The synthetic lethality of targeting cell cycle checkpoints and PARPs in cancer treatment

Continuous cell division is a hallmark of cancer, and the underlying mechanism is tumor genomics instability. Cell cycle checkpoints are critical for enabling an orderly cell cycle and maintaining genome stability during cell division. Based on their distinct functions in cell cycle control, cell cycle checkpoints are classified into two groups: DNA damage checkpoints and DNA replication stress checkpoints. The DNA damage checkpoints (ATM-CHK2-p53) primarily monitor genetic errors and arrest cell cycle progression to facilitate DNA repair. Unfortunately, genes involved in DNA damage checkpoints are frequently mutated in human malignancies. In contrast, genes associated with DNA replication stress checkpoints (ATR-CHK1-WEE1) are rarely mutated in tumors, and cancer cells are highly dependent on these genes to prevent replication catastrophe and secure genome integrity. At present, poly (ADP-ribose) polymerase inhibitors (PARPi) operate through “synthetic lethality” mechanism with mutant DNA repair pathways genes in cancer cells. However, an increasing number of patients are acquiring PARP inhibitor resistance after prolonged treatment. Recent work suggests that a combination therapy of targeting cell cycle checkpoints and PARPs act synergistically to increase the number of DNA errors, compromise the DNA repair machinery, and disrupt the cell cycle, thereby increasing the death rate of cancer cells with DNA repair deficiency or PARP inhibitor resistance. We highlight a combinational strategy involving PARP inhibitors and inhibition of two major cell cycle checkpoint pathways, ATM-CHK2-TP53 and ATR-CHK1-WEE1. The biological functions, resistance mechanisms against PARP inhibitors, advances in preclinical research, and clinical trials are also reviewed.

Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica

As a newly described Sillaginidae species, Chinese sillago (Sillago sinica) needs a better understanding of gene annotation information. In this study, we reported the first full-length transcriptome data of S. sinica using the PacBio isoform sequencing Iso-seq and a description of transcriptome structure analysis. A total of 454,979 high-quality full-length transcripts were obtained by single-molecule real-time (SMRT) sequencing, which was corrected by Illumina sequencing data. After that, 66,948 non-redundant full-length transcripts were generated after mapping to the reference genome of S. sinica, including 49 fusion isoforms and 9,250 novel isoforms. 63,459 isoforms were successfully annotated by one of the Nr, Nt, SwissProt, Pfam, KOG, GO, and KEGG databases. Additionally, 30,987 alternative polyadenylation (APA) sites, 451,867 alternative splicing (AS) events, 21,928 long non-coding RNAs (lncRNAs) and 12,911 transcription factors (TFs) were identified. The full-length transcripts of S. sinica would provide a precious resource for characterizing the transcriptome of S. sinica and for the further study of gene function and regulatory mechanism of this species.

Tuberculosis infection related hemophagocytic lymphohistiocytosis diagnosed in patient with GZMB mutation: A case report and literature review

BACKGROUND

Secondary hemophagocytic lymphohistiocytosis (HLH) is a life-threatening syndrome associated with infections, tumors and connective tissue disease. However rapid identification of the underlying infectious cause of HLH is challenging because traditional etiological diagnostics are time-consuming and sometimes fail to identify the pathogens. Metagenomic next-generation sequencing (mNGS) may be a potential optimal solution, which may help improve the clinical diagnosis of underlying infections in hematological diseases.

CASE PRESENTATION

A 28-year-old man presented with a 2-month history of intermittent fever and cytopenia. The HLH was diagnosed based on the manifestations of fever, splenomegaly, anemia, thrombocytopenia, hyperferritinemia, hyperglyceridemia, and elevated IL-2R levels. High-through-put sequencing analysis detected a GZMB mutation. While the initial detection of cultures and smears of tuberculosis was negative, TB infection was eventually identified by mNGS of blood sample. The symptoms rapidly abated during the initial administration of TB.

CONCLUSION

The present case proposed that mNGS might be an effective diagnostic tool for diagnosing rare infectious cause of secondary HLH. GZMB mutation was first discovered to be present in secondary HLH.

Transcriptional response of short-term nanoplastic exposure in Monodonta labio

Although nanoplastic (NP) pollution across aquatic environments has elicited widespread attention in recent years, its associated risks remain unclear. Using intertidal Monodonta labio as the test organism, RNA-Seq was performed to analyze the expression levels of genes under acute exposure to different concentrations of NPs in this study. A large quantity of differentially expressed genes (DEGs) were detected in response to three concentrations (0.1, 1, and 10 mg/L) of NPs. The expression levels of genes related to immunity, oxidative stress, and apoptosis were altered after NP exposure, and most of them were suppressed. These findings establish the foundation for future research on the biological effects of NP ingestion among aquatic organisms and their potential effects on humans via the consumption of these marine resources. However, further research on DEGs is needed to gain a better understanding of the molecular mechanisms behind their responses to NP toxicity in aquatic organisms.

Low expression and Hypermethylation of ATP2B1 in Intrahepatic Cholangiocarcinoma Correlated With Cold Tumor Microenvironment

Background

The efficacy of current therapeutic schedule is limited owing to fibroproliferative tumor microenvironment (TME) of cholangiocarcinoma, compelling a search for new therapeutic targets.

Methods

Gene expression profiles and methylation profiles were obtained from UCSC Xena. Consensus clustering was performed on the transcriptome data of cholangiocarcinoma to determine the different immune subtypes. The differentially expressed genes (DEGs) between hot tumor and cold tumors were identified. ESTIMATE was used to assess immune score, and the cases were separated into relatively superior and inferior immune score groups. Single-sample gene set enrichment analysis was applied to assess 28 immune cells in the cholangiocarcinoma microenvironment. Unsupervised consensus was applied for methylation profiling to distribute the high and low methylation groups. The correlation between DNA methylation and mRNA expression was investigated, and the relationship between the ATP2B1 gene and the immune microenvironment was explored. Finally, 77 cases of intrahepatic cholangiocarcinoma (ICC) were collected for verification.

Results

Seven subtypes were related to patient outcomes (P=0.005). The proportions of CD8⁺ T cells in the “hot” immune type was significantly greater than that in the “cold” immune type (P<0.05). Next, DEGs and DNA methylation-governed genes were intersected, and ATP2B1 was identified as a prognosis factor in ICC (P=0.035). ATP2B1 expression was positively correlated with immune scores (P=0.005, r=0.458), the levels of infiltrating CD8⁺ T cells (P=0.004, r=0.47), and CD4⁺ T cells (P=0.027, r=0.37). Immunohistochemistry confirmed that the amounts of CD8⁺ and CD4⁺ T cells were significantly higher in ICC tissue samples than in tissues with ATP2B1 overexpression (P<0.05).

Conclusions

ATP2B1 overexpression can activate immune signals and prompt cold tumor response.

Comparative transcriptome reveals the thermal stress response differences between Heilongjiang population and Xinjiang population of Lota lota

Some cold-water fishes are particularly sensitive to the water temperature increasing caused by current global warming. However, the alterations in the physiology and behavior of infraspecific populations living in heterogeneous landscapes in response to water temperature increasing were significantly different. Consequently, understanding the impact of temperature increasing on different populations may be crucial for the conservation of cold-water fishes in the context of global warming. The burbot is the only freshwater specie in Gadiformes. To better understand the differences of different populations of burbot under similar thermal stress, Lota lota was selected as the research objects. Firstly, RNA-seq was applied to identify the transcriptomic responses of Heilongjiang population exposed to three temperature gradients (0 °C, 18 °C and 28 °C). Compared with 0 °C, 4216 and 12,657 genes were significantly differentially expressed at 18 °C and 28 °C, respectively. Meanwhile, 49 genes were significantly differentially expressed in three temperature pairs and these genes were presumed to involve in stress response process, immunologic process, reproductive process, development process, material metabolism process, signal transduction process, spermatogenesis process and cell apoptosis process. The response differences of two L. lota populations to similar thermal stress were compared and the results showed that they have different gene expression responses (the number of differentially expression genes and biological processes). The lower annual temperature of the Heilongjiang River might make it more sensitive to temperature increasing. Based on the comparative transcriptome analyses, 12 orthologous genes were considered as the potential regulators of L. lota preference for cold-water environment and these genes are potentially related to the immunologic process, reproductive process, development process, signal transduction process, and cell apoptosis process. Those results can provide basic information for the rational development of conservation strategies of different L. lota populations under the background of global warming.

Genome-wide identification and low-salinity stress analysis of the Hsp70 gene family in swimming crab (Portunus trituberculatus)

No genome-wide identification and expression analysis have been performed on the heat shock protein 70 (Hsp70) gene family, which is essential to key cellular processes and responses to environmental change, in decapods. In the present study, we identified nine members of the Hsp70 gene family within the genome of swimming crab (Portunus trituberculatus) and provided insights into their response to long-term low-salinity stress. Results demonstrated that gene structure and motifs are conserved among members of this gene family in P. trituberculatus. Under low-salinity stress, the expression of this gene family in the gill of P. trituberculatus showed that hsc70l.2 was significantly upregulated, hyou1 was significantly downregulated. The hsc70l.4 was not expressed. Furthermore, selection test on duplicated genes showed a negative selection on hsc70l.1, hsc70l.2, hsc70l.3, and hsc70l.4, suggesting functional redundancy. This may be the first study that systematically identified and analyzed the Hsp70 gene family in decapods. These results can provide fundamental data for the biological research of P. trituberculatus and enhance understanding of the biological function of Hsp70 in crustaceans adapting to salinity changes.

Supplemented phase diagrams for vitrification CPA cocktails: DP6, VS55 and M22

DP6, VS55 and M22 are the most commonly used cryoprotective agent (CPA) cocktails for vitrification experiments in tissues and organs. However, complete phase diagrams for the three CPAs are often unavailable or incomplete (only available for full strength CPAs) thereby hampering optimization of vitrification and rewarming procedures. In this paper, we used differential scanning calorimetry (DSC) to measure the transition temperatures including heterogeneous nucleation temperatures (T_het), glass transition temperatures (T_g), rewarming phase crystallization (devitrification and/or recrystallization) temperatures (T_d) and melting temperatures (T_m) while cooling or warming the CPA sample at 5 °C/min and plotted the obtained transition temperatures for different concentrations of CPAs into the phase diagrams. We also used cryomicroscopy cooling or warming the sample at the same rate to record the ice crystallization during the whole process, and we presented the cryomicroscopic images at the transition temperatures, which agreed with the DSC presented phenomena.

Generation of immunodeficient pig with hereditary tyrosinemia type 1 and their preliminary application for humanized liver

Background

Mice with humanized livers are important models to study drug toxicology testing, development of hepatitis virus treatments, and hepatocyte transplantation therapy. However, the huge difference between mouse and human in size and anatomy limited the application of humanized mice in investigating human diseases. Therefore, it is urgent to construct humanized livers in pigs to precisely investigate hepatocyte regeneration and human hepatocyte therapy. CRISPR/Cas9 system and somatic cell cloning technology were used to generate two pig models with FAH deficiency and exhibiting severe immunodeficiency (FAH/RAG1 and FAH/RAG1/IL2RG deficiency). Human primary hepatocytes were then successfully transplanted into the FG pig model and constructed two pigs with human liver.

Results

The constructed FAH/RAG1/IL2RG triple-knockout pig models were characterized by chronic liver injury and severe immunodeficiency. Importantly, the FG pigs transplanted with primary human hepatocytes produced human albumin in a time dependent manner as early as 1 week after transplantation. Furthermore, the colonization of human hepatocytes was confirmed by immunochemistry staining.

Conclusions

We successfully generated pig models with severe immunodeficiency that could construct human liver tissues.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13578-022-00760-3.

HPV16-LINC00393 Integration Alters Local 3D Genome Architecture in Cervical Cancer Cells

High-risk human papillomavirus (hrHPV) infection and integration were considered as essential onset factors for the development of cervical cancer. However, the mechanism on how hrHPV integration influences the host genome structure remains not fully understood. In this study, we performed in situ high-throughput chromosome conformation capture (Hi-C) sequencing, chromatin immunoprecipitation and sequencing (ChIP-seq), and RNA-sequencing (RNA-seq) in two cervical cells, 1) NHEK normal human epidermal keratinocyte; and 2) HPV16-integrated SiHa tumorigenic cervical cancer cells. Our results reveal that the HPV-LINC00393 integrated chromosome 13 exhibited significant genomic variation and differential gene expression, which was verified by calibrated CTCF and H3K27ac ChIP-Seq chromatin restructuring. Importantly, HPV16 integration led to differential responses in topologically associated domain (TAD) boundaries, with a decrease in the tumor suppressor KLF12 expression downstream of LINC00393. Overall, this study provides significant insight into the understanding of HPV16 integration induced 3D structural changes and their contributions on tumorigenesis, which supplements the theory basis for the cervical carcinogenic mechanism of HPV16 integration.

Immune checkpoint inhibitor-related adverse events in lung cancer: Real-world incidence and management practices of 1905 patients in China

Background

Immune checkpoint inhibitors (ICIs) are the standard treatment for advanced lung cancer, but immune‐related adverse events (irAEs) remain poorly understood, especially in a real‐world setting.

Methods

A multicenter observational study was conducted. Medical records of lung cancer patients treated with ICIs at 26 hospitals from January 1, 2015, to February 28, 2021, were retrieved. Types of ICIs included antiprogrammed cell death 1 or antiprogrammed cell death ligand 1 (PD‐L1) monotherapy, anticytotoxic T‐lymphocyte antigen‐4 monotherapy, or combination therapy.

Results

In total, 1905 patients with advanced lung cancer were evaluated. The median age was 63 (range 28–87) years, and the male/female ratio was 3.1:1 (1442/463). The primary histological subtype was adenocarcinoma (915). A total of 26.9% (512/1905) of the patients developed 671 irAEs, and 5.8% (110/1905) developed 120 grade 3–5 irAEs. Median duration from ICI initiation to irAEs onset was 56 (range 0–1160) days. The most common irAEs were thyroid dysfunction (7.2%, 138/1905), pneumonitis (6.5%, 124/1905), and dermatological toxicities (6.0%, 115/1905). A total of 162 irAEs were treated with steroids and 11 irAEs led to death. Patients with positive PD‐L1 expression (≥1%) and who received first‐line ICI treatment developed more irAEs. Patients who developed irAEs had a better disease control rate (DCR, 71.3% [365/512] vs. 56.0% [780/1145]; p < 0.001).

Conclusions

The incidence rate of irAEs was 26.9% in a real‐world setting. IrAEs might be related to a better DCR, but clinicians should be more aware of irAE recognition and management in clinical practice.

Elevated serum CA19-9 indicates severe liver inflammation and worse survival after curative resection in hepatitis B-related hepatocellular carcinoma

We explored the prognostic value of preoperative CA19-9 in α-fetoprotein (AFP)-positive and -negative HCC with hepatitis B virus (HBV) background (HBV-HCC), and explored the underlying mechanism. Recurrence-free survival (RFS) and overall survival (OS) were assessed in HBV-HCC patients who underwent curative resection (Cohort 1). Immunohistochemical staining of CA19-9 in HCC and liver parenchyma were quantified in another cohort of 216 patients with resected HCC (Cohort 2). Immunohistochemical staining of CA19-9 and serum CA19-9 level was also compared between patients with HCC and intrahepatic cholangiocarcinoma (ICC) (Cohort 3). In Cohort 1, CA19-9 ≥ 39 U/mL was an independent risk factor for RFS (HR = 1.507, 95% CI = 1.087-2.091, p = 0.014) and OS (HR = 1.646, 95% CI = 1.146-2.366, p = 0.007). CA19-9 ≥ 39 U/mL was also associated with significantly higher incidence of macrovascular invasion (MaVI) compared with CA19-9 < 39 U/mL (23.0% vs. 7.2%, p = 0.002), and elevated aminotransferase and aspartate aminotransferase to platelet ratio index (APRI), and lower albumin. Immunohistochemical staining of CA19-9 revealed that CA19-9 expression was found exclusively in the background liver but not in HCC tumor cells. In contrast, tumor tissue was the main source of CA19-9 in ICC patients. CA19-9 ≥ 39 U/mL was associated with worse OS and RFS in both AFP-positive and negative HCC patients. CA19-9 indicated more severe inflammation and cirrhosis in the liver of HCC patients.

YY1-Induced Transcriptional Activation of FAM111B Contributes to the Malignancy of Breast Cancer

BACKGROUND

Family with sequence similarity 111 member B (FAM111B) is an oncoprotein associated with multiple malignancies. We investigated the potential mechanisms of FAM111B in breast cancer.

PATIENTS AND METHODS

We tested the expression of FAM111B in breast cancer tissues and the survival rate of breast cancer patients with high or low level of FAM111B through TCGA data. The expression of FAM111B in breast cancer tissues and adjacent tissues was detected using western blotting. Then we used siRNA to construct a low expression model of FAM111B in SKBR3 and MDA-MB-468. EdU, CCK-8, wound healing, and transwell assays were performed to monitor the proliferation, migration, and invasion of breast cancer cells. Western blotting was used to detect the expression of EMT-related indicators. Chromatin Immunoprecipitation (ChIP) and qPCR were used to evaluate the regulatory effect of Yin Yang 1 (YY1) on FAM111B.

RESULTS

The expression of FAM111B in breast cancer tissues was higher than that in normal tissues. Patients who had high FAM111B expression had a worse prognosis. Knockdown of FAM111B inhibited the proliferation, migration, and invasion of breast cancer cells. Knockdown of FAM111B resulted in increased expression of EMT-related protein E-cadherin and decreased expression of N-cadherin and Vimentin. ChIP-qPCR analysis demonstrated that YY1 could bind to the promoter of FAM111B gene and strengthen its transcription activity.

CONCLUSION

YY1-induced transcriptional activation of FAM111B accelerated the progression of breast cancer.

Landscape of Myeloid-derived Suppressor Cell in Tumor Immunotherapy

Myeloid-derived suppressor cells (MDSC) are a group of immature cells that produced by emergency myelopoiesis. Emerging evidences have identified the vital role of MDSC in cancer microenvironment, in which MDSC exerts both immunological and non-immunological activities to assist the progression of cancer. Advances in pre-clinical research have provided us the understanding of MDSC in cancer context from the perspective of molecular mechanism. In clinical scenario, MDSC and its subsets have been discovered to exist in peripheral blood and tumor site of patients from various types of cancers. In this review, we highlight the clinical value of MDSC in predicting prognosis of cancer patients and the responses of immunotherapies, therefore to propose the MDSC-inhibiting strategy in the scenario of cancer immunotherapies. Phenotypes and biological functions of MDSC in cancer microenvironment are comprehensively summarized to provide potential targets of MDSC-inhibiting strategy from the aspect of molecular mechanisms.