Inferring TF activation order in time series scRNA-Seq studies

Methods for the analysis of time series single cell expression data (scRNA-Seq) either do not utilize information about transcription factors (TFs) and their targets or only study these as a post-processing step. Using such information can both, improve the accuracy of the reconstructed model and cell assignments, while at the same time provide information on how and when the process is regulated. We developed the Continuous-State Hidden Markov Models TF (CSHMM-TF) method which integrates probabilistic modeling of scRNA-Seq data with the ability to assign TFs to specific activation points in the model. TFs are assumed to influence the emission probabilities for cells assigned to later time points allowing us to identify not just the TFs controlling each path but also their order of activation. We tested CSHMM-TF on several mouse and human datasets. As we show, the method was able to identify known and novel TFs for all processes, assigned time of activation agrees with both expression information and prior knowledge and combinatorial predictions are supported by known interactions. We also show that CSHMM-TF improves upon prior methods that do not utilize TF-gene interaction.

An important attribute of time series single cell RNA-Seq (scRNA-Seq) data, is the ability to infer continuous trajectories of genes based on orderings of the cells. While several methods have been developed for ordering cells and inferring such trajectories, to date it was not possible to use these to infer the temporal activity of several key TFs. These TFs are are only post-transcriptionally regulated and so their expression does not provide complete information on their activity. To address this we developed the Continuous-State Hidden Markov Models TF (CSHMM-TF) methods that assigns continuous activation time to TFs based on both, their expression and the expression of their targets. Applying our method to several time series scRNA-Seq datasets we show that it correctly identifies the key regulators for the processes being studied. We analyze the temporal assignments for these TFs and show that they provide new insights about combinatorial regulation and the ordering of TF activation. We used several complementary sources to validate some of these predictions and discuss a number of other novel suggestions based on the method. As we show, the method is able to scale to large and noisy datasets and so is appropriate for several studies utilizing time series scRNA-Seq data.

Staging and clinical correlations of lymphoscintigraphy for unilateral gynecological cancer-related lymphedema

BACKGROUND

This study was to investigate the lymphoscintigraphy findings for the diagnosis and severity in unilateral gynecological cancer-related lymphedema (GCRL) and to correlate lymphoscintigraphy stages with the clinical findings.

METHODS

Patients with unilateral GCRL who underwent lymphoscintigraphy were staged using the presence of ileo-inguinal lymph nodes, distal-lymphatic ducts, and dermal backflow findings. Taiwan Lymphoscintigraphy Staging (TLS) was divided into three patterns and seven stages: normal drainage (L-0); partial obstruction (P-1, P-2, and P-3); and total obstruction (T4, T-5, and T-6). Correlations between clinical lymphedema severity and TLS were evaluated using analysis of variance and multivariable linear regression analyses.

RESULTS

A total of 141 patients with unilateral GCRL were divided as follows: 6 (4.3%) in normal drainage, 56 (39.7%) in partial-obstruction, and 79 (56%) in total obstruction. Cellulitis episodes, circumferential difference, and computed tomography (CT) volumetric difference were shown to be statistically different between TLS stages (P < .001 for all). Total obstruction stages were the most significant factors associated with the severity of circumferential difference (β = 19.72, 25.54, 32.42, respectively; P < .05) and CT volumetric difference (β = 36.04, 45.12, 52.78, respectively; P < .01).

CONCLUSIONS

Total lymphatic obstruction was present in 56% of unilateral GCGL. Lymphoscintigraphy stages were statistically correlated with episodes of cellulitis, circumferential difference and CT volumetric difference in unilateral GCRL.

[Split-thickness scalp and allogenic acellular dermal matrix in repairing deep wounds of hands in patients with extremely extensive burns]

Objective: To explore the clinical effects of split-thickness scalp and allogenic acellular dermal matrix (ADM) in repairing deep wounds of hands in patients with extremely extensive burns. Methods: Six patients with extremely extensive burns complicated by deep burn in hands were admitted to our department from December 2014 to December 2017, including 4 males and 2 females, aged 21 to 58 years. Their total burn areas were from 85% to 95% total body surface area (TBSA), and the sum of deep-partial thickness and full-thickness wounds was larger than 50% TBSA. Under general anesthesia, deep wounds of 10 dorsal hands were repaired by combined transplantation of split-thickness scalp and allogenic ADM in 4 to 6 weeks after injury. The skin grafting range was beyond the metacarpophalangeal joint, including partial dorsal digital deep wounds. Survival of skin grafts on dorsal hands, follow-up of hand shape and functional recovery were observed and recorded. Results: Six patients were successfully treated. There was no infection on the dorsal deep wounds of 10 hands after surgery, and the grafts survived well. During follow-up of 1 to 2 years after operation, there were no recurrent tension blisters or dorsal extension deformity of the metacarpophalangeal joints in 10 hands, the shape and function of hands recovered well, and hand Carroll scores were from 90 to 99 points, with functional levels of Ⅴ and Ⅵ. Conclusions: The combined transplantation of split-thickness scalp and allogenic ADM is a good method for repairing deep hand wounds in patients with extremely extensive burns, which can alleviate the cicatrix hyperplasia and contracture of healed hand wounds, and improve the shape and function of hands.

Diffusion Properties of Normal-Appearing White Matter Microstructure and Severity of Motor Impairment in Acute Ischemic Stroke

BACKGROUND AND PURPOSE

The effect of white matter hyperintensities as measured by FLAIR MR imaging on functional impairment and recovery after ischemic stroke has been investigated thoroughly. However, there has been growing interest in investigating normal-appearing white matter microstructural integrity following ischemic stroke onset with techniques such as DTI.

MATERIALS AND METHODS

Fifty-two patients with acute ischemic stroke and 36 without stroke were evaluated with a DTI and FLAIR imaging protocol and clinically assessed for the severity of motor impairment using the Motricity Index within 72 hours of suspected symptom onset.

RESULTS

There were widespread decreases in fractional anisotropy and increases in mean diffusivity and radial diffusivity for the acute stroke group compared with the nonstroke group. There was a significant positive association between fractional anisotropy and motor function and a significant negative association between mean diffusivity/radial diffusivity and motor function. The normal-appearing white matter ROIs that were most sensitive to the Motricity Index were the anterior/posterior limb of the internal capsule in the infarcted hemisphere and the splenium of the corpus callosum, external capsule, posterior limb/retrolenticular part of the internal capsule, superior longitudinal fasciculus, and cingulum (hippocampus) of the intrahemisphere/contralateral hemisphere.

CONCLUSIONS

The microstructural integrity of normal-appearing white matter is a significant parameter to identify neural differences not only between those individuals with and without acute ischemic stroke but also correlated with the severity of acute motor impairment.

Improvement of Streptococcus suis glutamate dehydrogenase expression in Escherichia coli through genetic modification of acetate synthesis pathway

Escherichia coli generates acetate as an undesirable by-product that has several negative effects on protein expression, and the reduction of acetate accumulation by modifying genes of acetate synthesis pathway can improve the expression of recombinant proteins. In the present study, the effect of phosphotransacetylase (pta) or/and acetate kinase (ackA) deletion on glutamate dehydrogenase (GDH) expression was investigated. The results indicated that the disruptions of pta or/and ackA decreased the acetate accumulation and synthesis of per gram cell, and increased cell density, and GDH expression and synthesis of per gram cell. The pta gene was more important for acetate formation than the ackA gene. Using the strain with deletions of pta-ackA (SSGPA) for GDH expression, acetate accumulation (2·61 g l^-1 ) and acetate synthesis of per gram cell (0·229 g g^-1 ) were lowest, decreasing by 28·29 and 41·43% compared with those of the parental strain (SSG) respectively. The flux of acetate synthesis (6·6%) was decreased by 72·15% compared with that of SSG, and the highest cell density (11·38 g l^-1 ), GDH expression (2·78 mg ml^-1 ), and GDH formation of per gram cell (0·2442 mg mg^-1 ) were obtained, which were 1·22-, 1·43- and 1·17-times higher than the parental strain respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Significance and Impact of the Study: Acetate is the key undesirable by-product in Escherichia coli cultivation, and both biomass and production of desired products are increased by the reduction of acetate accumulation. In the present study, the strains with deletions of pta or/and ackA were constructed to reduce the acetate accumulation and improve the GDH expression, and the highest expression level of GDH was obtained using the strain with lesion in pta-ackA that was 1·17-times higher than that of the parental strain. The construction strategy of recombinant E. coli for decreasing the acetate excretion can be used for high expression level of other desired products.

Cell lineage inference from SNP and scRNA-Seq data

Several recent studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. Recently, CRISPR has also been used to reconstruct lineage trees by inserting random mutations. However, both approaches suffer from drawbacks that limit their use. Here, we develop a method to detect significant, cell type specific, sequence mutations from scRNA-Seq data. We show that only a few mutations are enough for reconstructing good branching models. Integrating these mutations with expression data further improves the accuracy of the reconstructed models. As we show, the majority of mutations we identify are likely RNA editing events indicating that such information can be used to distinguish cell types.

Imatinib enhances the anti-tumour effect of doxorubicin in canine B-cell lymphoma cell line

Canine lymphoma is one of the most common malignant tumours occurring in dogs and has a high incidence worldwide. Despite advances in cancer prevention, the treatment of neoplastic diseases still requires improvement. Some cancer cells may resist the effect of chemotherapeutic agents by up-regulating drug transporters leading to increased drug efflux, resulting in intrinsic or acquired drug resistance, which is a mechanism commonly seen in doxorubicin-resistant tumour cells. In this study, canine B-cell lymphoma cell line CLBL1-8.0, a doxorubicin-resistant B cell lymphoma cell line derived from CLBL-1 by increasing the doxorubicin concentration during culturing, exhibited high expression of P-glycoprotein (P-gp, ATP-binding cassette sub-family B member 1 [ABCB1]). These proteins are commonly involved in cancer cell resistance to doxorubicin. Imatinib, a tyrosine kinase inhibitor significantly potentiated the sensitivity of doxorubicin in P-gp-overexpressing doxorubicin-resistant cells. Moreover, a combination of these two drugs may increase the retention of doxorubicin by decreasing the efflux of doxorubicin without affecting P-gp protein overexpression. In conclusion, imatinib reversed doxorubicin resistance by decreasing drug efflux in P-gp-overexpressing doxorubicin-resistant canine lymphoma cells. These results suggest that combining doxorubicin, one of the most widely used chemotherapeutic drugs in the treatment of canine lymphoma, with imatinib might potentially overcome doxorubicin resistance in a clinical setting.

Identification of key pathways and genes changes in pancreatic cancer cells (BXPC-3) after cross-talk with primary pancreatic stellate cells using bioinformatics analysis

Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors with poor prognosis, and the interaction between activated pancreatic stellate cells (PSCs) and PDAC cells plays an important role in the development of PDAC. The aim of this study was to identify gene changes in BXPC-3 after cross-talk with PSCs and reveal their potential mechanisms. The gene expression profiling analysis of BXPC-3 was completed after co-culture with primary PSCs for 48 h. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed, and the differentially expressed genes (DEGs) were identified by Agilent GeneSpring GX software. In total, 3657 DEGs were identified in BXPC-3, including 1881 up-regulated genes and 1776 downregulated genes. GO analysis results showed that upregulated DEGs were significantly enriched in biological processes (BP), including peptide metabolic process, response to stress and electron transport chain; the downregulated DEGs were significantly enriched in biological processes, including signaling, multicellular organism development and anatomical structure development. KEGG pathway analysis revealed that 19 pathways were upregulated and 32 pathways were downregulated, and that upregulated DEGs were enriched in protein export and glutathione metabolism, while the downregulated DEGs were enriched in axon guidance and focal adhesion. The top 10 upregulated genes and the top 10 downregulated genes were identified. By constructing PPI network, we selected out 10 key genes (TP53, SRC, IL6, JUN, ISG15, CAD, STAT1, OAS3, OAS1, VIM) and significant pathways. The associated survival analysis was performed and the SRC, IL-6, ISG15, STAT1, OAS3, OAS1 and VIM were proved to be related to worse overall survival time of PDAC patients. In conclusion, the present study indicated that the identified DEGs promote our understanding of the molecular mechanisms underlying the interaction between pancreatic cancer cells and PSCs and might be used as molecular targets in the future to study the role of tumor microenvironment in the progression of PDAC.

Record Purcell factors in ultracompact hybrid plasmonic ring resonators

For integrated optical devices and traveling-wave resonators, realistic use of the superior wave-matter interaction offered by plasmonics is impeded by ohmic loss, which increases rapidly with mode volume reduction. In this work, we report composite hybrid plasmonic waveguides (CHPWs) that are not only capable of guiding subwavelength optical mode with long-range propagation but also unrestricted by stringent requirements in structural, material, or modal symmetry. In these asymmetric CHPWs, the versatility afforded by coupling dissimilar plasmonic modes provides improved fabrication tolerance and more degrees of device design optimization. Experimental realization of CHPWs demonstrates propagation loss and mode area of 0.03 dB/μm and 0.002 μm2, corresponding to the smallest combination among long-range plasmonic structures reported to date. CHPW ring resonators with 2.5-μm radius were realized with record Purcell factor compared with existing plasmonic and dielectric resonators of similar radii.

Intra-abdominal chylovenous bypass treats retroperitoneal lymphangiomatosis

BACKGROUND

Retroperitoneal lymphangiomatosis (RL) is a rare form of primary lymphedema featuring aberrant retroperitoneal lymphatic proliferation. It causes recurrent cellulitis, repeated interventions, and poor life quality. This study aimed to investigate proper diagnositc criteria and surgical outcomes for RL with extremity lymphedema.

METHODS

Between 2012 and 2018, 44 primary lower-extremity lymphedema cases received lymphoscintigraphy, magnetic resonance imaging, and single-photon electron computed tomography to detect RL. RL patients underwent vascularized lymph node transfers (VLNT) for extremity lymphedema and intra-abdominal side-to-end chylovenous bypasses (CVB) for chylous ascites. Complications, CVB patency, and quality of life were evaluated postoperatively.

RESULTS

Six RL patients (mean age of 30.3 years) had chylous ascites with five had lower-extremity lymphedema. All CVBs remained patent, though one required re-anastomosis, giving a 100% patency rate. Four unilateral and one bilateral extremity lymphedema underwent six VLNTs with 100% flap survival. Patients reported improved quality of life (P = 0.023), decreased cellulitis incidence (P = 0.041), and improved mean lymphedema circumference (P = 0.043). All patients resumed a normal diet and activity.

CONCLUSIONS

Evaluating primary lower-extremity lymphedema patients with MRI and SPECT could reveal a 13.6% prevalence of RL and guide treatment of refractory extremity lymphedema. Intra-abdominal CVB with VLNT effectively treated RL with chylous ascites and extremity lymphedema.