Pretreatment CT-based machine learning radiomics model predicts response in unresectable hepatocellular carcinoma treated with lenvatinib plus PD-1 inhibitors and interventional therapy.

BACKGROUND: Lenvatinib plus PD-1 inhibitors and interventional (LPI) therapy have demonstrated promising treatment effects in unresectable hepatocellular carcinoma (HCC). However, biomarkers for predicting the response to LPI therapy remain to be further explored. We aimed to develop a radiomics model to noninvasively predict the efficacy of LPI therapy. METHODS: Clinical data of patients with HCC receiving LPI therapy were collected in our institution. The clinical model was built with clinical information. Nine machine learning classifiers were tested and the multilayer perceptron classifier with optimal performance was used as the radiomics model. The clinical-radiomics model was constructed by integrating clinical and radiomics scores through logistic regression analysis. RESULTS: 151 patients were enrolled in this study (2:1 randomization, 101 and 50 in the training and validation cohorts), of which three achieved complete response, 69 showed partial response, 46 showed stable disease, and 33 showed progressive disease. The objective response rate, disease control rate, and conversion resection rates were 47.7, 78.1 and 23.2%. 14 features were selected from the initially extracted 1223 for radiomics model construction. The area under the curves of the radiomics model (0.900 for training and 0.893 for validation) were comparable to that of the clinical-radiomics model (0.912 for training and 0.892 for validation), and both were superior to the clinical model (0.669 for training and 0.585 for validation). Meanwhile, the radiomics model can categorize participants into high-risk and low-risk groups for progression-free survival (PFS) and overall survival (OS) in the training (HR 1.913, 95% CI 1.121 to 3.265, p=0.016 for PFS; HR 4.252, 95% CI 2.051 to 8.816, p=0.001 for OS) and validation sets (HR 2.347, 95% CI 1.095 to 5.031, p=0.012 for PFS; HR 2.592, 95% CI 1.050 to 6.394, p=0.019 for OS). CONCLUSION: The promising machine learning radiomics model was developed and validated to predict the efficacy of LPI therapy for patients with HCC and perform risk stratification, with comparable performance to clinical-radiomics model.

Immunotherapy in leukaemia.

Leukaemia is the common name for a group of malignant diseases of the haematopoietic system with complex classifications and characteristics. Remarkable progress has been made in basic research and preclinical studies for acute leukaemia compared to that of the many other types/subtypes of leukaemia, especially the exploration of the biological basis and application of immunotherapy in acute myeloid leukaemia (AML) and B-cell acute lymphoblastic leukaemia (B-ALL). In this review, we summarize the basic approaches to immunotherapy for leukaemia and focus on the research progress made in immunotherapy development for AML and ALL. Importantly, despite the advances made to date, big challenges still exist in the effectiveness of leukaemia immunotherapy, especially in AML. Therefore, we use AML as an example and summarize the mechanisms of tumour cell immune evasion, describe recently reported data and known therapeutic targets, and discuss the obstacles in finding suitable treatment targets and the results obtained in recent clinical trials for several types of single and combination immunotherapies, such as bispecific antibodies, cell therapies (CAR-T-cell treatment), and checkpoint blockade. Finally, we summarize novel immunotherapy strategies for treating lymphocytic leukaemia and clinical trial results.

Radiomic and clinical data integration using machine learning predict the efficacy of anti-PD-1 antibodies-based combinational treatment in advanced breast cancer: a multicentered study.

BACKGROUND: Immune checkpoint inhibitors (ICIs)-based therapy, is regarded as one of the major breakthroughs in cancer treatment. However, it is challenging to accurately identify patients who may benefit from ICIs. Current biomarkers for predicting the efficacy of ICIs require pathological slides, and their accuracy is limited. Here we aim to develop a radiomics model that could accurately predict response of ICIs for patients with advanced breast cancer (ABC). METHODS: Pretreatment contrast-enhanced CT (CECT) image and clinicopathological features of 240 patients with ABC who underwent ICIs-based treatment in three academic hospitals from February 2018 to January 2022 were assigned into a training cohort and an independent validation cohort. For radiomic features extraction, CECT images of patients 1 month prior to ICIs-based therapies were first delineated with regions of interest. Data dimension reduction, feature selection and radiomics model construction were carried out with multilayer perceptron. Combined the radiomics signatures with independent clinicopathological characteristics, the model was integrated by multivariable logistic regression analysis. RESULTS: Among the 240 patients, 171 from Sun Yat-sen Memorial Hospital and Sun Yat-sen University Cancer Center were evaluated as a training cohort, while other 69 from Sun Yat-sen University Cancer Center and the First Affiliated Hospital of Sun Yat-sen University were the validation cohort. The area under the curve (AUC) of radiomics model was 0.994 (95% CI: 0.988 to 1.000) in the training and 0.920 (95% CI: 0.824 to 1.000) in the validation set, respectively, which were significantly better than the performance of clinical model (0.672 for training and 0.634 for validation set). The integrated clinical-radiomics model showed increased but not statistical different predictive ability in both the training (AUC=0.997, 95% CI: 0.993 to 1.000) and validation set (AUC=0.961, 95% CI: 0.885 to 1.000) compared with the radiomics model. Furthermore, the radiomics model could divide patients under ICIs-therapies into high-risk and low-risk group with significantly different progression-free survival both in training (HR=2.705, 95% CI: 1.888 to 3.876, p<0.001) and validation set (HR=2.625, 95% CI: 1.506 to 4.574, p=0.001), respectively. Subgroup analyses showed that the radiomics model was not influenced by programmed death-ligand 1 status, tumor metastatic burden or molecular subtype. CONCLUSIONS: This radiomics model provided an innovative and accurate way that could stratify patients with ABC who may benefit more from ICIs-based therapies.

Spatial-Temporal Variation and Driving Factors of Ecological Vulnerability in Nansi Lake Basin, China.

Lake basins are one of the most significant areas of human-land interaction. It is essential for the region's ecological protection and high-quality development to assess their ecological vulnerability (EV) and analyze the key driving factors of EV. Considering the characteristics of the lake basin, we chose 17 indicators to evaluate the EV of the Nansi Lake Basin based on the "sensitivity-resilience-pressure" (SRP) model. Then, spatial principal component analysis (SPCA) and a transfer matrix were used to analyze the spatial-temporal variation characteristics of the EV. Moreover, the optimal parameters-based geographical detector (OPGD) was applied to investigate the factors influencing the spatial heterogeneity of the EV. The results indicated that the EV of the Nansi Lake Basin was characterized by a circling spatial structure, with low values distributed in the Nansi Lake and its surrounding areas, as well as high values concentrated in the northwest. The EV of the Nansi Lake Basin decreased from 2010 to 2020, indicating that the overall ecological pressure in the Nansi Lake Basin decreased. Climatic factors, land use type, and habitat quality were the primary factors that influenced the spatial heterogeneity of the EV in the basin. Our findings can serve as policy guidelines for ecological management and the sustainable development of the Nansi Lake Basin and also contribute to the EV assessment of lake basins.

Revalidation and redescription of Sarcocheilichthys sciistius (Abbott, 1901) (Cypriniformes: Cyprinidae) from the northern China.

Sarcocheilichthys sciistius was originally described by Abbott in 1901. It was considered as a synonym of S. nigripinnis by later researchers. However, some recent studies suggested that S. nigripinnis from the Haihe River Basin and Yellow River Basin were different to S. nigripinnis distributed in southern China, and that these populations show a closer relationship with the Heilongjiang (Amur) River endemic speciesS. czerskii and S. soldatovi. In this study, we examined one hundred and twenty-five specimens from nine sites of six river basins. Based on morphological and molecular systematic studies, we confirmed S. sciistius is a valid species, and S. czerskii, S. soldatovi were synonyms of S. sciistius. Sarcocheilichthys sciistius can be distinguished from S. nigripinnis by having more lateral-line scales (4042 vs. 3840), shorter lower lip and different pectoral and pelvic fins color. The phylogenetic trees reconstructed by Bayesian Inference and Maximum Likelihood based on the Cyt b gene also support S. sciistius as a distinct species.

Revalidation and redescription of a gobionine species Microphysogobio bicolor (Nichols, 1930) (Teleostei: Cypriniformes) from the Yangtze River Basin, China.

Microphysogobio bicolor (Nichols, 1930), a species which has long been synonymized with Microphysogobio fukiensis (Nichols, 1926), is revalidated in this study, based on morphological comparison and molecular phylogenetic analysis. The species can be distinguished from congeners by the following characters: mouth horseshoe-shaped, central portion of anterior papillae arranged in one row, tightly contact with each other, equal or slightly larger than all other papillae on upper lip; lateral-line scales 3638; branched anal-fin rays 5; posterior chamber of air-bladder length equal to eye diameter; vertebrae 4+32; body usually sharply bicolored. The significant Cyt b gene sequence divergence between M. bicolor and its congeners also strongly support that it is a valid species which represents an individual clade sister to the M. luhensisM. kachekensisM. yunnanensis clade. A redescription of M. bicolor and a diagnostic key to all valid Microphysogobio in the Yangtze River Basin are also provided in this study.

Taxonomic revision and redescription of Microphysogobio hsinglungshanensis, the type species of Microphysogobio Mori, 1934 (Cypriniformes: Cyprinidae).

The genus Microphysogobio was established by Mori [Mori, T. (1934). The fresh water fishes of Jehol. In Report of the first scientific expedition to Manchoukuo. 1: pp. 1-61] based on a single specimen (Microphysogobio hsinglungshanensis) collected in the Luanhe River basin, Xinglong County, Hebei Province, China. Because the genus characteristics were derived from its type species, M. hsinglungshanensis, the detailed description is essential. In addition, to distinguish M. hsinglungshanensis and Microphysogobio chinssuensis, the description based on holotype and more specimens is needed. M. hsinglungshanensis can be distinguished from all other congeners by the following combination of characters: mouth shallow arc shaped and inferior; medial pad on lower lip inverted trapezoid and usually grooved; barbel short, 6.9%-14.3% in head length; lateral-line scales 38-39; ventral region between pectoral-fin origin and pelvic-fin origin scaleless; scales above lateral line 4-4.5; predorsal scales 10-11; vertebrae 4 + 32 - 34; caudal-fin membrane with two or three rows of irregular black spots. The characteristics of this genus were redefined based on M. hsinglungshanensis in this study.

Hepato-specific microRNA-122 facilitates accumulation of newly synthesized miRNA through regulating PRKRA.

microRNAs (miRNAs) are a versatile class of non-coding RNAs involved in regulation of various biological processes. miRNA-122 (miR-122) is specifically and abundantly expressed in human liver. In this study, we employed 3'-end biotinylated synthetic miR-122 to identify its targets based on affinity purification. Quantitative RT-PCR analysis of the affinity purified RNAs demonstrated a specific enrichment of several known miR-122 targets such as CAT-1 (also called SLC7A1), ADAM17 and BCL-w. Using microarray analysis of affinity purified RNAs, we also discovered many candidate target genes of miR-122. Among these candidates, we confirmed that protein kinase, interferon-inducible double-stranded RNA-dependent activator (PRKRA), a Dicer-interacting protein, is a direct target gene of miR-122. miRNA quantitative-RT-PCR results indicated that miR-122 and small interfering RNA against PRKRA may facilitate the accumulation of newly synthesized miRNAs but did not detectably affect endogenous miRNAs levels. Our findings will lead to further understanding of multiple functions of this hepato-specific miRNA. We conclude that miR-122 could repress PRKRA expression and facilitate accumulation of newly synthesized miRNAs.

Promyelocytic leukemia protein interacts with werner syndrome helicase and regulates double-strand break repair in γ-irradiation-induced DNA damage responses.

We show here that γ-irradiation leads to the translocation of endogenous Werner syndrome helicase (WRN) from nucleoli to nucleoplasmic DNA double strand breaks (DSBs), and WRN plays a role in damage repair. The relocation of WRN after irradiation was perturbed by promyelocytic leukemia protein (PML) knockdown and enhanced by PML IV overexpression. PML IV physically interacted with WRN after irradiation. Amino acids (a.a.) 394 to 433 of PML were necessary for this interaction and the nucleoplasmic translocation of WRN and were involved in DSB repair and cellular sensitivity to γ-irradiation. Taken together, our results provide molecular support for a model in which PML IV physically interacts with and regulates the translocation of WRN for DNA damage repair through its 394-433 a.a. domain.

p53 Suppresses lung resistance-related protein expression through Y-box binding protein 1 in the MCF-7 breast tumor cell line.

Lung resistance-related protein (LRP) has roles in multi-drug resistance of tumor cells. Understanding the mechanisms that regulate LRP expression in tumor cells is an important research area. A putative p53 response element in the LRP promoter has been found. Thus, p53-related regulation of LRP expression was explored in this study. We first demonstrated that p53 overexpression inhibited LRP expression both at the protein and mRNA levels. Then, using a dual-luciferase reporter assay, we located the p53 response element to the Y-box (-263~-407) of the LRP promoter, the YB-1 binding site, but not the putative p53 response element. Furthermore, coimmunoprecipitation and chromatin immunoprecipitation showed p53 could bind to the Y-box of the LRP promoter through interaction of p53 with YB-1. YB-1 coexpression with p53 facilitated p53-induced suppression of endogenous LRP expression in MCF-7 cells. HDAC2, a corepressor of p53, was found to also interact with YB-1, and this interaction was mediated by p53. These results showed that the p53-HDAC2 transcriptional repressor complex can bind to the Y-box of the LRP promoter and repress LRP expression through interaction with YB-1. p53-related suppression of LRP expression was completely reversed by doxorubicin treatment and Adr, whereas CP and VP-16 treatment induced LRP expression increased significantly. Inhibition of LRP expression by siRNA facilitated Adr induced apoptosis of MCF-7 cells. All these findings indicated that loss of p53-related suppression of LRP may be the reason for LRP expression increase, and, therefore, chemotherapy resistance in tumor cells.

Functional proteomic analysis of promyelocytic leukaemia nuclear bodies in irradiation-induced MCF-7 cells.

It is well established that promyelocytic leukaemia nuclear bodies (PML NBs) play important roles in DNA damage responses (DDR). After irradiation, PML NBs dynamically recruit or release important proteins involved in cell-cycle regulation, DNA repair and apoptosis. As PML protein is the key molecule of PML NBs' dynamic assembling, we aimed to characterize the PML-interacting proteins in (60)Co-irradiated MCF-7 cells. A proteomic approach using CoIP, mono-dimensional electrophoresis and tandem mass spectrometry, allowed us to identify a total of 124 proteins that may associate with PML after irradiation. Bioinformatic analysis of the identified proteins showed that most of them were related to characterized PML functions, such as transcriptional regulation, cell-cycle regulation, cell-death regulation and response to stress. Four proteins, B23, MVP, G3BP1 and DHX9, were verified to co-localize with PML differentially before and after ionizing radiation (IR) treatment. The proteins identified in this study will significantly improve our understanding of the dynamic organization and multiple functions of PML NBs in DDR.

MicroRNA-193b regulates proliferation, migration and invasion in human hepatocellular carcinoma cells.

BACKGROUND AND AIMS: Recently, some miRNAs have been reported to be connected closely with the development of human hepatocellular carcinoma. However, the functions of these miRNAs in HCC remain largely undefined. METHODS: The expression profiles of miR-193b were compared between HCC tissues and adjacent normal liver tissues using qRT-PCR method. This method was also be used to screen the potential target genes of miR-193b. A luciferase reporter assay was conducted to confirm target association. Finally, the functional effect of miR-193b in hepatoma cells was examined further. RESULTS: miR-193b was significantly down-regulated in most of the HCC tissues compared to the matching non-tumoural liver tissues. Furthermore, ectopic expression of miR-193b dramatically suppressed the ability of hepatoma cells to form colonies in vitro and to develop tumours in nude mice. CCND1 and ETS1 were revealed to be regulated by miR-193b directly. By regulating the expressions of these oncogenes, miR-193b induced cell cycle arrest and inhibited the invasion and migration of hepatoma cells. CONCLUSIONS: miR-193b may function as a tumour suppressor in the development of HCC by acting on multiple tumourigenic pathways.

miR-183 inhibits TGF-beta1-induced apoptosis by downregulation of PDCD4 expression in human hepatocellular carcinoma cells.

BACKGROUND: In recent years, some miRNAs have been reported to be connected closely with the development of human hepatocellular carcinoma. In our previous studies, a set of miRNAs were revealed to be dysregulated in HCC tissues. However, the functions of these miRNAs in HCC remain largely undefined. METHODS: The expression profiles of miR-183 were compared between HCC tissues and adjacent normal liver tissues using qRT-PCR method. This method was used to screen the potential target genes of miR-183. A luciferase reporter assay was conducted to confirm target association. Finally, the functional effect of miR-183 in hepatoma cells was examined. RESULTS: Among the 25 HCC samples analyzed, microRNA-183 was significantly up-regulated (twofold to 367-fold) in 17 samples compared with the matching nontumoral liver tissues. Programmed cell death 4 (PDCD4) was identified as the target gene of miR-183. Moreover, PDCD4 is a proapoptotic molecule involved in TGF-beta1-induced apoptosis in human HCC cells, we found that miR-183 transfectants were resistant to apoptosis induced by TGF-beta1. CONCLUSIONS: We conclude that miR-183 can inhibit apoptosis in human HCC cells by repressing the PDCD4 expression, and miR-183 may play an important role in HCC development.

Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array.

BACKGROUND: The balance between endothelial cell survival and apoptosis during stress is an important cellular process for vessel integrity and vascular homeostasis, and it is also pivotal in angiogenesis during the development of many vascular diseases. However, the underlying molecular mechanisms remain largely unknown. Although both transcription and alternative splicing are important in regulating gene expression in endothelial cells under stress, the regulatory mechanisms underlying this state and their interactions have not yet been studied on a genome-wide basis. RESULTS: Human umbilical vein endothelial cells (HUVECs) were treated with cobalt chloride (CoCl2) both to mimic hypoxia and to induce cell apoptosis and alternative splicing responses. Cell apoptosis rate analysis indicated that HUVECs exposed to 300 microM CoCl2 for 24 hrs were initially counterbalancing apoptosis with cell survival. We therefore used the Affymetrix exon array system to determine genome-wide transcript- and exon-level differential expression. Other than 1583 differentially expressed transcripts, 342 alternatively spliced exons were detected and classified by different splicing types. Sixteen alternatively spliced exons were validated by RT-PCR. Furthermore, direct evidence for the ongoing balance between HUVEC survival and apoptosis was provided by Gene Ontology (GO) and protein function, as well as protein domain and pathway enrichment analyses of the differentially expressed transcripts. Importantly, a novel molecular module, in which the heat shock protein (HSP) families play a significant role, was found to be activated under mimicked hypoxia conditions. In addition, 46% of the transcripts containing stress-modulated exons were differentially expressed, indicating the possibility of combinatorial regulation of transcription and splicing. CONCLUSION: The exon array system effectively profiles gene expression and splicing on the genome-wide scale. Based on this approach, our data suggest that transcription and splicing not only regulate gene expression, but also carry out combinational regulation of the balance between survival and apoptosis of HUVECs under mimicked hypoxia conditions. Since cell survival following the apoptotic challenge is pivotal in angiogenesis during the development of many vascular diseases, our results may advance the knowledge of multilevel gene regulation in endothelial cells under physiological and pathological conditions.

MicroRNA-101 regulates expression of the v-fos FBJ murine osteosarcoma viral oncogene homolog (FOS) oncogene in human hepatocellular carcinoma.

UNLABELLED: MicroRNAs (miRNAs) have recently been proposed as a versatile class of molecules involved in regulation of various biological processes. Although there is emerging evidence that some microRNAs can function as oncogenes or tumor suppressors, the specific role of miRNA in human hepatocellular carcinoma (HCC) is unclear at this point. In this study, we examined the microRNA expression profiles in a set of 20 human HCC specimens by miRNA microarray and quantitative real-time polymerase chain reaction. The results showed that among the 20 HCC samples analyzed, microRNA-101 was significantly down-regulated twofold or more (twofold to 20-fold) in 16 samples compared with the matching nontumoral liver tissues. Using both a luciferase reporter assay and Western blot analysis, we showed that microRNA-101 repressed the expression of v-fos FBJ murine osteosarcoma viral oncogene homolog (FOS) oncogene, a key component of the activator protein-1 (AP-1) transcription factor. Moreover, using a luciferase expression vector (pAP-1-Luc) driven by seven copies of an AP-1 cis-element, we observed that microRNA-101 expression inhibited phorbol 12-myristate 13-acetate (PMA)-induced AP-1 activity. In in vitro Matrigel invasion and Transwell migration assays, enhanced microRNA-101 expression inhibited the invasion and migration of cultured HCC cells, respectively. These findings suggest that microRNA-101 may play an important role in HCC. CONCLUSION: MicroRNA-101, which is aberrantly expressed in HCC, could repress the expression of the FOS oncogene.

Stress induces tRNA cleavage by angiogenin in mammalian cells.

tRNAs play a central role in protein translation, acting as the carrier of amino acids. By cloning microRNAs, we unexpectedly obtained some tRNA fragments generated by tRNA cleavage in the anticodon loop. These tRNA fragments are present in many cell lines and different mouse tissues. In addition, various stress conditions can induce this tRNA cleavage event in mammalian cells. More importantly, angiogenin (ANG), a member of RNase A superfamily, appears to be the nuclease which cleaves tRNAs into tRNA halves in vitro and in vivo. These results imply that angiogenin plays an important physiological role in cell stress response, except for the known function of inducing angiogenesis.

miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes.

MicroRNAs (miRNAs) are a class of small regulatory RNAs that are thought to be involved in diverse biological processes by regulating gene expression. Numerous miRNAs have been identified in various species, and many more miRNAs remain to be detected. Generally, hundreds of mRNAs have been predicted to be potential targets of one miRNA, so it is a great challenge to identify the genuine miRNA targets. Here, we generated the cell lines depleted of Drosha protein and screened dozens of transcripts (including Cyclin D1) regulated potentially by miRNA-mediated RNA silencing pathway. On the basis of miRNA expressing library, we established a miRNA targets reverse screening method by using luciferase reporter assay. By this method, we found that the expression of Cyclin D1 (CCND1) was regulated by miR-16 family directly, and miR-16 induced G1 arrest in A549 cells partially by CCND1. Furthermore, several other cell cycle genes were revealed to be regulated by miR-16 family, including Cyclin D3 (CCND3), Cyclin E1 (CCNE1) and CDK6. Taken together, our data suggests that miR-16 family triggers an accumulation of cells in G0/G1 by silencing multiple cell cycle genes simultaneously, rather than the individual target.