ß-Catenin in Dendritic Cells Negatively Regulates CD8 T Cell Immune Responses through the Immune Checkpoint Molecule Tim-3.

Recent studies have demonstrated that ß-catenin in dendritic cells (DCs) serves as a key mediator in promoting both CD4 and CD8 T cell tolerance, although the mechanisms underlying how ß-catenin exerts its functions remain incompletely understood. Here, we report that activation of ß-catenin leads to the up-regulation of inhibitory molecule T-cell immunoglobulin and mucin domain 3 (Tim-3) in type 1 conventional DCs (cDC1s). Using a cDC1-targeted vaccine model with anti-DEC-205 engineered to express the melanoma antigen human gp100 (anti-DEC-205-hgp100), we demonstrated that CD11c-ß-cateninactive mice exhibited impaired cross-priming and memory responses of gp100-specific CD8 T (Pmel-1) cells upon immunization with anti-DEC-205-hgp100. Single-cell RNA sequencing (scRNA-seq) analysis revealed that ß-catenin in DCs negatively regulated transcription programs for effector function and proliferation of primed Pmel-1 cells, correlating with suppressed CD8 T cell immunity in CD11c-ß-cateninactive mice. Further experiments showed that treating CD11c-ß-cateninactive mice with an anti-Tim-3 antibody upon anti-DEC-205-hgp100 vaccination led to restored cross-priming and memory responses of gp100-specific CD8 T cells, suggesting that anti-Tim-3 treatment likely synergizes with DC vaccines to improve their efficacy. Indeed, treating B16F10-bearing mice with DC vaccines using anti-DEC-205-hgp100 in combination with anti-Tim-3 treatment resulted in significantly reduced tumor growth compared with treatment with the DC vaccine alone. Taken together, we identified the ß-catenin/Tim-3 axis as a potentially novel mechanism to inhibit anti-tumor CD8 T cell immunity and that combination immunotherapy of a DC-targeted vaccine with anti-Tim-3 treatment leads to improved anti-tumor efficacy.

Robust self-supervised denoising of voltage imaging data using CellMincer.

Voltage imaging enables high-throughput investigation of neuronal activity, yet its utility is often constrained by a low signal-to-noise ratio (SNR). Conventional denoising algorithms, such as those based on matrix factorization, impose limiting assumptions about the noise process and the spatiotemporal structure of the signal. While deep learning based denoising techniques offer greater adaptability, existing approaches fail to fully exploit the fast temporal dynamics and unique short- and long-range dependencies within voltage imaging datasets. Here, we introduce CellMincer, a novel self-supervised deep learning method designed specifically for denoising voltage imaging datasets. CellMincer operates on the principle of masking and predicting sparse sets of pixels across short temporal windows and conditions the denoiser on precomputed spatiotemporal auto-correlations to effectively model long-range dependencies without the need for large temporal denoising contexts. We develop and utilize a physics-based simulation framework to generate realistic datasets for rigorous hyperparameter optimization and ablation studies, highlighting the key role of conditioning the denoiser on precomputed spatiotemporal auto-correlations to achieve 3-fold further reduction in noise. Comprehensive benchmarking on both simulated and real voltage imaging datasets, including those with paired patch-clamp electrophysiology (EP) as ground truth, demonstrates CellMincer's state-of-the-art performance. It achieves substantial noise reduction across the entire frequency spectrum, enhanced detection of subthreshold events, and superior cross-correlation with ground-truth EP recordings. Finally, we demonstrate how CellMincer's addition to a typical voltage imaging data analysis workflow improves neuronal segmentation, peak detection, and ultimately leads to significantly enhanced separation of functional phenotypes.

FoxO3 Regulates Mouse Bone Mesenchymal Stem Cell Fate and Bone-Fat Balance During Skeletal Aging.

Age-related osteoporosis is characterized by an imbalance between osteogenic and adipogenic differentiation in bone mesenchymal stem cells (BMSCs). Forkhead box O 3 (FoxO3) transcription factor is involved in lifespan and cell differentiation. In this study, we explore whether FoxO3 regulates age-related bone loss and marrow fat accumulation. The expression levels of FoxO3 in BMSCs during aging were detected in vivo and in vitro. To explore the role of FoxO3 in osteogenic and adipogenic differentiation, primary BMSCs were isolated from young and aged mice. FoxO3 expression was modulated by adenoviral vector transfection. The role of FoxO3 in bone-fat balance was evaluated by alizarin red S staining, oil red O staining, quantitative reverse transcription-polymerase chain reaction, Western blot, and histological analysis. Age-related bone loss and fat deposit are associated with downregulation of FoxO3. Overexpression of FoxO3 alleviated age-related bone loss and marrow fat accumulation in aged mice. Mechanistically, FoxO3 reduced adipogenesis and enhanced osteogenesis of BMSCs via downregulation of PPAR-γ and Notch signaling, respectively. In conclusion, FoxO3 is an essential factor controlling the fate of BMSCs and is a potential target for the prevention of age-related osteoporosis.

Percutaneous Transforaminal Endoscopic Surgery (PTES) for Treatment of Lumbar Degenerative Disease in Patients with Underlying Diseases: A Retrospective Cohort Study of 196 Cases.

Objective: To evaluate the postoperative outcomes, safety and feasibility of percutaneous transforaminal endoscopic surgery (PTES) for the treatment of lumbar degenerative disease (LDD) in the patients with underlying diseases. Methods: From June 2017 to April 2019, PTES was performed to treat 226 patients of single-level LDD. According to clinical background, the patients were divided into two groups. A total of 102 patients with underlying diseases were included in group A. The other 124 LDD patients without underlying diseases were included in group B. The occurrence of postoperative complications was recorded. Leg pain was assessed before, immediately, 1 month, 2 months, 3 months, 6 months, 1 year, and 2 years after PTES using VAS, and ODI before PTES and 2 years after PTES were recorded. The therapeutic quality (Excellent, Good, Moderate or Poor) was defined according to MacNab grade at 2-year follow-up. Results: No aggravation of underlying diseases or serious complications was observed in all patients within 6 months after the operation. Altogether, 196 patients were followed up for more than 2 years, 89 patients in group A and 107 patients in group B. The VAS score of leg pain and ODI dropped significantly after surgery (P<0.001) in both groups. One case of group B received PTES again due to recurrence 52 months after surgery. According to MacNab, the excellent and good rate was 97.75% (87/89) in group A and 96.26% (103/107) in group B. In operative duration, frequency of intraoperative fluoroscopy, blood loss, incision length, hospital stay, VAS, ODI, and the excellent and good rate, there was no statistical difference between the two groups. Conclusion: PTES is safe, effective and feasible for the treatment of LDD with underlying diseases, which is comparable to PTES for LDD without underlying diseases. The entrance point of PTES (Gu's Point) is located at the corner of the flat back turning to the lateral side. PTES is not only a minimally invasive surgical technique but also includes a postoperative care system for preventing LDD recurrence.

Exosomes derived from bone marrow mesenchymal stem cells pretreated with decellularized extracellular matrix enhance the alleviation of osteoarthritis through miR-3473b/phosphatase and tensin homolog axis.

BACKGROUND: Osteoarthritis (OA) is a prevalent degenerative articular disease for which there is no effective treatment. Progress has been made in mesenchymal stem cell (MSC)-based therapy in OA, and the efficacy has been demonstrated to be a result of paracrine exosomes from MSCs. Decellularized extracellular matrix (dECM) provides an optimum microenvironment for the expansion of MSCs. In the present study, we aimed to investigate whether exosomes isolated from bone marrow mesenchymal stem cells (BMSCs) with dECM pretreatment (dECM-BMSC-Exos) enhance the amelioration of OA. METHODS: Exosomes from BMSCs with or without dECM pretreatment were isolated. We measured and compared the effect of the BMSC-Exo and dECM-BMSC-Exo on interleukin (IL)-1ß-induced chondrocytes by analyzing proliferation, anabolism and catabolism, migration and apoptosis in vitro. The in vivo experiment was performed by articular injection of exosomes into DMM mice, followed by histological evaluation of cartilage. MicroRNA sequencing of exosomes was performed on BMSC-Exo and dECM-BMSC-Exo to investigate the underlying mechanism. The function of miR-3473b was validated by rescue studies in vitro and in vivo using antagomir-3473b. RESULTS: IL-1ß-treated chondrocytes treated with dECM-BMSC-Exos showed enhanced proliferation, anabolism, migration and anti-apoptosis properties compared to BMSC-Exos. DMM mice injected with dECM-BMSC-Exo showed better cartilage regeneration than those injected with BMSC-Exo. Interestingly, miR-3473b was significantly elevated in dECM-BMSC-Exos and was found to mediate the protective effect in chondrocytes by targeting phosphatase and tensin homolog (PTEN), which activated the PTEN/AKT signaling pathway. CONCLUSIONS: dECM-BMSC-Exo can enhance the alleviation of osteoarthritis via promoting migration, improving anabolism and inhibiting apoptosis of chondrocytes by upregulating miR-3473b, which targets PTEN.

Dahuang Zhechong pill attenuates hepatic sinusoidal capillarization in liver cirrhosis and hepatocellular carcinoma rat model via the MK/integrin signaling pathway.

ETHNOPHARMACOLOGICAL RELEVANCE: Dahuang Zhechong pill (DHZCP), a traditional Chinese medicine, was derived from the famous book Unk "Synopsis of Prescriptions of the Golden Chamber" during the Han dynasty. Owing to its ability to invigorate the circulation of blood in Chinese medicine, DHZCP is usually used for treating liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Clinical application have shown that DHZCP exhibits satisfactory therapeutic effects in HCC adjuvant therapy; however, little is known about its underlying mechanisms. AIM OF THE STUDY: We aimed to clarify the mechanism of DHZCP against hepatic sinusoidal capillarization in rats with LC and HCC by inhibiting the MK/integrin signaling pathway of liver sinusoidal endothelial cells (LSECs). MATERIALS AND METHODS: The contents of 29 characteristic components in DHZCP were determined by ultraperformance liquid chromatography-tandem mass spectrometry. DEN (Diethylnitrosamine)-induced LC and HCC rat models were constructed, and DHZCP was administered when the disease entered the LC stage. After 4 or 12 weeks of administration, hematoxylin and eosin staining, Masson staining, Metavir score, and SSCP (Single strand conformation polymorphism) gene mutation detection were used to confirm tissue fibrosis and cancer. The levels of NO, ET-1 and TXA2, which can regulate vasomotor functions and activate the MK/Itgα6/Src signaling pathway were evaluated by using immunohistochemistry, chemiluminescence, immunofluorescence, Western blot analysis, and enzyme-linked immunosorbent assay (ELISA). Similar methods were also used to evaluate the levels of VEGF, VEGFR, Ang-2 and Tie, which can promote pathological angiogenesis and activate the MK/Itgα4/NF-κB signaling pathway. In vitro cell experiments were performed using potential pharmacodynamic molecules targeting integrins in DHZCP were selected by molecular docking, and the effects of these molecules on the function of LSECs were studied by Itgα4+ and Itgα6+ cell models. RESULTS: At the stage of LC, the animal experiments demonstrated that DHZCP mainly inhibited the MK/Itgα6 signaling pathway to increase the number and size of hepatic sinus fenestration, reversed the ET-1/NO and TXA2/NO ratios, regulated hepatic sinus relaxation and contraction balance, reduced the portal vein pressure, and inhibited cirrhotic carcinogenesis. At the HCC stage, DHZCP could also significantly inhibit the MK/Itgα4 signaling pathway, reduce pathological angiogenesis, and alleviate disease progression. The results of the cell experiments showed that Rhein, Naringenin, Liquiritin and Emodin-8-O-ß-D-glucoside (PMEG) were involved in vascular regulation by affecting the MK/integrin signaling pathway. Liquiritin and PMEG mainly blocked the MK/α6 signal, which is important in regulating the vasomotor function of the liver sinus. Naringenin and Rhein mainly acted by blocked the signaling of MK/α4 action signal, which are potent molecules that inhibit pathological angiogenesis. CONCLUSIONS: DHZCP could improve the hepatic sinusoidal capillarization of LC and HCC by inhibiting the MK/Itgα signaling pathway and inhibited disease progression. Rhein, Naringenin, Liquiritin and PMEG were the main active molecules that affected the MK/Itgα signaling pathway.

Dendritic Cell-Based Vaccines Against Cancer: Challenges, Advances and Future Opportunities.

As the most potent professional antigen presenting cells, dendritic cells (DCs) have the ability to activate both naive CD4 and CD8 T cells. Recognized for their exceptional ability to cross-present exogenous antigens to prime naive antigen-specific CD8 T cells, DCs play a critical role in generating CD8 T cell immunity, as well as mediating CD8 T cell tolerance to tumor antigens. Despite the ability to potentiate host CD8 T cell-mediated anti-tumor immunity, current DC-based cancer vaccines have not yet achieved the promised success clinically with the exception of FDA-approved Provenge. Interestingly, recent studies have shown that type 1 conventional DCs (cDC1s) play a critical role in cross-priming tumor-specific CD8 T cells and determining the anti-tumor efficacy of cancer immunotherapies including immune checkpoint blockade (ICB). Together with promising clinical results in neoantigen-based cancer vaccines, there is a great need for DC-based vaccines to be further developed and refined either as monotherapies or in combination with other immunotherapies. In this review, we will present a brief review of DC development and function, discuss recent progress, and provide a perspective on future directions to realize the promising potential of DC-based cancer vaccines.

How to predict the culprit segment in percutaneous transforaminal endoscopic surgery under local anesthesia for surgical treatment of lumbar degenerative diseases? Radiologic images or clinical symptoms.

Objective: Percutaneous transforaminal endoscopic surgery (PTES) is a novel, minimally invasive technique used to treat lumbar degenerative diseases (LDDs). PTES under local anesthesia was performed to treat the culprit segment of LDDs predicted by radiologic images or clinical symptoms, and the efficacy, security, and feasibility were evaluated. Methods: Eighty-seven cases of LDDs with nerve root symptoms, which were not consistent with lumbar degenerative levels and degrees on MRI and CT, were treated with PTES under local anesthesia in a day surgery ward from January 2015 to December 2019. Forty-two patients, whose culprit segments were predicted by radiologic images, were included in group A. The other 45 patients, whose culprit segments were predicted by clinical symptoms, were included in group B. Leg pain VAS and ODI scores before and after PTES were recorded. The outcome was defined according to the MacNab grade at the 2-year follow-up. Postoperative complications were recorded. Results: In group A, 2 patients underwent PTES for one segment, 37 patients underwent PTES for two segments, and 3 patients underwent PTES for three segments. One of the one-segment PTES patients had no relief from symptoms and underwent another PTES for other culprit segments 3 months after surgery. In group B, 44 of 45 patients were treated using PTES for one segment and 1 patient was treated for two segments. Group B showed significantly less operative duration, less blood loss, and less fluoroscopy frequency than group A (p < 0.001). The leg pain VAS score and the ODI score significantly decreased after the operation in both groups (p < 0.001), and the excellent and good rates were 97.6% (41/42) in group A and 100% (45/45) in group B at the 2-year follow-up. The leg pain VAS score of group B was significantly lower than that of group A immediately and 1 week, 1 month, 2 months, and 3 months after surgery (p < 0.001). There was no statistical difference in ODI scores and the excellent and good rates between the two groups. No complications, such as wound infection or permanent nerve injury, were observed. Conclusion: It is much more accurate to predict the culprit segment according to clinical symptoms than radiologic images in PTES under local anesthesia for surgical treatment of LDDs.

Efficacy and safety of percutaneous transforaminal endoscopic surgery (PTES) compared with MIS-TLIF for surgical treatment of lumbar degenerative disease in elderly patients: A retrospective cohort study.

Objectives: To evaluate the efficacy and safety of PTES for surgical treatment of lumbar degenerative disease (LDD) including lumbar disc herniation, lateral recess stenosis, intervertebral foraminal stenosis and central spinal canal stenosis in elderly patients compared with MIS-TLIF. Methods: From November 2016 to December 2018, 84 elderly patients (>70 years old) of single-level LDD with neurologic symptoms underwent the surgical treatment. 45 patients were treated using PTES under local anesthesia in group 1 and 39 patients treated using MIS-TLIF in group 2. Preoperative, postoperative back and leg pain were evaluated using Visual analog scale (VAS) and the results were determined with Oswestry disability index (ODI) at 2-year follow-up. All complications were recorded. Results: PTES group shows significantly less operation time (55.6 ± 9.7 min vs. 97.2 ± 14.3 min, P < 0.001), less blood loss [11(2-32) ml vs. 70(35-300) ml, P < 0.001], shorter incision length (8.4 ± 1.4 mm vs. 40.6 ± 2.7 mm, P < 0.001), less fluoroscopy frequency [5(5-10) times vs. 7(6-11) times, P < 0.001] and shorter hospital stay[3(2-4) days vs. 7(5-18) days, P < 0.001] than MIS-TLIF group does. Although there was no statistical difference of leg VAS scores between two groups, back VAS scores in PTES group were significantly lower than those in MIS-TLIF group during follow-ups after surgery (P < 0.001). ODI of PTES group was also significantly lower than that of MIS-TLIF group at 2-year follow-up (12.3 ± 3.6% vs. 15.7 ± 4.8%, P < 0.001). Conclusion: Both PTES and MIS-TLIF show favorable clinical outcomes for LDD in elderly patients. Compared with MIS-TLIF, PTES has the advantages including less damage of paraspinal muscle and bone, less blood loss, faster recovery, lower complication rate, which can be performed under local anesthesia.

Accumulation of LDL/ox-LDL in the necrotic region participates in osteonecrosis of the femoral head: a pathological and in vitro study.

BACKGROUND: Osteonecrosis of the femoral head (ONFH) is a common but intractable disease that appears to involve lipid metabolic disorders. Although numerous studies have demonstrated that high blood levels of low-density lipoprotein (LDL) are closely associated with ONFH, there is limited evidence to explain the pathological role of LDL. Pathological and in vitro studies were performed to investigate the role of disordered metabolism of LDL and oxidized LDL (ox-LDL) in the femoral head in the pathology of ONFH. METHODS: Nineteen femoral head specimens from patients with ONFH were obtained for immunohistochemistry analysis. Murine long-bone osteocyte Y4 cells were used to study the effects of LDL/ox-LDL on cell viability, apoptosis, and metabolism process of LDL/ox-LDL in osteocytes in normoxic and hypoxic environments. RESULTS: In the pathological specimens, marked accumulation of LDL/ox-LDL was observed in osteocytes/lacunae of necrotic regions compared with healthy regions. In vitro studies showed that ox-LDL, rather than LDL, reduced the viability and enhanced apoptosis of osteocytes. Pathological sections indicated that the accumulation of ox-LDL was significantly associated with impaired blood supply. Exposure to a hypoxic environment appeared to be a key factor leading to LDL/ox-LDL accumulation by enhancing internalisation and oxidation of LDL in osteocytes. CONCLUSIONS: The accumulation of LDL/ox-LDL in the necrotic region may contribute to the pathology of ONFH. These findings could provide new insights into the prevention and treatment of ONFH.

Connexin 36 Mediates Orofacial Pain Hypersensitivity Through GluK2 and TRPA1.

Trigeminal neuralgia is a debilitating condition, and the pain easily spreads to other parts of the face. Here, we established a mouse model of partial transection of the infraorbital nerve (pT-ION) and found that the Connexin 36 (Cx36) inhibitor mefloquine caused greater alleviation of pT-ION-induced cold allodynia compared to the reduction of mechanical allodynia. Mefloquine reversed the pT-ION-induced upregulation of Cx36, glutamate receptor ionotropic kainate 2 (GluK2), transient receptor potential ankyrin 1 (TRPA1), and phosphorylated extracellular signal regulated kinase (p-ERK) in the trigeminal ganglion. Cold allodynia but not mechanical allodynia induced by pT-ION or by virus-mediated overexpression of Cx36 in the trigeminal ganglion was reversed by the GluK2 antagonist NS102, and knocking down Cx36 expression in Nav1.8-expressing nociceptors by injecting virus into the orofacial skin area of Nav1.8-Cre mice attenuated cold allodynia but not mechanical allodynia. In conclusion, we show that Cx36 contributes greatly to the development of orofacial pain hypersensitivity through GluK2, TRPA1, and p-ERK signaling.

Integrate multi-omics data with biological interaction networks using Multi-view Factorization AutoEncoder (MAE).

BACKGROUND: Comprehensive molecular profiling of various cancers and other diseases has generated vast amounts of multi-omics data. Each type of -omics data corresponds to one feature space, such as gene expression, miRNA expression, DNA methylation, etc. Integrating multi-omics data can link different layers of molecular feature spaces and is crucial to elucidate molecular pathways underlying various diseases. Machine learning approaches to mining multi-omics data hold great promises in uncovering intricate relationships among molecular features. However, due to the "big p, small n" problem (i.e., small sample sizes with high-dimensional features), training a large-scale generalizable deep learning model with multi-omics data alone is very challenging. RESULTS: We developed a method called Multi-view Factorization AutoEncoder (MAE) with network constraints that can seamlessly integrate multi-omics data and domain knowledge such as molecular interaction networks. Our method learns feature and patient embeddings simultaneously with deep representation learning. Both feature representations and patient representations are subject to certain constraints specified as regularization terms in the training objective. By incorporating domain knowledge into the training objective, we implicitly introduced a good inductive bias into the machine learning model, which helps improve model generalizability. We performed extensive experiments on the TCGA datasets and demonstrated the power of integrating multi-omics data and biological interaction networks using our proposed method for predicting target clinical variables. CONCLUSIONS: To alleviate the overfitting problem in deep learning on multi-omics data with the "big p, small n" problem, it is helpful to incorporate biological domain knowledge into the model as inductive biases. It is very promising to design machine learning models that facilitate the seamless integration of large-scale multi-omics data and biomedical domain knowledge for uncovering intricate relationships among molecular features and clinical features.

Affinity network fusion and semi-supervised learning for cancer patient clustering.

Defining subtypes of complex diseases such as cancer and stratifying patient groups with the same disease but different subtypes for targeted treatments is important for personalized and precision medicine. Approaches that incorporate multi-omic data are more advantageous to those using only one data type for patient clustering and disease subtype discovery. However, it is challenging to integrate multi-omic data as they are heterogeneous and noisy. In this paper, we present Affinity Network Fusion (ANF) to integrate multi-omic data for patient clustering. ANF first constructs patient affinity networks for each omic data type, and then calculates a fused network for spectral clustering. We applied ANF to a processed harmonized cancer dataset downloaded from GDC data portal consisting of 2193 patients, and generated promising results on clustering patients into correct disease types. Moreover, we developed a semi-supervised model combining ANF and neural network for few-shot learning. In several cases, the model can achieve greater than 90% accuracy on test set with training less than 1% of the data. This demonstrates the power of ANF in learning a good representation of patients, and shows the great potential of semi-supervised learning in cancer patient clustering. .

Universal screening of both endometrial and colon cancers increases the detection of Lynch syndrome.

BACKGROUND: Lynch syndrome (LS) is the most common hereditary cause of colorectal cancer (CRC) and endometrial cancer (EC). Screening of all CRCs for LS is currently recommended, but screening of ECs is inconsistent. The objective of this study was to determine the added value of screening both CRC and EC tumors in the same population. METHODS: A prospective, immunohistochemistry (IHC)-based screening program for all patients with newly diagnosed CRCs and ECs was initiated in 2011 and 2013, respectively, at 2 centers (primary and tertiary). Genetic testing was recommended for those who had tumors with absent mutS homolog 2 (MSH2), MSH6, or postmeiotoic segregation increased 2 (PMS2) expression and for those who had tumors with absent mutL homolog 1 (MLH1) expression and no v-Raf murine sarcoma viral oncogene homolog B (BRAF) mutation or MLH1 promoter methylation. Amsterdam II criteria, revised Bethesda criteria, and scores from prediction models for gene mutations (the PREMM1,2,6 and PREMM5 prediction models) were ascertained in patients with LS. RESULTS: In total, 1290 patients with CRC and 484 with EC were screened for LS, and genetic testing was recommended for 137 patients (10.6%) and 32 patients (6.6%), respectively (P = .01). LS was identified in 16 patients (1.2%) with CRC and in 8 patients (1.7%) with EC. Among patients for whom genetic testing was recommended, the LS diagnosis rate was higher among those with EC (25.0% vs 11.7%, P = .052). The Amsterdam II criteria, revised Bethesda criteria, and both PREMM calculators would have missed 62.5%, 50.0%, and 12.5% of the identified patients with LS, respectively. CONCLUSIONS: Expanding a universal screening program for LS to include patients who had EC identified 50% more patients with LS, and many of these patients would have been missed by risk assessment tools (including PREMM5 ). Universal screening programs for LS should include both CRC and EC. Cancer 2018. © 2018 American Cancer Society.

Reconstructing context-specific gene regulatory network and identifying modules and network rewiring through data integration.

Reconstructing context-specific transcriptional regulatory network is crucial for deciphering principles of regulatory mechanisms underlying various conditions. Recently studies that reconstructed transcriptional networks have focused on individual organisms or cell types and relied on data repositories of context-free regulatory relationships. Here we present a comprehensive framework to systematically derive putative regulator-target pairs in any given context by integrating context-specific transcriptional profiling and public data repositories of gene regulatory networks. Moreover, our framework can identify core regulatory modules and signature genes underlying global regulatory circuitry, and detect network rewiring and core rewired modules in different contexts by considering gene modules and edge (gene interaction) modules collaboratively. We applied our methods to analyzing Autism RNA-seq experiment data and produced biologically meaningful results. In particular, all 11 hub genes in a predicted rewired autistic regulatory subnetwork have been linked to autism based on literature review. The predicted rewired autistic regulatory network may shed some new insight into disease mechanism.

A tailored approach to BRAF and MLH1 methylation testing in a universal screening program for Lynch syndrome.

To determine the correlation between BRAF genotype and MLH1 promoter methylation in a screening program for Lynch syndrome (LS), a universal screening program for LS was established in two medical centers. Tumors with abnormal MLH1 staining were evaluated for both BRAF V600E genotype and MLH1 promoter methylation. Tumors positive for both were considered sporadic, and genetic testing was recommended for all others. A total 1011 colorectal cancer cases were screened for Lynch syndrome, and 148 (14.6%) exhibited absent MLH1 immunostaining. Both BRAF and MLH1 methylation testing were completed in 126 cases. Concordant results (both positive or both negative) were obtained in 86 (68.3%) and 16 (12.7%) cases, respectively, with 81% concordance overall. The positive and negative predictive values for a BRAF mutation in predicting MLH1 promoter methylation were 98.9% and 41%, respectively, and the negative predictive value fell to 15% in patients ≥70 years old. Using BRAF genotyping as a sole test to evaluate cases with absent MLH1 staining would have increased referral rates for genetic testing by 2.3-fold compared with MLH1 methylation testing alone (31% vs 13.5%, respectively, P<0.01). However, a hybrid approach that reserves MLH1 methylation testing for BRAF wild-type cases only would significantly decrease the number of methylation assays performed and reduce the referral rate for genetic testing to 12.7%. A BRAF mutation has an excellent positive predictive value but poor negative predictive value in predicting MLH1 promoter methylation. A hybrid use of these tests may reduce the number of low-risk patients referred to genetic counseling and facilitate wider implementation of Lynch syndrome screening programs.

Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems.

Omic data analyses pose great informatics challenges. As an emerging subfield of bioinformatics, omics informatics focuses on analyzing multi-omic data efficiently and effectively, and is gaining momentum. There are two underlying trends in the expansion of omics informatics landscape: the explosion of scattered individual omics informatics tools with each of which focuses on a specific task in both single- and multi- omic settings, and the fast-evolving integrated software platforms such as workflow management systems that can assemble multiple tools into pipelines and streamline integrative analysis for complicated tasks. In this survey, we give a holistic view of omics informatics, from scattered individual informatics tools to integrated workflow management systems. We not only outline the landscape and challenges of omics informatics, but also sample a number of widely used and cutting-edge algorithms in omics data analysis to give readers a fine-grained view. We survey various workflow management systems (WMSs), classify them into three levels of WMSs from simple software toolkits to integrated multi-omic analytical platforms, and point out the emerging needs for developing intelligent workflow management systems. We also discuss the challenges, strategies and some existing work in systematic evaluation of omics informatics tools. We conclude by providing future perspectives of emerging fields and new frontiers in omics informatics.

Detection of KRAS mutations using double-stranded toehold-exchange probes.

Detection of KRAS mutations in cancer tissues is immensely valuable for the identification of personalized genotype-based therapy. Here, we employed a double-stranded toehold-exchange probe, which is labeled with fluorescent molecules (FAM) and quenchers (Dabcyl), to detect KRAS mutations in cancer tissues. This probe was able to differentiate the intended mutation in a sample containing as little as 5% mutant alleles in a background of wild-type DNA. This probe also performed robustly at a wide range of conditions, for examples, from 4 °C to 37 °C, from 200 mM Na(+) to 1M Na(+), and from 200 mM K(+) to 500 mM K(+). Furthermore, we validated the practicality of this probe in a clinical setting using 8 pairs of cancer tissue samples and their NT (corresponding adjacent nontumorous tissue) samples. All the results generated from the probe detection agreed with those from direct sequencing. Combining features of extreme high specificity and robustness, this probe is a valuable tool for reliable diagnosis of cancer-related mutations.

Identification of biomarkers for the detection of early stage lung adenocarcinoma by microarray profiling of long noncoding RNAs.

BACKGROUND: Lung adenocarcinoma has one of the poorest outcomes of any cancer worldwide, in part due to the lack of a reliable means of early detection. Long noncoding RNAs (lncRNAs) have been shown to be deregulated in some types of cancer; however, the contributions of lncRNAs to lung adenocarcinoma remain unknown. METHODS: We described the expression profile of lncRNAs in human lung adenocarcinoma at an early stage and the corresponding adjacent nontumorous tissues (NT) by microarray. From the microarray analysis, a total of 1170 lncRNAs were significantly differentially expressed in three early stage lung adenocarcinoma tissues compared with NT (fold-change≥2.0, p≤0.05). Candidate biomarkers were selected from the significantly differentially expressed lncRNAs based on our established filtering pipeline; subsequently, marker optimization and validation by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) on a total of 102 pairs of early stage lung adenocarcinoma and NT samples. RESULTS: A panel of 5-lncRNA was identified that could distinguish early stage lung adenocarcinoma from NT samples with high sensitivity and specificity. The area under the receiver operating characteristic curve (AUC) for tumor identification in the training and validation sets were 0.978 and 0.987, respectively. CONCLUSIONS: Our results are the first to reveal differentially expressed lncRNAs in early stage lung adenocarcinoma and suggest that lncRNAs may be novel candidate biomarkers for the early detection of this disease.

Early Detection of Lung Cancer in Serum by a Panel of MicroRNA Biomarkers.

INTRODUCTION: The objective of the study was to develop a panel of microRNAs (miRNAs) as highly sensitive and specific biomarkers for lung cancer early detection. MATERIALS AND METHODS: The study contained 2 phases: first, preliminary marker selection based on previous reports on the serum of 24 early stage lung cancer patients and 24 healthy control subjects by TaqMan probe-based real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR); and second, validation of miRNA markers on 94 early stage lung cancer, 48 stage III to IV lung cancer, and 111 healthy control serum samples. RESULTS: A total of 3 miRNAs (miR-125a-5p, miR-25, and miR-126) were selected for further analysis in this study. The combination of the 3 miRNAs could produce 0.936 area under the receiver operating characteristic curve value in distinguishing early stage lung cancer patients from control subjects with 87.5% sensitivity and 87.5% specificity, respectively. The diagnostic value of the miRNA panel in an independent set of lung cancer patients confirmed the sensitivity and specificity. CONCLUSION: The results demonstrated that the panel of miRNA biomarkers had the potential for the early detection of lung cancer.