Monitoring hepatocellular carcinoma using tumor content in circulating cell-free DNA.

PURPOSE: To evaluate the utility of tumor content in circulating cell-free DNA (ccfDNA) for monitoring hepatocellular carcinoma (HCC) throughout its natural history. METHODS: We included 67 hepatitis B virus (HBV)-related HCC patients, of whom 17 had paired pre- and post-treatment samples, and 90 controls. Additionally, in a prospective cohort with HBV surface antigen-positive participants recruited in 2012 and followed up biannually with blood sample collections until 2019, we included 270 repeated samples before diagnosis from 63 participants who later developed HCC (pre-HCC samples). Shallow whole-genome sequencing and the ichorCNA method were used to analyze genome-wide copy number and tumor content in ccfDNA. RESULTS: High tumor content was associated with advanced tumor stage (P < 0.001) and a poor survival after HCC diagnosis (HR=12.35; 95% confidence interval [CI]=1.413-107.9; P = 0.023). Tumor content turned negative after surgery (P = 0.027), while remained positive after transarterial chemoembolization treatment (P = 0.578). In non-HCC samples, the mean tumor content (±SD) was 0.011 (±0.007) and had a specificity of 97.8% (95%CI=92.2%-99.7%). In pre-HCC samples, tumor content increased from 0.014 in 4 years before diagnosis to 0.026 in 1 year before diagnosis. The sensitivity of tumor content in detecting HCC increased from 22.7% (95%CI=11.5%-37.8%) within one year before diagnosis to 30.4% (95%CI=13.2%-52.9%) at BCLC stage 0/A, 81.8% (95%CI=59.7%-94.8%) at stage B, and 95.5% (95%CI=77.2%-99.9%) at stage C. CONCLUSIONS: The tumor content in ccfDNA is correlated with tumor burden and may help in monitoring HCC one year earlier than clinical diagnosis and in predicting patient prognosis.

Treatment of intracranial aneurysms with pipeline embolization device: a single-center experience.

Background: Endovascular therapy is the primary treatment modality for intracranial aneurysms (IA). The objective of this study was to assess the effectiveness and safety of a pipeline embolization device (PED) for the treatment of IA. Methods: This retrospective study was conducted at a single center. Data were collected for all patients who underwent PED treatment at the Fourth Affiliated Hospital of Xinjiang Medical University between December 2018 and January 2022. Clinical characteristics, aneurysm-related characteristics, treatment details, and clinical and imaging outcomes were collected and analyzed. Results: A total of 60 consecutive patients with 60 IAs were treated with a PED. The mean age of the participants was 61.8 years, with 53% being female. The average size of the aneurysms was 14.7 mm, with 54 located in the anterior circulation and six in the posterior circulation. The median last follow-up time was 13.0 months (range, 11-24 months). All patients underwent final digital subtraction angiography (DSA) for angiographic follow-up, and 50 aneurysms (83.3%) were completely occluded. The overall complication rate was 3.3%, and there were no reported mortalities. Among the 12 cases of ruptured aneurysms, all of which underwent adjunctive coil embolization, the complete occlusion rate was 91.7% with a complication rate of 16.6% [ischemic complication and modified Rankin scale (mRS) deteriorated]. In the 6 cases of posterior circulation aneurysms (2 in the basilar artery), 5 cases achieved complete occlusion and 1 case achieved near-complete occlusion, with no reported complications or mortality. Conclusions: The use of PEDs appears to be an effective treatment option for IA, demonstrating high occlusion rates and low complication rates. While the application of PEDs for the treatment of ruptured aneurysms did not increase the risk of secondary aneurysm rupture, caution is still warranted due to a higher complication rate. In the treatment of aneurysms of the vertebrobasilar artery using PEDs, this study achieved favorable efficacy outcomes without complications nor patient mortality. However, further studies are needed to validate these findings.

Promising immunotherapy targets: TIM3, LAG3, and TIGIT joined the party.

Immune checkpoint inhibitors (ICIs) have shown great promise as immunotherapy for restoring T cell function and reactivating anti-tumor immunity. The US Food and Drug Administration (FDA) approved the first immune checkpoint inhibitor, ipilimumab, in 2011 for advanced melanoma patients, leading to significant improvements in survival rates. Subsequently, other immune checkpoint-targeting antibodies were tested. Currently, seven ICIs, namely ipilimumab (anti-cytotoxic T lymphocyte-associated protein 4 [CTLA4]), pembrolizumab, nivolumab (anti-programmed cell death protein 1 [PD-1]), atezolizumab, avelumab, durvalumab, and cemiplimab (anti-PD-L1), have been approved for various cancer types. However, the efficacy of antibodies targeting CTLA4 or PD-1/programmed death-ligand 1 (PD-L1) remains suboptimal. Consequently, ongoing studies are evaluating the next generation of ICIs, such as lymphocyte activation gene-3 (LAG3), T cell immunoglobulin and mucin-domain containing 3 (TIM3), and T cell immunoglobulin and ITIM domain (TIGIT). Our review provides a summary of clinical trials evaluating these novel immune checkpoints in cancer treatment.

Coupling coordination and underlying mechanisms of urbanization development and land use efficiency in the Gansu section of the Yellow River Basin.

This swift progression of urbanization has led to increasingly prominent conflicts over the use of land, particularly around its supply and demand. Researchers, both in China and internationally, have underscored the inherent interconnection between urbanization and land utilization. This relationship has gradually become more complex with the development of urbanization. With the implementation of the Yellow River Basin's strategy to preserve the environment while ensuring high-quality development, the Yellow River Basin has become a focal point of attention for numerous scholars. This study centers on the 57 county-level administrative divisions within the Gansu segment of the Yellow River Basin. We employed an extensive array of methodologies, such as GIS technology, the entropy method, data envelopment analysis, the coupling coordination degree model, and the panel vector autoregressive model. We established an index system and a measurement model to evaluate the degree of urbanization and the efficiency of land use. We also investigated the coupling coordinated dynamics between these two variables, to further explore the dynamic interplay between urbanization and land use and reveal their underlying mechanisms. The conclusions are as follows. The urbanization level and efficiency of land use in the Gansu section of the Yellow River Basin have exhibited a consistent upward trajectory, albeit at levels that are not particularly high, indicating substantial room for improvement in the future. The level of coupling coordination between urbanization and land use efficiency in the Gansu section of the Yellow River Basin has shown a generally upward trend. However, the overall coordination level remains relatively low, characterized by an imbalance, with "high coupling but low coordination". Regarding spatial distribution patterns, considerable disparities exist in the level of coordination development, which generally decreases from the eastern toward the western regions. A strong reciprocal and interactive relationship exists between the urbanization level and land use efficiency. An elevated level of economic urbanization can initially stimulate land use efficiency. Similarly, the improvement in the level of population urbanization, social urbanization, and ecological urbanization tends to exert a restraining influence on the augmentation of land use efficiency. Conversely, the enhancement of land use efficiency makes a distinct contribution to promoting the elevation of the urbanization level.

Chronic Central Serous Chorioretinopathy in Elderly Subjects: Structure and Blood Flow Characteristics of Retina and Choroid.

INTRODUCTION: With advancements in imaging technology, researchers have been able to identify more distinctive imaging features of central serous chorioretinopathy (CSC). However, existing research primarily concentrates on young patients aged 50 years and below, leaving a dearth of studies on elderly CSC patients. Previous studies indicate that elderly CSC patients may exhibit unique imaging characteristics and have a clinical prognosis that significantly differs from younger patients. This study aimed to evaluate the characteristics of retina, choroid structure, and blood flow in elderly patients with chronic CSC (cCSC) examined multimode imaging and try to find new pathogenesis information of it. METHODS: Using a cut-off age of 50 years, patients with chronic central serous chorioretinopathy were divided into two groups: older and younger. The control group consisted of 40 healthy individuals, with their right eyes assigned. Various clinical features were recorded, including the incidence of ellipsoid zone rupture (EZ-), fibrin in the subretinal fluid (SRF), pachydrusen, subretinal drusenoid deposits (SDD), pigment epithelial detachment (PED), double-layer sign (DLS), and choroidal lipid globule cavern. Measurements were taken for the thickness of the outer nuclear layer (ONL), the length of the extended outer photoreceptor segment (POS), the height and width of SRF, the vascular density of each layer of the retinal capillary plexus, the central macular thickness (CMT), and the subfoveal choroidal thickness (SFCT). RESULTS: The proportion of females in the elderly group (43.75%) was significantly higher than that in the youth group (22.41%) (p = 0.034). The degree of hyperopia in the elderly group (1.03 ± 0.73) was higher than that in the youth group (0.26 ± 1.06), with a significant difference in BCVA (p = 0.05). The thickness of SFCT, CMT, ONL in the elderly group, and the length of photoreceptor outer segment in the elderly group were thinner than those in the youth group (p < 0.05). Choroidal capillary perfusion area (CCPA), macular area, and paramacular area were lower in the elderly group than those in the youth group in the full scan range (p < 0.05). The blood flow densities of deep capillary plexus (DCP), intermediate capillary plexus (ICP), and superficial capillary plexus (SCP) in the whole scan range, macular area, and paramacular area were lower in the elderly group than in the youth group, but the differences were not statistically significant. CONCLUSIONS: In conclusion, our data suggest that elderly patients with cCSC may experience different disease outcomes. Elderly cCSC patients exhibit less gender bias, poorer vision, more severe structural damage and ischemia in the choroid and retina, and have a higher risk of developing choroidal neovascularization.

Circulating Tumor DNA Profiling Approach Based on In Silico Background Elimination Guides Chemotherapy in Nasopharyngeal Carcinoma.

Circulating tumor DNA (ctDNA) analysis increasingly provides a promising minimally invasive alternative to tissue biopsies in precision oncology. However, there are no ctDNA analysis approaches available in nasopharyngeal carcinoma (NPC) and current methods of ctDNA mutation profiling have limited resolution because of the high background noise and false-positive rate caused by benign variants in plasma cell-free DNA (cfDNA), majorly generated during clonal hematopoiesis. Although personalized parallel white blood cell genome sequencing suppresses the noise of clonal hematopoiesis variances, the system cost and complexity restrict its extensive application in clinical settings. We developed Matched WBC Genome sequencing Independent CtDNA profiling (MaGIC) approaches, which synergically integrated a ctDNA capturing panel for a hybrid capture cfDNA deep sequencing, in silico background elimination, and a reliable readout measurement. We profiled the ctDNAs of 80 plasma samples from 40 patients with NPC before and during chemotherapy by MaGICs. In addition, the public cfDNA sequencing data and The Cancer Genome Atlas project data were analyzed by MaGICs to evaluate their application in other scenarios of patient classification. The MaGIC version-2 has the ability to predict the chemosensitivity of patients with NPC with high accuracy by utilizing a single sample of liquid biopsy from each patient prior to a standardized treatment regimen. Moreover, both versions of MaGICs are of ideal performance in the diagnosis of patients with prostate cancer by liquid biopsy and prognosis prediction of multiple cancers by tissue biopsy. This study has the potential to enhance the sensitivity and expand the application scope of ctDNA detection, independently of other paired genome sequencing methods. As a result, it might further increase the clinical utilization of liquid biopsy based on ctDNA.

Endovascular re-canalization for symptomatic non-acute intracranial large artery occlusion: a single-center retrospective study.

Background: Managing patients with symptomatic non-acute intracranial large artery occlusion (SNA-ILAO) poses a significant challenge due to the high morbidity and risk of recurrent critical ischemic events, even with standard medical therapy. This unique subgroup of patients requires specialized attention. The aim of this study is to evaluate the feasibility and safety of endovascular interventional recanalization for SNA-ILAO. Methods: We retrospectively collected data of patients with SNA-ILAO who underwent endovascular interventional therapy at the Fourth Affiliated Hospital of Xinjiang Medical University from 2018 to 2021. The collected data included clinical demography, imaging data, treatment details, and prognosis. Follow-up imaging assessments were conducted for the patients, and descriptive statistics were performed. Results: A total of 24 patients were enrolled, with a majority being male (58.3%) and a mean age of 62.0±9.3 years. The pre-treatment median modified Rankin scale (mRS) and the National Institutes of Health Stroke Scale (NIHSS) scores at baseline were 3 and 1, respectively. The most common occlusion location was the middle cerebral artery (MCA), including M1 (70.8%), M2 (20.8%), and M3 (4.7%). Successful recanalization was achieved in all 24 patients, with 21 cases (87.5%) achieving thrombolysis in cerebral infarction (TICI) 3 reperfusion and the remaining 3 cases (12.5%) achieving TICI 2b reperfusion. Asymptomatic intracranial hemorrhage (ICH) occurred in 2 patients (8.3%). During the first 30-day clinical follow-up, none of these patients experienced any recurrent cerebral ischemic events. During the 29.5-month follow-up period for vessel imaging, only 12.5% (3/24) of patients who had follow-up imaging experienced re-stenosis. Conclusions: Endovascular recanalization is a potentially safe and effective procedure for patients with SNA-ILAO. However, it is important to note that there is still a non-negligible rate of complications associated with this treatment. Therefore, exercising caution and implementing strict controls when administering this procedure is crucial.

RNF8 depletion attenuates hepatocellular carcinoma progression by inhibiting epithelial-mesenchymal transition and enhancing drug sensitivity.

Despite substantial advances that have been made in understanding the etiology of hepatocellular carcinoma (HCC), the early-stage diagnosis and treatment of advanced-stage HCC remain a major challenge. RNF8, an E3 ligase important for the DNA damage response, has been proven to facilitate the progression of breast and lung cancer, but its role in HCC remains unclear. In this study, we find that the expression of RNF8 is up-regulated in HCC tissues and positively correlated with poor prognosis of HCC. Furthermore, silencing RNF8 by siRNAs attenuates the migration of HCC cells and inhibits epithelial-mesenchymal transition (EMT) by regulating the expressions of proteins including N-cadherin, ß-catenin, snail, and ZO-1. Moreover, Kaplan‒Meier survival analysis shows that high RNF8 expression predicts poor survival benefits from sorafenib. Finally, cell viability assay demonstrates that RNF8 depletion enhances the sensitivity of HCC cells to sorafenib and lenvatinib treatment. We hypothesize that the inhibitory role of RNF8 in EMT and its enhancing effects on anti-cancer drugs orchestrate the protective effects of RNF8 deficiency in HCC, which indicates its potential in clinical application.

Effect of Energy Utilization and Economic Growth on the Ecological Environment in the Yellow River Basin.

In the 21st century, problems relating to energy, economy, and the environment have become increasingly severe across the world, and critical issues around environmental pollution, ecological imbalance, and an energy crisis have emerged. The Yellow River basin is an important ecological barrier, economic region, and energy base in Northern China. Environmental pollution in the Yellow River basin has become increasingly problematic, especially since the reform and opening up of China, along with the rapid development of the industrial economy and mining for energy resources. In this study, 64 of the 73 prefecture-level cities in the Yellow River basin were selected as the research object, including 18 cities in the downstream region, 26 cities in the midstream region, and 20 cities in the upstream region. The data used in this study were from 2004 to 2019. On the basis of temporal variation and spatial differentiation of the three factors of economy, energy, and environment, the impulse response function and the generalized method of moments (GMM) were adopted to evaluate the effects of energy utilization and economic growth on the ecological environment. Their roles in affecting the ecological environment were analyzed along with the underlying mechanisms. Overall, energy utilization, economic growth, and ecological environment are in good condition, showing a steady upward trend. Regional differences still exist, but the gap is gradually narrowing. There are some differences in the impulse response of the ecological environment to the economic growth and energy utilization in the upstream, midstream, and downstream regions of the Yellow River basin. The effect is leveled out or weakened in the middle and later phases of the impact. Compared with the downstream and upstream regions, economic growth and energy utilization in the midstream regions have less impact on the ecological environment. The two factors of energy utilization potential and economic potential have significant positive impacts on the ecological environment. The current situation of energy utilization has to some extent a positive impact on the ecological environment. Economic scale has a certain negative impact on the ecological environment.

An experimental model for ovarian cancer: propagation of ovarian cancer initiating cells and generation of ovarian cancer organoids.

BACKGROUND: Ovarian cancer (OC) is the most lethal gynecological cancer due to the recurrence of drug-resistance. Cancer initiating cells (CICs) are proposed to be responsible for the aggressiveness of OC. The rarity and difficulty of in vitro long-term cultivation of CICs challenge the development of CIC-targeting therapeutics. Reprogramming cancer cells into induced cancer initiating cell (iCICs) could be an approach to solve these. Several inducible CICs have been acquired by activating the expression of stemness genes in different cancer cells. However, few reports have demonstrated the feasibility in OC. METHODS: Patients with primary OC receiving surgery were enrolled. Tumor tissue were collected, and OCT4, SOX2, and NANOG expressions were assessed by immunohistochemistry (IHC) staining to investigate the association of stemness markers with overall survival (OS). An high-grade serous ovarian cancer (HGSOC) cell line, OVCAR-3 was reprogrammed by transducing Yamanaka four factors OCT4, SOX2, KLF4 and MYC (OSKM) to establish an iOCIC model, iOVCAR-3-OSKM. CIC characteristics of iOVCAR-3-OSKM were evaluated by RT-PCR, sphere formation assay and animal experiments. Drug-resistance and migration ability were accessed by dye-efflux activity assay, MTT assay and migration assay. Gene profile was presented through RNA-sequencing. Lineage differentiation ability and organoid culture were determined by in vitro differentiation assays. RESULTS: In OC patients, the co-expression of multiple stem-related transcription factors (OCT4, SOX2, and NANOG) was associated with worse OS. iOVCAR-3-OSKM cells generated by reprogramming successfully exhibited stemness characteristics with strong sphere-forming and tumorigenesis ability. iOVCAR-3-OSKM cells also showed malignant potential with higher drug resistance to chemodrug, Paclitaxel (PTX) and migration ability. iOVCAR-3-OSKM was maintainable and expandable on feeder-dependent culture condition, it also preserved ovarian lineage differentiation abilities, which could well differentiate into OC cells with CK-7 and CA125 expressions and develop into an organoid mimic poor prognostic OC histological feature. CONCLUSIONS: The establishment of iOVCAR-3-OSKM not only allows us to fill the gap in the information on induced CICs in OC but also provides a potential strategy to develop personalized CICs and organoid models for treating OC in the near future.

Prime Editing: An All-Rounder for Genome Editing.

Prime editing (PE), as a "search-and-replace" genome editing technology, has shown the attractive potential of versatile genome editing ability, which is, in principle, currently superior to other well-established genome-editing technologies in the all-in-one operation scope. However, essential technological solutions of PE technology, such as the improvement of genome editing efficiency, the inhibition of potential off-targets and intended edits accounting for unexpected side-effects, and the development of effective delivery systems, are necessary to broaden its application. Since the advent of PE, many optimizations have been performed on PE systems to improve their performance, resulting in bright prospects for application in many fields. This review briefly discusses the development of PE technology, including its functional principle, noteworthy barriers restraining its application, current efforts in technical optimization, and its application directions and potential risks. This review may provide a concise and informative insight into the burgeoning field of PE, highlight the exciting prospects for this powerful tool, and provide clues for questions that may propel the field forward.

A functional reference map of the RNF8 interactome in cancer.

BACKGROUND: RNF8 is an E3 ligase identified as a critical DNA damage-responsive protein. Recently, multiple reports have shown that RNF8 could be used as an important therapeutic target for cancer chemo/radiotherapy. However, the understanding of RNF8 remains limited due to the lack of its interactome reference map and comprehensive analysis of RNF8 in diverse cancers, which underscores the need to map the interactome of RNF8 via high-throughput methods. RESULTS: A two-way identification method based on LC-MS was designed for the identification of the RNF8 interactome with high-specificity. By in silico analysis and in vitro validation, we identified a new reference map of the RNF8 interactome network containing many new targets, such as YBX1, DNMT1, and HDCA1, new biological functions and the gene-disease associations of RNF8. Our results revealed a close relationship between RNF8 and neurodegenerative diseases or tumor-infiltrating immune cells using bulk RNA-seq and scRNA-seq datasets. As a proof of concept of our interactome map, we validated the direct binding between RNF8 and YBX1 and showed that RNF8 catalyzed the ubiquitination of YBX1. These results demonstrated that RNF8 might be a crucial regulator of YBX1. CONCLUSIONS: Our work provides a unique framework for researchers and clinicians who seek to better explore or understand RNF8-regulated biological functions in cancers. This study will hopefully facilitate the rational design and further development of anti-RNF8 therapy in cancers.

The Transcription Factor ThPOK Regulates ILC3 Lineage Homeostasis and Function During Intestinal Infection.

Innate lymphoid cells (ILCs) have been identified as a heterogeneous population of lymphocytes that mirrors the cytokine and transcriptional profile of adaptive T cells. The dynamic balance between key transcription factors determines the heterogeneity, plasticity, and functions of ILC subsets. The transcription factor ThPOK is highly conserved in biological evolution and exerts pivotal functions in the differentiation of T cells. However, the function of ThPOK in ILC3s has not been identified. Here, we found that ThPOK regulated the homeostasis of ILC3s, as mice lacking ThPOK showed decreased NKp46+ ILC3s and increased CCR6- NKp46- ILC3s. ThPOK-deficient mice were more sensitive to S. typhimurium infection due to the impaired IFN-γ secretion of NKp46+ ILC3s. Furthermore, ThPOK participates in ILC3-mediated control of C. rodentium infection by negatively regulating IL-17A secretion. ThPOK preserves the identity of NKp46+ ILC3s by repressing RORγt, which indirectly releases T-bet expression. On the molecular level, ThPOK directly binds to Rorc and Il23r to restrain their expression which further modulates IL-17A secretion. Collectively, our analysis revealed a critical role of ThPOK in the homeostasis and functions of ILC3 subsets.

Effects of Industrial Structure Adjustment on Pollutants Discharged to the Aquatic Environment in Northwest China.

Northwest China is located along China's Belt and Road Initiative routes and represents the frontier and core region for China's construction and development of the Silk Road Economic Belt. In recent years, the conflict between economic development and environmental pollution has become increasingly intense in this region, with the latter mainly caused by disorderly industrialization brought about by rapid urbanization processes. Inappropriate industrial structure is the primary reason for environmental degradation in Northwest China, which has limited precipitation and available water. Due to its fragile aquatic environment and unsustainable use of water resources, the pollution and degradation of the aquatic environment has become a bottleneck that severely restricts the sustainable development of China's northwest region. In the present study, five provinces or autonomous regions in Northwest China were selected as the study objects. Based on the vector autoregressive (VAR) model, quantitative research methods, such as impulse response function and variance decomposition analysis, were applied to quantify the dynamics between industrial structure adjustment and changes in industrial pollutant discharges to the aquatic environment, so that the impact of industrial structure adjustment on pollutants discharged to the aquatic environment could be quantified and characterized. Therefore, the present study has both theoretical and practical significance. The conclusions are as follows: (1) In general, industrial structure in most provinces in Northwest China imposes a positive effect over the discharge of pollutants to the aquatic environment. Adjusting industrial structure and reducing the proportion of secondary industry present can to some extent promote reductions in the discharge of pollutants to the aquatic environment. However, such beneficial effects may vary among different provinces. (2) Specifically, for Gansu, province industrial structure adjustment could help reduce the discharge of pollutants to the aquatic environment effectively during the early stages, but this positive effect gradually weakens and disappears during the later stages. In Qinghai province, industrial structure adjustment could not help reduce the discharge of pollutants to the aquatic environment effectively during the early stages, but a positive effect gradually increases and continues to function later. The performance in Shaanxi and Xinjiang provinces was quite similar, with industrial structure adjustment helping to effectively reduce the discharge of pollutants to the aquatic environment over a long period of time. This positive effect can play a more sustained and stable role. For Ningxia province, industrial structure adjustment can not only help significantly reduce the discharge of pollutants to the aquatic environment but also displays a significant positive effect. (3) Given the specific conditions and characteristics of the region under study, relevant policies for industrial structure adjustment should be formulated and implemented.

Characterizing Relevant MicroRNA Editing Sites in Parkinson's Disease.

MicroRNAs (miRNAs) are extensively edited in human brains. However, the functional relevance of the miRNA editome is largely unknown in Parkinson's disease (PD). By analyzing small RNA sequencing profiles of brain tissues of 43 PD patients and 88 normal controls, we found that the editing levels of five A-to-I and two C-to-U editing sites are significantly correlated with the ages of normal controls, which is disrupted in PD patients. We totally identified 362 miRNA editing sites with significantly different editing levels in prefrontal cortices of PD patients (PD-PC) compared to results of normal controls. We experimentally validated that A-to-I edited miR-497-5p, with significantly higher expression levels in PD-PC compared to normal controls, directly represses OPA1 and VAPB. Furthermore, overexpression of A-to-I edited miR-497-5p downregulates OPA1 and VAPB in two cell lines, and inhibits proliferation of glioma cells. These results suggest that the hyperediting of miR-497-5p in PD contributes to enhanced progressive neurodegeneration of PD patients. Our results provide new insights into the mechanistic understanding, novel diagnostics, and therapeutic clues of PD.

Deep RNA Sequencing Revealed Fusion Junctional Heterogeneity May Predict Crizotinib Treatment Efficacy in ALK-Rearranged NSCLC.

INTRODUCTION: Gene fusion variants in ALK-rearranged NSCLC may predict patient outcomes, but previous results have been inconclusive. Fusion isoforms coexisting in the same tumor may affect the efficacy of targeted therapy, but they have not been investigated. METHODS: Patients with ALK-rearranged NSCLC who received crizotinib treatments were recruited. Precrizotinib tumor tissues were analyzed by the anchored multiplex polymerase chain reaction for targeted RNA sequencing. Kaplan-Meier and Cox regression were used to compare overall and progression-free survivals. RESULTS: Of the 51 studied subjects, EML4-ALK variant types v1, v2, v3, and others were detected in 23 (45.1%), five (9.8%), 19 (37.3%), and four patients (7.8%), respectively. Multiple EML4-ALK RNA isoforms were detected in 24 tumors (47.1%), and single isoform in 27 (52.9%). Most of the v3 tumors (16 of 19) harbored both v3a and v3b RNA isoforms. Multiple isoforms were also detected in eight non-v3 tumors (33.3% of all 24 multiple isoforms; five v1, two v5', and one v2). Compared with patients with single isoform, those with multiple isoforms had worse progression-free (hazard ratio and 95% confidence interval: 2.45 [1.06-5.69]) and overall (hazard ratio [95% confidence interval]: 3.74 [1.26-11.13]) survivals after adjusting for potential confounders including variant type. Using the patient-derived H2228 cells known to express v3a and v3b, our single-cell polymerase chain reaction detected either v3a or v3b in most single cells. Treatment of H2228 cells by three ALK inhibitors revealed increased ratios of v3a-to-v3b expression over time. CONCLUSIONS: Intratumoral EML4-ALK isoforms may predict the efficacy of targeted therapy in ALK-rearranged NSCLC. Temporal changes of intratumoral fusion isoforms may result from differential selection pressures that a drug might have on one isoform over another. Larger studies on fusion heterogeneity using RNA sequencing are warranted.

Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson's disease.

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease. However, it is unclear whether microbiota and metabolites have demonstrated changes at early PD due to the difficulties in diagnosis and identification of early PD in clinical practice. In a previous study, we generated A53T transgenic monkeys with early Parkinson's symptoms, including anxiety and cognitive impairment. Here we analyzed the gut microbiota by metagenomic sequencing and metabolites by targeted gas chromatography. The gut microbiota analysis showed that the A53T monkeys have higher degree of diversity in gut microbiota with significantly elevated Sybergistetes, Akkermansia, and Eggerthella lenta compared with control monkeys. Prevotella significantly decreased in A53T transgenic monkeys. Glyceric acid, L-Aspartic acid, and p-Hydroxyphenylacetic acid were significantly elevated, whereas Myristic acid and 3-Methylindole were significantly decreased in A53T monkeys. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (KO0131) and the oxidative phosphorylation reaction (KO2147) were significantly increased in metabolic pathways of A53T monkeys. Our study suggested that the transgenic A53T and α-syn aggregation may affect the intestine microbiota and metabolites of rhesus monkeys, and the identified five compositional different metabolites that are mainly associated with mitochondrial dysfunction may be related to the pathogenesis of PD.

Application of Data Science in Circulating Tumor DNA Detection: A Promising Avenue Towards Liquid Biopsy.

The circulating tumor DNA (ctDNA), as a promising biomarker of liquid biopsy, has potential clinical relevance on the molecular diagnosis and monitoring of cancer. However, the trace concentration level of ctDNA in the peripheral blood restricts its extensive clinical application. Recently, high-throughput-based methodologies have been leveraged to improve the sensitivity and specificity of ctDNA detection, showing a promising avenue towards liquid biopsy. This review briefly summarizes the high-throughput data features concerned by current ctDNA detection strategies and the technical obstacles, potential solutions, and clinical relevance of current ctDNA profiling technologies. We also highlight future directions improving the limit of detection of ctDNA for better clinical application. This review may serve as a reference for the crosslinks between data science and ctDNA-based liquid biopsy, benefiting clinical translation in advanced cancer diagnosis.

Attenuation of Antiviral Immune Response Caused by Perturbation of TRIM25-Mediated RIG-I Activation under Simulated Microgravity.

Microgravity is a major environmental factor of space flight that triggers dysregulation of the immune system and increases clinical risks for deep-space-exploration crews. However, systematic studies and molecular mechanisms of the adverse effects of microgravity on the immune system in animal models are limited. Here, we establish a ground-based zebrafish disease model of microgravity for the research of space immunology. RNA sequencing analysis demonstrates that the retinoic-acid-inducible gene (RIG)-I-like receptor (RLR) and the Toll-like receptor (TLR) signaling pathways are significantly compromised by simulated microgravity (Sµg). TRIM25, an essential E3 for RLR signaling, is inhibited under Sµg, hampering the K63-linked ubiquitination of RIG-I and the following function-induction positive feedback loop of antiviral immune response. These mechanisms provide insights into better understanding of the effects and principles of microgravity on host antiviral immunity and present broad potential implications for developing strategies that can prevent and control viral diseases during space flight.