Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

ACAP1 Deficiency Predicts Inferior Immunotherapy Response in Solid Tumors

Background: ACAP1 plays a key role in endocytic recycling, which is essential for the normal function of lymphocytes. However, the expression and function of ACAP1 in lymphocytes have rarely been studied. Methods: Large-scale genomic data, including multiple bulk RNA-sequencing datasets, single-cell sequencing datasets, and immunotherapy cohorts, were exploited to comprehensively characterize ACAP1 expression, regulation, and function. Gene set enrichment analysis (GSEA) was used to uncover the pathways associated with ACAP1 expression. Eight algorithms, including TIMER, CIBERSORT, CIBERSORT-ABS, QUANTISEQ, xCELL, MCPCOUNTER, EPIC, and TIDE, were applied to estimate the infiltrating level of immune cells. Western blotting, qPCR, and ChIP-PCR were used to validate the findings from bioinformatic analyses. A T-cell co-culture killing assay was used to investigate the function of ACAP1 in lymphocytes. Results: ACAP1 was highly expressed in immune-related tissues and cells and minimally in other tissues. Moreover, single-cell sequencing analysis in tumor samples revealed that ACAP1 is expressed primarily in tumor-infiltrating lymphocytes (TILs), including T, B, and NK cells. ACAP1 expression is negatively regulated by promoter DNA methylation, with its promoter hypo-methylated in immune cells but hyper-methylated in other cells. Furthermore, SPI1 binds to the ACAP1 promoter and positively regulates its expression in immune cells. ACAP1 levels positively correlate with the infiltrating levels of TILs, especially CD8+ T cells, across a broad range of solid cancer types. ACAP1 deficiency is associated with poor prognosis and immunotherapeutic response in multiple cancer types treated with checkpoint blockade therapy (ICT). Functionally, the depletion of ACAP1 by RNA interference significantly impairs the T cell-mediated killing of tumor cells. Conclusions: Our study demonstrates that ACAP1 is essential for the normal function of TILs, and its deficiency indicates an immunologically “cold” status of tumors that are resistant to ICT

Refinement and validation of a comprehensive clinical diagnostic model (GAMAD) based on gender, age, multitarget circulating tumour DNA methylation signature and commonly used serological biomarkers for early detection of hepatocellular carcinoma: a multicentre, prospective observational study protocol

Introduction Prompt detection of hepatocellular carcinoma (HCC) in patients with chronic liver diseases is critical for enhancing prognosis. Existing imaging techniques and serum markers fall short of clinical needs. This study aims to establish a non-invasive diagnostic model for early HCC detection in the Chinese population.Methods and analysis This prospective, multicentre, observational study will enrol 2000 participants, including HCC patients, those with chronic liver diseases (hepatitis, cirrhosis and benign liver space-occupying lesions), and healthy individuals. The study will collect demographic data and blood samples, which will be used to test α-fetoprotein (AFP), des-γ-carboxy-prothrombin (DCP) and circulating tumour DNA (ctDNA) methylation. The GAMAD (Gender+Age+Methylation+AFP+DCP) model involving gender, age, ctDNA methylation signature, AFP and DCP will be developed and blindly validated in training and validation sets (1400 and 600 cases, respectively). Primary endpoints include sensitivity, specificity and accuracy (receiver operating characteristic curves; area under the curve value) of GAMAD for HCC and/or high-risk HCC groups. Secondary endpoints involve comparing GAMAD with the established GALAD (Gender+Age+AFP-L3+AFP+DCP) model and each blood index (AFP, DCP and methylation signature) to evaluate: (1) GAMAD’s clinical utility for HCC patients in all stages according to different staging systems; (2) GAMAD’s discrimination ability for patients in various subgroups, including liver cirrhosis (LC) related HCC and LC, hepatitis B virus (HBV) related HCC and HBV, hepatitis C virus (HCV) related HCC and HCV, and non-alcoholic fatty liver disease (NAFLD) related HCC and NAFLD.Ethics and dissemination This trial has been approved by the Medical Ethics Committees of the First Hospital of Jilin University (#22K073-001), the Eastern Hepatobiliary Surgery Hospital, Naval Medical University (#EHBHKY2023-H0003-P001) and Tianjin Third Central Hospital (#IRB2023-007-01). All participants in the trial will provide written informed consent. Results of this study will be disseminated in peer-reviewed scientific journals and at conferences nationally and internationally.Trial registration number NCT05626985

Sorafenib Nanomicelles Effectively Shrink Tumors by Vaginal Administration for Preoperative Chemotherapy of Cervical Cancer

To investigate the potential of sorafenib (SF) in preoperative chemotherapy for cervical cancer to reduce tumor volume, sorafenib micelles (SF micelles) with good stability and high drug loading were designed. SF micelles were prepared by film hydration followed by the ultrasonic method. The results showed that the SF micelles were spherical with an average particle size of 67.18 ± 0.66 nm (PDI 0.17 ± 0.01), a considerable drug loading of 15.9 ± 0.46% (w/w%) and satisfactory stability in buffers containing plasma or not for at least 2 days. In vitro release showed that SF was gradually released from SF micelles and almost completely released on the third day. The results of in vitro cellular intake, cytotoxicity and proliferation of cervical cancer cell TC-1 showed that SF micelles were superior to sorafenib (Free SF). For intravaginal administration, SF micelles were dispersed in HPMC (SF micelles/HPMC), showed good viscosity sustained-release profiles in vitro and exhibited extended residence in intravaginal in vivo. Compared with SF micelles dispersed in N.S. (SF micelles/N.S.), SF micelles/HPMC significantly reduced tumor size with a tumor weight inhibition rate of 73%. The results suggested that SF micelles had good potential for preoperative tumor shrinkage and improving the quality life of patients

Sequential Release of Paclitaxel and Imatinib from Core–Shell Microparticles Prepared by Coaxial Electrospray for Vaginal Therapy of Cervical Cancer

To optimize the anti-tumor efficacy of combination therapy with paclitaxel (PTX) and imatinib (IMN), we used coaxial electrospray to prepare sequential-release core–shell microparticles composed of a PTX-loaded sodium hyaluronate outer layer and an IMN-loaded PLGA core. The morphology, size distribution, drug loading, differential scanning calorimetry (DSC), Fourier transform infrared spectra (FTIR), in vitro release, PLGA degradation, cellular growth inhibition, in vivo vaginal retention, anti-tumor efficacy, and local irritation in a murine orthotopic cervicovaginal tumor model after vaginal administration were characterized. The results show that such core–shell microparticles were of spherical appearance, with an average size of 14.65 μm and a significant drug-loading ratio (2.36% for PTX, 19.5% for IMN, w/w), which might benefit cytotoxicity against cervical-cancer-related TC-1 cells. The DSC curves indicate changes in the phase state of PTX and IMN after encapsulation in microparticles. The FTIR spectra show that drug and excipients are compatible with each other. The release profiles show sequential characteristics in that PTX was almost completely released in 1 h and IMN was continuously released for 7 days. These core–shell microparticles showed synergistic inhibition in the growth of TC-1 cells. Such microparticles exhibited prolonged intravaginal residence, a >90% tumor inhibitory rate, and minimal mucosal irritation after intravaginal administration. All results suggest that such microparticles potentially provide a non-invasive local chemotherapeutic delivery system for the treatment of cervical cancer by the sequential release of PTX and IMN

Frequency-dependent and time-variant alterations of neural activity in post-stroke depression: A resting-state fMRI study

Background: Post-stroke depression (PSD) is one of the most frequent psychiatric disorders after stroke. However, the underlying brain mechanism of PSD remains unclarified. Using the amplitude of low-frequency fluctuation (ALFF) approach, we aimed to investigate the abnormalities of neural activity in PSD patients, and further explored the frequency and time properties of ALFF changes in PSD. Methods: Resting-state fMRI data and clinical data were collected from 39 PSD patients (PSD), 82 S patients without depression (Stroke), and 74 age- and sex-matched healthy controls (HC). ALFF across three frequency bands (ALFF-Classic: 0.01–0.08 Hz; ALFF-Slow4: 0.027–0.073 Hz; ALFF-Slow5: 0.01–0.027 Hz) and dynamic ALFF (dALFF) were computed and compared among three groups. Ridge regression analyses and spearman’s correlation analyses were further applied to explore the relationship between PSD-specific alterations and depression severity in PSD. Results: We found that PSD-specific alterations of ALFF were frequency-dependent and time-variant. Specially, compared to both Stroke and HC groups, PSD exhibited increased ALFF in the contralesional dorsolateral prefrontal cortex (DLPFC) and insula in all three frequency bands. Increased ALFF in ipsilesional DLPFC were observed in both slow-4 and classic frequency bands which were positively correlated with depression scales in PSD, while increased ALFF in the bilateral hippocampus and contralesional rolandic operculum were only found in slow-5 frequency band. These PSD-specific alterations in different frequency bands could predict depression severity. Moreover, decreased dALFF in contralesional superior temporal gyrus were observed in PSD group. Limitations: Longitudinal studies are required to explore the alterations of ALFF in PSD as the disease progress. Conclusions: The frequency-dependent and time-variant properties of ALFF could reflect the PSD-specific alterations in complementary ways, which may assist to elucidate underlying neural mechanisms and be helpful for early diagnosis and interventions for the disease

Different scoring systems to predict 6-week mortality in cirrhosis patients with acute variceal bleeding: a retrospective analysis of 202 patients

<p><b>Objective:</b> Determine the optimal scoring system for evaluation of 6-week bleeding-related mortality in liver cirrhosis patients with acute variceal bleeding (AVB). Prediction effects of six scoring systems, AIMS65 score, Glasgow-Blatchford (GBS) score, full Rockall (FRS) score, the model for end-stage liver disease (MELD), the MELD-Na model and the Child-Turcotte-Pugh (CTP) score were analyzed in this study.</p> <p><b>Methods:</b> A total of 202 liver cirrhosis patients with AVB were enrolled between 1 January 2014, and 31 December 2014. All subjects were scored according to AIMS65, GBS, FRS, MELD, MELD-Na and CTP scoring systems on the first day of admission. The primary endpoint of the study was 6-week mortality. The prediction effect of these scoring systems for 6-week mortality was compared by ROC curve and the area under the curve (AUC).</p> <p><b>Results:</b> The scores of nonsurvival group evaluated by the AIMS65, GBS, FRS, MELD, MELD-Na and CTP (2.6 ± 1.1, 12.9 ± 2.7, 6.6 ± 1.8, 26.9 ± 6.5, 31.6 ± 9.3, 9.6 ± 2.2, respectively) were higher than those of the survival group (1.2 ± 1.1, 10.2 ± 3.4, 5.1 ± 1.6, 21.0 ± 6.4, 22.8 ± 8.2, 7.7 ± 2.0, respectively) (<i>p</i> < .01). The values of AUC and Youden index of AIMS65 and MELD-Na scoring systems [(0.808, 0.453) and (0.781, 0.516), respectively] were superior to those of MELD (0.761, 0.454), CTP (0.748, 0.399), FRS (0.738, 0.358) and GBS scoring systems (0.726, 0.370).</p> <p><b>Conclusions:</b> AIMS65 and MELD-Na scoring systems are recommended for evaluation of 6-week bleeding-related mortality in liver cirrhosis patients with AVB.</p

Deformation of Ultrahigh Molecular Weight Polyethylene Precursor Fiber: Crystal Slip with or without Melting

Temperature effects on deformation behaviors of extracted ultrahigh molecular weight polyethylene (UHMWPE) precursor fibers are studied with the <i>in situ</i> synchrotron radiation wide-angle X-ray scattering technique (WAXS) during tensile deformation at temperatures from 25 to 130 °C. The structural and mechanical evolution behaviors during tensile deformation can be divided into four temperature regions with boundaries located at temperatures of α_I and α_II relaxations and the onset of melting, respectively, which reveal that the deformation behaviors of polymer crystals are determined by the interplay between intrinsic structural dynamic or chains mobility and external stress field. Irrespective of temperature, yield and strain-softening proceed via partial melting while crystal slip via cutting crystal planes occurs in the strain-hardening zone. Finally we construct morphological diagrams containing crystallinity, crystal size, and orientation in temperature–strain space, which may serve as a roadmap for UHMWPE fibers processing