), ASPIRE 3-year FUP (KRd) and TOURMALINE-MM1 (IRd). Only drug acquisition costs (with wastage) were considered in the analysis (according to drug label dosage) and were retrieved from the Brazilian official price list (Jul/19). Cost per PFS was calculated by dividing the total cost in the PFS period by time in PFS (in months). Cost in 18 months was assessed because it is the maximum time that carfilzomib is recommended to be used.

RESULTS: DRd showed the best PFS result compared with ERd, KRd and IRd (42.0 vs. 19.4, 26.1, 20.6, respectively). Total costs in the period of PFS for each of the comparators were BRL 2.02 million (DRd), BRL 1.29 million (ERd), BRL 1.14 million (KRd) and BRL 0.98 million (IRd). Costs per PFS- were BRL 48,060, BRL 66,343, BRL 43,822, BRL 47,760 and costs in the 18 first months were BRL 1.01 million, BRL 1,13 million, BRL 0.95 million and BRL 0.84 million for DRd, ERd, KRd and IRd, respectively.

CONCLUSIONS: DRd showed the best PFS result, however its cost per PFS is the 3rd lowest among the comparators. As costs are directly dependent on PFS, the longer the PFS the higher are the costs. Additionally, daratumumab has continuous usage meanwhile carfilzomib has label recommended usage for just 18 cycles due to toxicity and tolerability-related events.

Disclosures

Santana: Janssen pharmaceuticals: Employment. Saad:Janssen pharmaceuticals: Employment. Kolanian:Janssen pharmaceuticals: Employment. Fioratti:Janssen pharmaceuticals: Employment. Junqueira:Janssen pharmaceuticals: Employment. Decimoni:Janssen Pharmaceuticals: Employment.
Outcomes of Haploidentical Haematopoietic Stem Cell Transplantation for Paroxysmal Nocturnal Haemoglobinuria
Authors: Liu Limin , Zhou Huifen , Miao Miao , Wu Depei , Tang Xiaowen , Qiu Huiying , Han Yue , Jin Zhengming , Chen Suning , Sun Aining , Wang Qingyuan
Published: November 2019

Background: Haematopoietic stem cell transplantation (HSCT) is the only curative therapy for paroxysmal nocturnal haemoglobinuria (PNH). Haploidentical HSCT (haplo-HSCT) is an alternative treatment method for PNH patients lacking suitable identical donors. The current study evaluated the feasibility of haplo-HSCT in PNH patients.

Methods: We retrospectively analysed the outcomes of 28 PNH patients who received haplo-HSCT between October 2010 and December 2018.

Results: The median age was 28 (range 6-54) years. One patient (underwent HSCT in December 2018) was not evaluable for engraftment or haematopoietic recovery because of early death on day +14 due to septicaemia. The 27 evaluable patients all achieved myeloid engraftment and complete chimerism, and one patient experienced secondary graft failure. Three patients demonstrated delayed platelet recovery, and one patient demonstrated platelet graft failure. The median time to neutrophil recovery was 12 (range, 9-26) days, and the median time to platelet recovery was 16 (range, 11-75) days. The cumulative incidences were 29.63% for grades I to IV acute graft-versus-host disease (aGVHD) and 14.82% for grades II to IV aGVHD. No patient experienced grades III to IV aGVHD. With a median follow-up time of 37 (range 4-78) months, the cumulative incidence of chronic graft-versus-host disease (cGVHD) was 28.81%, and the cumulative incidence of moderate-severe cGVHD was 11.73%. No patient relapsed during the follow-up period. The 12-month transplantation-related mortality (TRM) rate was 15.25%. The probabilities of 3-year overall survival (OS) and graft-versus-host disease-free, failure-free survival (GFFS) were 84.8 ± 7.1% and 77.0 ± 8.3%, respectively.

Conclusions: The preliminary results indicated that haplo-HSCT is a feasible option for PNH patients lacking suitable identical donors.

Disclosures

No relevant conflicts of interest to declare.
Complete Hematologic and Cytogenetic Remission of Acute Myeloid Leukemia in an Elderly Patient Treated with Decitabine and Venetoclax: A Case Report
Authors: Paredes Hanrry Jerry , Gonzalez M. Francisco
Published: November 2019

We present the case of a 77 year old woman, Caucasian, with medical history of diabetes mellitus, hyperthyroidism, hypertension and hyperlipidemia, that suddenly develops progressive articular pain, dyspnea at rest, easy bruising /ecchymosis in soft tissues, weakness and nose bleeding. At admission no visceromegaly was noted, gums and lymph nodes were normal. Initial lab workup showed severe anemia (Hb 7.7 g/dL), leukocytosis (19.1 x 10^3/uL) with monocytosis (51%) and left shift, severe thrombocytopenia (Plt 33 x 10^3/uL), hyperfibrinogenemia, hyperglycemia and hyperuricemia. Bone marrow morphology was conclusive of Acute Myeloid Leukemia with 45 % of blasts, hypercellular with progressive trilineage hematopoiesis and no ringed sideroblasts. Flow cytometry of peripheral blood detected only 0.8 % of blasts (CD34+) with positive myeloid markers. Flow cytometry of bone marrow detected 17 % of myeloid blasts expressing CD34+, HLA-DR, CD117, cytoplasmic (cy) MPO, CD13, partial CD11b, negative for cyTdT and cy CD79a. Genetically, 5q31/EGR1 deletion (86%) and gain of 20q12 (64%), with no other anomalies or mutations were found.

Patient was treated with Decitabine 20mg/m2 IV daily x 10 d, followed by Venetoclax starting gradually from 100 mg escalating up to 300 mg oral as induction therapy. Complications during this phase were pleural effusion, C. difficile-associated diarrhea, urinary infection due to Enterococcus faecium, anemia, thrombocytopenia that required blood and platelet transfusions. After the first cycle of therapy a new bone marrow done showed morphologically < 2 % of blasts with moderate pancytopenia, but presence still of 10 % of CD34+ myeloblasts detected by flow cytometry. After a second course of therapy Decitabine/Venetoclax, peripheral blood leukocytes and platelets normalized, persisting only moderate anemia with no transfusion requirements. Bone marrow FISH report was normal, Del 5q disappeared, no detection of aberrations associated to myelodysplastic syndrome, and no detection of other abnormalities (results below the cut-off) were described, however a new pathogenic alteration in the DNMT3A gene not described before in other cases was detected with the New Generation System analysis.

At the moment of presenting this case report there is a leukemia-free survival of 6 months, with impressing improvement in the general status.

Conclusion: Therapy with the combination Decitabine/Venetoclax is a good alternative for treating elderly patients with AML, sparing the aggressiveness of regular induction chemotherapies and a tremendous impact in inducing cytogenetic remission.

Disclosures

No relevant conflicts of interest to declare.
Management of Delayed Elimination of High-Dose Methotrexate in Community Oncology Practices Can Mitigate Its Effect on Length of Hospital Stay, Treatment Dose-Density, Acute Kidney Injury, Dialysis, and Death
Authors: Howard Scott , Harry McKeon Tad , John Sfondouris , Marada Suresh , Napier Nicholas
Published: November 2019

Background

High-dose methotrexate (HDMTX, doses higher than 500 mg/m2) is an essential component of therapy for several hematologic cancers but requires meticulous supportive care and therapeutic drug monitoring to deliver safely. Community oncologists manage 85% of adults with cancer in the USA but may lack infrastructure to support HDMTX administration and patient outcomes can be compromised by avoidance of HDMTX when it would have been appropriate, toxicities, and early discontinuation after toxicity occurs.

Methods

We evaluated HDMTX use and outcomes in the Guardian Research Network, (www.GuardianResearch.org), a non-profit USA clinical trials consortium of 110 community oncology centers with a database containing patients' entire medical, including all demographics, diagnoses, labs, medications, procedures, encounters, and notes of all kinds (clinical, radiology reports). Anonymized, de-identified data about HDMTX doses, administration, supportive care, and outcomes was analyzed to determine its safety and efficacy in the community setting.

Results

Of 529784 cancer patients diagnosed from 2011 through 2019, 230 received at 1 to 18 courses of HDMTX (median 3) for acute lymphoblastic leukemia (n=41), NHL (n=142), or other cancers (n=47). Patient characteristics are shown in the Table. In 106 cases (46%), patients received only 1 or 2 doses of HDMTX, usually due to delayed methotrexate clearance and acute kidney injury (AKI). Only 2 patients (1%) received dialysis, but 23 (10%) died within 28 days of a HDMTX course. Survival at 3 years for patients who received only 1 or 2 doses of HDMTX was 50% (Standard error, SE 6%), compared to 71% for those who received 3 or 4 doses (SE 6%) and 64% for patients who received 5 or more doses (SE 7%), p=0.002. Age older than 80 years predicted survival (p=0.02), but no other patient features, including: race (p=0.40), sex (p=0.72), cancer type (p=0.82). In multivariable Cox proportional hazards analysis, receiving 2 or less HDMTX courses was associated with a hazard ratio (HR) of 2.0 (95% CI 1.3 to 3.3, p=0.004) and age increased the risk of death for each decade older than 50 years (HR 4.8 for patients older than 80 years, 95% CI 1.6 to 14, p=0.004.

Conclusions

HDMTX can be safely delivered in community oncology practices, but requires meticulous supportive care to allow completion of all doses and maximize survival

Figure

Disclosures

Howard: BTG: Consultancy, Research Funding; Servier: Consultancy, Speakers Bureau; Sanofi: Consultancy, Speakers Bureau; EUSA: Consultancy; Resonance: Equity Ownership.
Outcome of Morbidly Obese Patients with Acute Venous Thromboembolism Managed with Direct Oral Anticoagulants
Authors: Anusim Nwabundo , Ionescu Filip , Jindal Vishal , Gupta Ruby , Jaiyesimi Ishmael , Gaikazian Susanna
Published: November 2019

Background.

Obesity is a major epidemic affecting all age groups in the USA. It has been associated with venous thromboembolism (VTE), which requires prolonged anticoagulation. Classic options (vitamin K antagonists, heparins) are increasingly replaced by direct oral anticoagulants (DOACs), which have not been well studied in patients with body mass index (BMI) > 40kg/m2 or weight above 120 kg. Despite limited safety and efficacy data, patients and their caregivers often opted for this medication owing to its ease of administration, lack of requirement for frequent laboratory testing and for dietary restrictions.

Methods.

This is a retrospective study of all morbidly obese patients (BMI > 40kg/m2) diagnosed with acute VTE managed with DOACs at Beaumont hospital between January of 2018 and December of 2018. Data regarding demographics, specific DOAC, major bleeding (hemoglobin decrease by 2 g/dL) and new or progressive thrombosis were recorded during a sixty-day follow up. Data was analyzed using JMP statistical software.

Results

A total of 42 patients diagnosed with acute VTE received DOACs during the study period. Most were female (76%); the median BMI was 44 (IQR 42-60) and mean age was 57. Most patients had a BMI of 40-50 kg/m2 (n=34, 81%) compared to BMI 50-60 kg/m2 (n=6, 14%) and BMI >60kg/m2 (n=6, 14%). Apixaban was the most frequently used DOAC (n=27, 65%). No clinically significant bleeding occurred during the study period. There were 2 thrombotic episodes (5% of patients) within 60 days of starting a DOAC; both occurred in patients receiving rivaroxaban. One event was present in the BMI 40-50kg/m2 group and one in the >60kg/m2 group.

Conclusions

DOACs appear to be safe and efficacious for the management of VTE in the morbidly obese population. Future studies may focus on the comparative efficacy of apixaban and rivaroxaban in the morbidly obese population.

Disclosures

No relevant conflicts of interest to declare.
EZH2 Gain-of-Function Mutations Generate a Lymphoma-Permissive Immune Niche
Authors: Béguelin Wendy , Teater Matthew R , Meydan Cem , Phillip Jude M , Melnick Ari
Published: November 2019

The polycomb histone methyltransferase protein EZH2 is highly expressed and mutated in approximately 25% of the two most common subtypes of non-Hodgkin's lymphoma: follicular lymphoma (FL) and diffuse large B cell lymphoma (DLBCL). Both of these tumor types originate from germinal center (GC) B-cells, which are highly proliferative cells that form transiently during the T-cell dependent humoral immune response. Wild type EZH2 plays a critical role in the formation of GC B-cells and mutant EZH2 drives malignant transformation of these cells in vivo. These lymphoma-associated mutations of EZH2 are gain-of-function and enhance EZH2 methyltransferase activity, which cause abnormally efficient H3K27me3, enhancing repression of transcription. Of note, EZH2 mutant lymphomas manifest aberrant suppression of antigen presentation pathways, such as loss or reduced expression of MHC-I and MHC-II, and reduced T-cell infiltrates. We show that mice engineered to conditionally express mutant Ezh2Y641F specifically in GC B-cells exhibited massive GC hyperplasia with expansion of the "light zone" -the GC niche where B-cells are selected based on the affinity of their antibodies- and extended follicular dendritic cells network. With chimeric bone marrow transplantation experiments we found that Ezh2Y641F provides a competitive advantage to activated B-cells in seeding and expanding the T-cell dependent GC reaction. Liquid chromatography separation and mass spectrometry of histone tryptic peptides revealed a massive increase in H3K27me3 in Ezh2Y641F GC B-cells, at the expense of a reduction in H3K27me2. Remarkably, we observed increased unmodified and decreased H3K27me1, indicating a loss-of-function mono-methylase activity of Ezh2Y641F. We confirmed an extensive global gain of H3K27me3 by ChIP-seq, with massive spreading of the mark both upstream and downstream TSS. RNA-seq analysis showed differential expression of genes involved in antigen processing and presentation and immune response, suggesting that B-cell selection process is altered in Ezh2Y641F GC light zone. Therefore, we hypothesized that, through an epigenetic mechanism, Ezh2 mutation makes B-cells less dependent of T-cells by aberrantly suppressing genes involved in the immune synapse. Indeed, inhibition of the interaction between TFH and GC B-cell in vivo using anti CD40L antibody, abrogated GC reaction in WT but not in Ezh2Y641F mice. Of note, EZH2 mutant GCs manifest a massive expansion of the follicular dendritic cell network in spite of lack of T-cell dependence, a finding that reflects low grade FL histology. Hence, EZH2 mutant lymphomas might progress due to acquired immune escape, which is a critical consideration when designing precision, tailored immune-therapy regimens.

Disclosures

Melnick: Constellation: Consultancy; Janssen: Research Funding; Epizyme: Consultancy.
Results from a multidisciplinary clinic guided by geriatric assessment before stem cell transplantation in older adults
Authors: Derman Benjamin A. , Kordas Keriann , Ridgeway Jean , Chow Selina , Dale William , Lee Sang Mee , Aguada Elingel , Jakubowiak Andrzej J. , Jasielec Jagoda , Kline Justin , Kosuri Satyajit , Larson Richard A. , Liu Hongtao , Mortel Mylove , Odenike Olatoyosi , Pisano Jennifer , Riedell Peter , Stock Wendy , Bishop Michael R. , Artz Andrew S.
Published: November 2019

Key Points

GA to guide an MDC evaluation to optimize older adult candidates for hematopoietic cellular therapy is feasible and practical. An MDC evaluation for older adults before transplantation holds promise to mitigate transplant-related morbidity and mortality.
Inhibition of phosphatidylinositol 3-kinase by PX-866 suppresses temozolomide-induced autophagy and promotes apoptosis in glioblastoma cells
Authors: Harder Bryan G. , Peng Sen , Sereduk Christopher P. , Sodoma Andrej M. , Kitange Gaspar J. , Loftus Joseph C. , Sarkaria Jann N. , Tran Nhan L.
Published: November 2019

Background

Temozolomide (TMZ) is the most commonly used chemotherapeutic agent used to treat glioblastoma (GBM), which causes significant DNA damage to highly proliferative cells. Our observations have added to accumulating evidence that TMZ induces stress-responsive cellular programs known to promote cell survival, including autophagy. As such, targeting these survival pathways may represent new vulnerabilities of GBM after treatment with TMZ.

Methods

Using the T98G human glioma cell line, we assessed the molecular signaling associated with TMZ treatment, the cellular consequences of using the pan-PI3K inhibitor PX-866, and performed clonogenic assays to determine the effect sequential treatment of TMZ and PX-866 had on colony formation. Additionally, we also use subcutaneous GBM patient derived xenograft (PDX) tumors to show relative LC3 protein expression and correlations between survival pathways and molecular markers which dictate clinical responsiveness to TMZ.

Results

Here, we report that TMZ can induce autophagic flux in T98G glioma cells. GBM patient-derived xenograft (PDX) tumors treated with TMZ also display an increase in the autophagosome marker LC3 II. Additionally, O6-methylguanine-DNA-methyltransferase (MGMT) expression correlates with PI3K/AKT activity, suggesting that patients with inherent resistance to TMZ (MGMT-high) would benefit from PI3K/AKT inhibitors in addition to TMZ. Accordingly, we have identified that the blood-brain barrier (BBB) penetrant pan-PI3K inhibitor, PX-866, is an early-stage inhibitor of autophagic flux, while maintaining its ability to inhibit PI3K/AKT signaling in glioma cells. Lastly, due to the induction of autophagic flux by TMZ, we provide evidence for sequential treatment of TMZ followed by PX-866, rather than combined co-treatment, as a means to shut down autophagy-induced survival in GBM cells and to enhance apoptosis.

Conclusions

The understanding of how TMZ induces survival pathways, such as autophagy, may offer new therapeutic vulnerabilities and opportunities to use sequential inhibition of alternate pro-survival pathways that regulate autophagy. As such, identification of additional ways to inhibit TMZ-induced autophagy could enhance the efficacy of TMZ.
The assessment of efficient representation of drug features using deep learning for drug repositioning
Authors: Moridi Mahroo , Ghadirinia Marzieh , Sharifi-Zarchi Ali , Zare-Mirakabad Fatemeh
Published: November 2019

Background

De novo drug discovery is a time-consuming and expensive process. Nowadays, drug repositioning is utilized as a common strategy to discover a new drug indication for existing drugs. This strategy is mostly used in cases with a limited number of candidate pairs of drugs and diseases. In other words, they are not scalable to a large number of drugs and diseases. Most of the in-silico methods mainly focus on linear approaches while non-linear models are still scarce for new indication predictions. Therefore, applying non-linear computational approaches can offer an opportunity to predict possible drug repositioning candidates.

Results

In this study, we present a non-linear method for drug repositioning. We extract four drug features and two disease features to find the semantic relations between drugs and diseases. We utilize deep learning to extract an efficient representation for each feature. These representations reduce the dimension and heterogeneity of biological data. Then, we assess the performance of different combinations of drug features to introduce a pipeline for drug repositioning. In the available database, there are different numbers of known drug-disease associations corresponding to each combination of drug features. Our assessment shows that as the numbers of drug features increase, the numbers of available drugs decrease. Thus, the proposed method with large numbers of drug features is as accurate as small numbers.

Conclusion

Our pipeline predicts new indications for existing drugs systematically, in a more cost-effective way and shorter timeline. We assess the pipeline to discover the potential drug-disease associations based on cross-validation experiments and some clinical trial studies.
MLW-gcForest: a multi-weighted gcForest model towards the staging of lung adenocarcinoma based on multi-modal genetic data
Authors: Dong Yunyun , Yang Wenkai , Wang Jiawen , Zhao Juanjuan , Qiang Yan , Zhao Zijuan , Kazihise Ntikurako Guy Fernand , Cui Yanfen , Yang Xiaotong , Liu Siyuan
Published: November 2019

Background

Lung cancer is one of the most common types of cancer, among which lung adenocarcinoma accounts for the largest proportion. Currently, accurate staging is a prerequisite for effective diagnosis and treatment of lung adenocarcinoma. Previous research has used mainly single-modal data, such as gene expression data, for classification and prediction. Integrating multi-modal genetic data (gene expression RNA-seq, methylation data and copy number variation) from the same patient provides the possibility of using multi-modal genetic data for cancer prediction. A new machine learning method called gcForest has recently been proposed. This method has been proven to be suitable for classification in some fields. However, the model may face challenges when applied to small samples and high-dimensional genetic data.

Results

In this paper, we propose a multi-weighted gcForest algorithm (MLW-gcForest) to construct a lung adenocarcinoma staging model using multi-modal genetic data. The new algorithm is based on the standard gcForest algorithm. First, different weights are assigned to different random forests according to the classification performance of these forests in the standard gcForest model. Second, because the feature vectors generated under different scanning granularities have a diverse influence on the final classification result, the feature vectors are given weights according to the proposed sorting optimization algorithm. Then, we train three MLW-gcForest models based on three single-modal datasets (gene expression RNA-seq, methylation data, and copy number variation) and then perform decision fusion to stage lung adenocarcinoma. Experimental results suggest that the MLW-gcForest model is superior to the standard gcForest model in constructing a staging model of lung adenocarcinoma and is better than the traditional classification methods. The accuracy, precision, recall, and AUC reached 0.908, 0.896, 0.882, and 0.96, respectively.

Conclusions

The MLW-gcForest model has great potential in lung adenocarcinoma staging, which is helpful for the diagnosis and personalized treatment of lung adenocarcinoma. The results suggest that the MLW-gcForest algorithm is effective on multi-modal genetic data, which consist of small samples and are high dimensional.
Design and structural characterisation of olfactomedin-1 variants as tools for functional studies
Authors: Pronker Matti F. , van den Hoek Hugo , Janssen Bert J. C.
Published: November 2019

Background

Olfactomedin-1 (Olfm1; also known as Noelin or Pancortin) is a highly-expressed secreted brain and retina protein and its four isoforms have different roles in nervous system development and function. Structural studies showed that the long Olfm1 isoform BMZ forms a disulfide-linked tetramer with a V-shaped architecture. The tips of the Olfm1 “V” each consist of two C-terminal β-propeller domains that enclose a calcium binding site. Functional characterisation of Olfm1 may be aided by new biochemical tools derived from these core structural elements.

Results

Here we present the production, purification and structural analysis of three novel monomeric, dimeric and tetrameric forms of mammalian Olfm1 for functional studies. We characterise these constructs structurally by high-resolution X-ray crystallography and small-angle X-ray scattering. The crystal structure of the Olfm1 β-propeller domain (to 1.25 Å) represents the highest-resolution structure of an olfactomedin family member to date, revealing features such as a hydrophilic tunnel containing water molecules running into the core of the domain where the calcium binding site resides. The shorter Olfactomedin-1 isoform BMY is a disulfide-linked tetramer with a shape similar to the corresponding region in the longer BMZ isoform.

Conclusions

These recombinantly-expressed protein tools should assist future studies, for example of biophysical, electrophysiological or morphological nature, to help elucidate the functions of Olfm1 in the mature mammalian brain. The control over the oligomeric state of Olfm1 provides a firm basis to better understand the role of Olfm1 in the (trans-synaptic) tethering or avidity-mediated clustering of synaptic receptors such as post-synaptic AMPA receptors and pre-synaptic amyloid precursor protein. In addition, the variation in domain composition of these protein tools provides a means to dissect the Olfm1 regions important for receptor binding.
Transcriptional profiling predicts running promotes cerebrovascular remodeling in young but not midlife mice
Authors: Foley Kate E. , Yang Hongtian Stanley , Graham Leah C. , Howell Gareth R.
Published: November 2019

Background

The incidence of dementia and cognitive decline is increasing with no therapy or cure. One of the reasons treatment remains elusive is because there are various pathologies that contribute to age-related cognitive decline. Specifically, with Alzheimer’s disease, targeting to reduce amyloid beta plaques and phosphorylated tau aggregates in clinical trials has not yielded results to slow symptomology, suggesting a new approach is needed. Interestingly, exercise has been proposed as a potential therapeutic intervention to improve brain health and reduce the risk for dementia, however the benefits throughout aging are not well understood.

Results

To better understand the effects of exercise, we preformed transcriptional profiling on young (1–2 months) and midlife (12 months) C57BL/6 J (B6) male mice after 12 weeks of voluntary running. Data was compared to age-matched sedentary controls. Interestingly, the midlife running group naturally broke into two cohorts based on distance ran - either running a lot and more intensely (high runners) or running less and less intensely (low runners). Midlife high runners had lower LDL cholesterol as well as lower adiposity (%fat) compared to sedentary, than midlife low runners compared to sedentary suggesting more intense running lowered systemic markers of risk for age-related diseases including dementias. Differential gene analysis of transcriptional profiles generated from the cortex and hippocampus showed thousands of differentially expressed (DE) genes when comparing young runners to sedentary controls. However, only a few hundred genes were DE comparing either midlife high runners or midlife low runners to midlife sedentary controls. This indicates that, in our study, the effects of running are reduced through aging. Gene set enrichment analyses identified enrichment of genes involved in extracellular matrix (ECM), vascular remodeling and angiogenesis in young runners but not midlife runners. These genes are known to be expressed in multiple vascular-related cell types including astrocytes, endothelial cells, pericytes and smooth muscle cells.

Conclusions

Taken together these results suggest running may best serve as a preventative measure to reduce risk for cerebrovascular decline. Ultimately, this work shows that exercise may be more effective to prevent dementia if introduced at younger ages.
A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)
Authors: Chen Xi , Sun Shuo , Liu Fangjie , Shen Enhui , Liu Lu , Ye Chuyu , Xiao Bingguang , Timko Michael P. , Zhu Qian-Hao , Fan Longjiang , Cao Peijian
Published: November 2019

Background

Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed.

Results

A total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host geneQS, were sharply increased following the topping treatment.

Conclusions

These results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.
Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats
Authors: Zeng Hong , Yu Bao-fu , Liu Nan , Yang Yan-yan , Xing Hua-yi , Liu Xiao-xie , Zhou Mou-wang
Published: November 2019

Background

Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on transcriptional levels after SCI and to determine the mechanisms underlying α-Syn activity based on RNA-seq.

Result

The establishment of a rat model of lentiviral vector-mediated knockdown of α-Syn in Sprague-Dawley rats with T3 spinal cord contusion (LV_SCI group). The results of the RNA-seq analysis showed that there were 337 differentially expressed genes (DEGs) between the SCI group and the LV_SCI group, and 153 DEGs specific to LV_SCI between the (SCI vs LV_SCI) and (SCI vs CON) comparisons. The top 20 biological transition terms were identified by Gene ontology (GO) analysis. The Kyoto Gene and Genomic Encyclopedia (KEGG) analysis showed that the LV_SCI group significantly upregulated the cholinergic synaptic & nicotine addiction and the neuroactive ligand receptor interaction signaling pathway. Enriched chord analysis analyzes key genes. Further cluster analysis, gene and protein interaction network analysis and RT-qPCR results showed that Chrm2 and Chrnb2 together significantly in both pathways. The proliferation of muscarinic cholinergic receptor subtype 2 (Chrm2) and nicotinic cholinergic receptor subtype β2 (Chrnb2), and the neurogenesis were elevated in the injury site of LV_SCI group by immunofluorescence. Further by subcellular localization, the LV_SCI group enhanced the expression of Chrnb2 at the cell membrane.

Conclusion

Knockdown of α-Syn after SCI enhance motor function and promote neurogenesis probably through enhancing cholinergic signaling pathways and neuroreceptor interactions. This study not only further clarifies the understanding of the mechanism of knockdown of α-Syn on SCI but also helps to guide the treatment strategy for SCI.
Changes of intestinal bacterial microbiota in coronary heart disease complicated with nonalcoholic fatty liver disease
Authors: Zhang Yiwen , Xu Jun , Wang Xuemei , Ren Xinhua , Liu Yulan
Published: November 2019

Background

Previous study reported that patients who suffered coronary heart disease (CHD) complicated with non-alcoholic fatty liver disease (NAFLD) had worse cardiac function and clinical outcomes than patients with CHD only. Notably, the mechanism is still unclear. This study aimed to investigate the changes and roles of intestinal bacterial microbiota in CHD-NAFLD patients.

Methods and results

People were recruited and divided into three groups, including CHD patients (without NAFLD), CHD-NAFLD patients and healthy controls (HCs). Each group contained 24 people. Fecal samples and clinical information were carefully collected. The Illumina sequencing of 16S rRNA was applied to profile the overall structure of the fecal bacterial microbiota and the characteristics of the bacterial microbiota based on the Operational Taxonomic Units. In clinical information, the CHD-NAFLD patients showed an increase in BMI, uric acid and triglyceride. There was a significant reduction in the abundance ofParabacteroidesandCollinsellain overall CHD patients (including CHD-NAFLD and CHD patients). The intestinal bacterial microbiota in CHD-NAFLD patients showed an increase in the abundance ofCopococcusandVeillonella, and a reduction in the abundance ofParabacteroides,Bacteroides fragilis,Ruminococcus gnavus, Bacteroides dorei, andBifidobacterium longum subsp infantis. Among them, the abundance ofRuminococcus gnavusandBacteroides doreiwas significantly lower than that in CHD patients. Additionally, BMI positively correlated with the abundance ofCopococcusand negatively correlated with the abundance ofBifidobacterium longum subsp infantis. The abundance ofVeillonellapositively correlated with AST. The abundance ofBacteroides doreinegatively correlated with ALT and AST. It indicates that the abundance of intestinal microbiota was related to the changes in clinical indexes.

Conclusions

Changes of intestinal bacterial microbiota in CHD-NAFLD patients may be important factors affecting the degree of metabolic disorder, which may be one of the important reasons for the worse clinical outcome and disease progression in CHD-NAFLD patients than in CHD patients.
Identification and evaluation of reference genes for quantitative real-time PCR analysis in Polygonum cuspidatum based on transcriptome data
Authors: Wang Xiaowei , Wu Zhijun , Bao Wenqi , Hu Hongyan , Chen Mo , Chai Tuanyao , Wang Hong
Published: November 2019

Background

Polygonum cuspidatum of the Polygonaceae family is a traditional medicinal plant with many bioactive compounds that play important roles in human health and stress responses. Research has attempted to identify biosynthesis genes and metabolic pathways in this species, and quantitative real-time PCR (RT-qPCR) has commonly been used to detect gene expression because of its speed, sensitivity, and specificity. However, no P. cuspidatum reference genes have been identified, which hinders gene expression studies. Here, we aimed to identify suitable reference genes for accurate and reliable normalization of P. cuspidatum RT-qPCR data.

Results

Twelve candidate reference genes, including nine common (ACT, TUA, TUB, GAPDH, EF-1γ, UBQ, UBC, 60SrRNA, and eIF6A) and three novel (SKD1, YLS8, and NDUFA13), were analyzed in different tissues (root, stem, and leaf) without treatment and in leaves under abiotic stresses (salt, ultraviolet [UV], cold, heat, and drought) and hormone stimuli (abscisic acid [ABA], ethylene [ETH], gibberellin [GA3], methyl jasmonate [MeJA], and salicylic acid [SA]). Expression stability in 65 samples was calculated using the △CT method, geNorm, NormFinder, BestKeeper, and RefFinder. Two reference genes (NDUFA13 and EF-1γ) were sufficient to normalize gene expression across all sample sets. They were also the two most stable genes for abiotic stresses and different tissues, whereas NDUFA13 and SKD1 were the top two choices for hormone stimuli. Considering individual experimental sets, GAPDH was the top-ranked gene under ABA, ETH, and GA3 treatments, while 60SrRNA showed good stability under MeJA and cold treatments. ACT, UBC, and TUB were suitable genes for drought, UV, and ABA treatments, respectively. TUA was not suitable because of its considerable variation in expression under different conditions. The expression patterns of PcPAL, PcSTS, and PcMYB4 under UV and SA treatments and in different tissues normalized by stable and unstable reference genes demonstrated the suitability of the optimal reference genes.

Conclusions

We propose NDUFA13 and EF-1γ as reference genes to normalize P. cuspidatum expression data. To our knowledge, this is the first systematic study of reference genes in P. cuspidatum which could help advance molecular biology research in P. cuspidatum and allied species.
Genome-wide identification and expression analysis of SWEET gene family in Litchi chinensis reveal the involvement of LcSWEET2a/3b in early seed development
Authors: Xie Hanhan , Wang Dan , Qin Yaqi , Ma Anna , Fu Jiaxin , Qin Yonghua , Hu Guibing , Zhao Jietang
Published: November 2019

Background

SWEETs (Sugar Will Eventually be Exported transporters) function as sugar efflux transporters that perform diverse physiological functions, including phloem loading, nectar secretion, seed filling, and pathogen nutrition. The SWEET gene family has been identified and characterized in a number of plant species, but little is known about in Litchi chinensis, which is an important evergreen fruit crop.

Results

In this study, 16 LcSWEET genes were identified and nominated according to its homologous genes in Arabidopsis and grapevine. Multiple sequence alignment showed that the 7 alpha-helical transmembrane domains (7-TMs) were basically conserved in LcSWEETs. The LcSWEETs were divided into four clades (Clade I to Clade IV) by phylogenetic tree analysis. A total of 8 predicted motifs were detected in the litchi LcSWEET genes. The 16 LcSWEET genes were unevenly distributed in 9 chromosomes and there was one pairs of segmental duplicated events by synteny analysis. The expression patterns of the 16 LcSWEET genes showed higher expression levels in reproductive organs. The temporal and spatial expression patterns of LcSWEET2a and LcSWEET3b indicated they play central roles during early seed development.

Conclusions

The litchi genome contained 16 SWEET genes, and most of the genes were expressed in different tissues. Gene expression suggested that LcSWEETs played important roles in the growth and development of litchi fruits. Genes that regulate early seed development were preliminarily identified. This work provides a comprehensive understanding of the SWEET gene family in litchi, laying a strong foundation for further functional studies of LcSWEET genes and improvement of litchi fruits.
To what extent is multi-morbidity associated with new onset depression in patients attending cardiac rehabilitation?
Authors: Sever Serdar , Doherty Patrick , Harrison Alexander Stephen , Golder Su
Published: November 2019

Background

Depression is associated with increased mortality and poor prognosis in patients with cardiovascular disease (CVD). However, little is known about the patient characteristics associated with new onset post heart event depressive symptoms, specifically medical comorbidities, among cardiac rehabilitation (CR) participants. Therefore, this paper examines the comorbidity profile and characteristics associated with new onset depressive symptoms in patients attending CR.

Methods

An observational study using the routine practice data of British Heart Foundation National Audit of Cardiac Rehabilitation (NACR) from the last six years between April 2012 and March 2018. Patients with new onset post heart event depression and no previous documented history of depression were selected as the study population. An independent samples t-test and chi square tests were used to compare the association between new onset depressive symptoms and patient variables including demographics, clinical measures and comorbidities. A binary logistic regression was conducted to investigate the predictors of new onset depressive symptoms employing log-likelihood ratio statistic.

Results

The analyses included 109,055 CR patients with new onset depression measured by Hospital Anxiety and Depression Scale (HADS). At baseline assessment, comorbidity measures associated with new onset depressive symptoms were increased total number of comorbidities and a range of comorbidities - including diabetes, angina, arthritis, chronic back problems, asthma, stroke, anxiety, rheumatism, claudication, osteoporosis, chronic bronchitis and emphysema. After multivariate adjustments were done, at the start of CR, the significant predictors of new onset depressive symptoms were physical inactivity, high HADS anxiety score measurement, increased weight, total number of comorbidities, diabetes, stroke, chronic back problems, being from areas with higher levels of social deprivation, being single, and male.

Conclusion

The research findings establish new insights into the association between patient demographic and clinical variables across a range of comorbidities in patients with new onset post heart event depressive symptoms. At the start of CR, patients with new onset depressive symptoms need to be assessed skilfully as they tend to have a complex multi-morbid presentation linked to psychosocial risk factors known to hinder CR engagement.
Methods for diagnosing bile acid malabsorption: a systematic review
Authors: Lyutakov Ivan , Ursini Francesco , Penchev Plamen , Caio Giacomo , Carroccio Antonio , Volta Umberto , De Giorgio Roberto
Published: November 2019

Background

Bile acid malabsorption (BAM) and bile acid-related diarrhea represent an under-recognized cause of chronic diarrhea mainly because of limited guidance on appropriate diagnostic and laboratory tests. We aimed to perform a systematic review of the literature in order to identify and compare the diagnostic accuracy of different diagnostic methods for patients with BAM, despite a proven gold standard test is still lacking.

Methods

A PubMed literature review and a manual search were carried out. Relevant full papers, evaluating the diagnostic accuracy of different methods for BAM, were assessed. Available data were analyzed to estimate the sensitivity and specificity of each published test.

Results

Overall, more than one test was considered in published papers on BAM. The search strategy retrieved 574 articles; of these, only 16 were full papers (with a total of 2.332 patients) included in the final review. Specifically, n = 8 studies used 75Selenium-homotaurocholic-acid-test (75SeHCAT) with a < 10% retention threshold; n = 8 studies evaluated fasting serum 7-α-hydroxy-4-cholesten-3-one (C4); n = 3 studies involved total fecal bile acid (BA) excretion over 48 h; n = 4 studies assessed fibroblast growth factor 19 (FGF19). 75SeHCAT showed an average sensitivity and specificity of 87.32 and 93.2%, respectively, followed by serum C4 (85.2 and 71.1%) and total fecal BA (66.6 and 79.3%). Fasting serum FGF19 had the lowest sensitivity and specificity (63.8 and 72.3%). All the extracted data were associated with substantial heterogeneity.

Conclusions

Our systematic review indicates that 75SeHCAT has the highest diagnostic accuracy for BAM, followed by serum C4 assay. The diagnostic yield of fecal BA and FGF19 assays is still under investigation. Our review reinforces the need for novel biomarkers aimed to an objective detection of BAM and therefore improving the management of this condition.