Development and Evaluation of a Quantitative Systems Pharmacology Model for Mechanism Interpretation and Efficacy Prediction of Atezolizumab in Combination with Carboplatin and Nab-Paclitaxel in Patients with Non-Small-Cell Lung Cancer.

Immunotherapy has shown clinical benefit in patients with non-small-cell lung cancer (NSCLC). Due to the limited response of monotherapy, combining immune checkpoint inhibitors (ICIs) and chemotherapy is considered a treatment option for advanced NSCLC. However, the mechanism of combined therapy and the potential patient population that could benefit from combined therapy remain undetermined. Here, we developed an NSCLC model based on the published quantitative systems pharmacology (QSP)-immuno-oncology platform by making necessary adjustments. After calibration and validation, the established QSP model could adequately characterise the biological mechanisms of action of the triple combination of atezolizumab, nab-paclitaxel, and carboplatin in patients with NSCLC, and identify predictive biomarkers for precision dosing. The established model could efficiently characterise the objective response rate and duration of response of the IMpower131 trial, reproducing the efficacy of alternative dosing. Furthermore, CD8+ and CD4+ T cell densities in tumours were found to be significantly related to the response status. This significant extension of the QSP model not only broadens its applicability but also more accurately reflects real-world clinical settings. Importantly, it positions the model as a critical foundation for model-informed drug development and the customisation of treatment plans, especially in the context of combining single-agent ICIs with platinum-doublet chemotherapy.

Forces driving transposable element load variation during Arabidopsis range expansion.

Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.

Case Report: CTC1 mutations in a patient with diffuse hepatic and splenic hemangiomatosis complicated by Kasabach-Merritt syndrome.

Diffuse hemangiomatosis of the liver and spleen is rare. Currently, few studies are available on diffuse hepatic and splenic hemangiomatosis accompanied by Kasabach-Merritt syndrome (KMS). The conserved telomere maintenance component 1 (CTC1) gene contributes to telomere maintenance and replication by forming the telomeric capping complex. Herein, we report a case of diffuse hemangiomatosis in the liver and spleen accompanied by KMS in a 59-year-old woman who carried two novel heterozygous CTC1 variants: c.435+9A>C and c.3074C>T (p.Ala1025Val). Using next-generation sequencing, we detected mutations in the CTC1 gene in our patient, who had chief complaints of fatigue and abdominal distension complicated by severe thrombocytopenia and consumptive coagulopathy. Clinical symptoms, laboratory tests, and imaging findings led to the diagnosis of diffuse hepatic and splenic hemangiomatosis accompanied by KMS. The patient was treated with prednisone, thalidomide, and sirolimus, and her general condition was ameliorated at the 4-month follow-up with improved platelet count and coagulation function. A CTC1 gene mutation may be involved in the pathological process of vascular diseases. A combination treatment regimen of prednisone, thalidomide, and sirolimus may be effective for KMS.

Use of diffusion-weighted magnetic resonance imaging (DW-MRI) to predict early response to anti-tumor therapy in advanced non-small cell lung cancer (NSCLC): a comparison of intravoxel incoherent motion-derived parameters and apparent diffusion coefficient.

BACKGROUND: The intravoxel incoherent motion (IVIM) method of magnetic resonance imaging (MRI) analysis can provide information regarding many physiological and pathological processes. This study aimed to investigate whether IVIM-derived parameters and the apparent diffusion coefficient (ADC) can act as imaging biomarkers for predicting non-small cell lung cancer (NSCLC) response to anti-tumor therapy and compare their performances. METHODS: This prospective study included 45 patients with NSCLC treated with chemotherapy (29 men and 16 women, mean age 57.9±9.7 years). Diffusion-weighted imaging was performed with 13 b-values before and 2-4 weeks after treatment. The IVIM parameter pseudo-diffusion coefficient (D*), perfusion fraction (f), diffusion coefficient (D), and ADC from a mono-exponential model were obtained. Responses 2 months after chemotherapy were assessed. The diagnostic performance was evaluated, and optimal cut-off values were determined by receiver operating characteristic (ROC) curve analysis, and the differences of progression-free survival (PFS) in groups of responders and non-responders were tested by Cox regression and Kaplan-Meier survival analyses. RESULTS: Of 45 patients, 30 (66.7%) were categorized as responders, and 15 as non-responders. Differences in the diffusion coefficient D and ADC between responders and non-responders were statistically significant (all P<0.05). Conversely, differences in f and D* between responders and non-responders were both not statistically significance (all P>0.05). The ROC analyses showed the change in D value (ΔD) was the best predictor of early response to anti-tumor therapy [area under the ROC curve (AUC), 0.764]. The Cox-regression model showed that all ADC and D parameters were independent predictors of PFS, with a range of reduction in risk from 56.2% to 82.7%, and ΔD criteria responders had the highest reduction (82.7%). CONCLUSIONS: ADC and D derived from IVIM are potentially useful for the prediction of NSCLC treatment response to anti-tumor therapy. Although ΔD is best at predicting response to treatment, ΔADC measurement may simplify manual efforts and reduce the workload.

Fruquintinib with gefitinib as first-line therapy in patients carrying EGFR mutations with advanced non-small cell lung cancer: a single-arm, phase II study.

BACKGROUND: Fruquintinib is an oral vascular endothelial growth factor receptor inhibitor. Previous gefitinib studies with anti-angiogenics show promising efficacy. This phase II trial assessed efficacy and safety of fruquintinib in combination with gefitinib, in patients with advanced non-small cell lung cancer (NSCLC). METHODS: Fifty patients with stage IIIB/IV NSCLC and an epidermal growth factor receptor (EGFR) exon-19 deletion or exon-21 L858R mutation were enrolled between January 2017 and June 2019. Per protocol (version 1.0), patients received 4 mg fruquintinib once daily (qd) Days 1-21 of Cycle 1, using a 3-week-on/1-week-off schedule, plus continuous gefitinib 250 mg qd. If tolerated, patients proceeded to fruquintinib 5 mg qd (fruquintinib 5 mg group, n=26). Following protocol updates, dose escalation of fruquintinib from 4 mg qd to 5 mg qd was not allowed. The primary efficacy endpoint was objective response rate (ORR); secondary endpoints included progression-free survival (PFS), disease control rate (DCR), time to response, duration of response and adverse events (AEs). RESULTS: ORR was 73.5% (95% CI, 58.9-85.1) and DCR was 98.0% (95% CI, 89.2-100.0). Median PFS was 14.7 months for both groups; PFS was highest for patients with exon-19 deletion (16.5 months; 95% CI, 12.9-21.2). Grade ≥3 treatment-emergent AEs occurred in 17 (65.3%; fruquintinib 5 mg,) and 11 patients (45.8%; 4 mg). Serious AEs were recorded for nine patients (fruquintinib 5 mg, six patients; 4 mg, three). CONCLUSIONS: Fruquintinib and gefitinib treatment showed an acceptable safety profile and promising efficacy in patients with NSCLC.

Transposable elements drive rapid phenotypic variation in Capsella rubella.

Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown. Capsella rubella, an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (i) highly enriched in C. rubella compared with its outcrossing sister species Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at FLOWERING LOCUS C (FLC) in natural populations of C. rubella could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3' UTR of FLC affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.

Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes.

According to the less-is-more hypothesis, gene loss is an engine for evolutionary change. Loss-of-function (LoF) mutations resulting in the natural knockout of protein-coding genes not only provide information about gene function but also play important roles in adaptation and phenotypic diversification. Although the less-is-more hypothesis was proposed two decades ago, it remains to be explored on a large scale. In this study, we identified 60,819 LoF variants in 1071 Arabidopsis (Arabidopsis thaliana) genomes and found that 34% of Arabidopsis protein-coding genes annotated in the Columbia-0 genome do not have any LoF variants. We found that nucleotide diversity, transposable element density, and gene family size are strongly correlated with the presence of LoF variants. Intriguingly, 0.9% of LoF variants with minor allele frequency larger than 0.5% are associated with climate change. In addition, in the Yangtze River basin population, 1% of genes with LoF mutations were under positive selection, providing important insights into the contribution of LoF mutations to adaptation. In particular, our results demonstrate that LoF mutations shape diverse phenotypic traits. Overall, our results highlight the importance of the LoF variants for the adaptation and phenotypic diversification of plants.

Parallel Evolution of Common Allelic Variants Confers Flowering Diversity in Capsella rubella.

Flowering time is an adaptive life history trait. Capsella rubella, a close relative of Arabidopsis thaliana and a young species, displays extensive variation for flowering time but low standing genetic variation due to an extreme bottleneck event, providing an excellent opportunity to understand how phenotypic diversity can occur with a limited initial gene pool. Here, we demonstrate that common allelic variation and parallel evolution at the FLC locus confer variation in flowering time in C. rubella. We show that two overlapping deletions in the 5' untranslated region (UTR) of C. rubella FLC, which are associated with local changes in chromatin conformation and histone modifications, reduce its expression levels and promote flowering. We further show that these two pervasive variants originated independently in natural C. rubella populations after speciation and spread to an intermediate frequency, suggesting a role of this parallel cis-regulatory change in adaptive evolution. Our results provide an example of how parallel mutations in the same 5' UTR region can shape phenotypic evolution in plants.

Adaptation of Arabidopsis thaliana to the Yangtze River basin.

BACKGROUND: Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different. RESULTS: We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping. CONCLUSIONS: A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.

Adjuvant therapy for EGFR mutant and ALK positive NSCLC: Current data and future prospects.

Tyrosine kinase inhibitors (TKIs) against targetable mutations such as epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) are highly effective in treating advanced stage lung cancers harboring such mutations. Questions remain, however, about whether these agents can improve cure rates for early stage lung cancers in the adjuvant setting. Here, we examine the current data and ongoing trials addressing this issue.

17-AAG suppresses growth and invasion of lung adenocarcinoma cells via regulation of the LATS1/YAP pathway.

The large tumour suppressor 1 (LATS1) signalling network has been proved to be an essential regulator within the cell, participating in multiple cellular phenotypes. However, it is unclear concerning the clinical significance of LATS1 and the regulatory mechanisms of 17-Allylamino-17- demethoxygeldanamycin (17-AAG) in lung adenocarcinoma (LAC). The aim of the present study was to investigate the correlation of LATS1 and yes-associated protein (YAP) expression with clinicopathological characteristics in LAC patients, and the effects of 17-AAG on biological behaviours of LAC cells. Subcutaneous LAC tumour models were further established to observe the tumour growth in nude mice. The results showed that the positive expression of LATS1 was significantly lowered (26.7% versus 68.0%, P < 0.001), while that of YAP was elevated (76.0% versus 56.0%, P = 0.03) in LAC tissues compared to the adjacent non-cancerous tissues; LAST1 expression was negatively correlated with YAP expression (r = 0.432, P < 0.001) and lymphatic invasion of the tumour (P = 0.015). In addition, 17-AAG inhibited proliferation and invasion, and induced cell apoptosis and cycle arrest in LAC cells together with increased expression of E-cadherin and p-LATS1, and decreased expression of YAP and connective tissue growth factor. Tumour volumes and weight were much smaller in 17-AAG-treated groups than those in untreated group (P < 0.01). Taken together, our findings indicate that decreased expression of LATS1 is associated with lymphatic invasion of LAC, and 17-AAG suppresses growth and invasion of LAC cells via regulation of the LATS1/YAP pathway in vitro and in vivo, suggesting that we may provide a promising therapeutic strategy for the treatment of human LAC.

Acetylcholine receptor pathway in lung cancer: New twists to an old story.

Genome-wide association studies revealed that allelic variation in the α5-α3-ß4 nicotine acetylcholine receptor (nAChR) cluster on chromosome 15q24-15q25.1 was associated with lung cancer risk. nAChRs are membrane ligand-gated cation channels whose activation is triggered by the binding of the endogenous neurotransmitter acetylcholine (ACh) or other biologic compounds including nicotine. nAChRs have been found on lung cancer cells, underscoring the idea that the non-neuronal nAChR pathway has important implications for lung cancer. Several studies focusing on the treatment with nAChR antagonists with improved selectivity might trigger novel strategies for the intervention and prevention of lung cancer. Here we review the genetic risk factors for lung cancer in the nAChR gene cluster, the roles of nicotine receptors, and the molecular mechanisms of acetylcholine receptor pathways to lead to more opportunities for intervention and prevention of lung cancer.

FBXL5-mediated degradation of single-stranded DNA-binding protein hSSB1 controls DNA damage response.

Human single-strand (ss) DNA binding proteins 1 (hSSB1) has been shown to participate in DNA damage response and maintenance of genome stability by regulating the initiation of ATM-dependent signaling. ATM phosphorylates hSSB1 and prevents hSSB1 from ubiquitin-proteasome-mediated degradation. However, the E3 ligase that targets hSSB1 for destruction is still unknown. Here, we report that hSSB1 is the bona fide substrate for an Fbxl5-containing SCF (Skp1-Cul1-F box) E3 ligase. Fbxl5 interacts with and targets hSSB1 for ubiquitination and degradation, which could be prevented by ATM-mediated hSSB1 T117 phosphorylation. Furthermore, cells overexpression of Fbxl5 abrogated the cellular response to DSBs, including activation of ATM and phosphorylation of ATM targets and exhibited increased radiosensitivity, chemosensitivity and defective checkpoint activation after genotoxic stress stimuli. Moreover, the protein levels of hSSB1 and Fbxl5 showed an inverse correlation in lung cancer cells lines and clinical lung cancer samples. Therefore, Fbxl5 may negatively modulate hSSB1 to regulate DNA damage response, implicating Fbxl5 as a novel, promising therapeutic target for lung cancers.

[Spatial autocorrelation of genetic structure of Prunus padus population in broadleaved Korean pine forest of Changbai Mountains].

All 396 Prunus padus individuals of the population with DBH (diameter at breast height) > or = 1 cm were sampled in a 25 hm2 broadleaved Korean pine forest plot of Changbai Mountains and divided into three DBH classes: 1-3 cm, 3-10 cm, and >10 cm. They were then genotyped using microsatellite loci. The spatial autocorrelation of their genetic structure was analyzed at different distance classes and life stages. The results showed that positive autocorrelation mainly occurred at scales less than 70 m, while negative autocorrelation occurred at scales larger than 110 m. The spatial genetic structure (SGS) at different life stages was similar due to limited pollen/seed dispersal and asexual reproduction. No significant self-thinning occurred in the studied population.

CYP19A1 gene polymorphisms and risk of lung cancer.

OBJECTIVES: To investigate the association between polymorphisms of aromatase (encoded by the CYP19A1 gene and a key enzyme in biosynthesis of oestradiol) and the risk of lung cancer, and whether there were differences stratified by sex and smoking history. METHODS: This case-control study included consecutive, nonselected and pathologically-confirmed lung cancer patients and healthy people. Participants were classed as nonsmokers or smokers by questionnaire. Peripheral blood samples from all participants were genotyped for three single-nucleotide polymorphism (SNPs; rs727479, rs730154 and rs10046); allelic frequencies were compared across genotype and clinical records. RESULTS: A total of 529 patients with lung cancer and 567 age- and sex-matched controls were included. After adjustment for age, sex and smoking history, rs727479 was significantly associated with the incidence of lung cancer (for alleles AC vs AA). There was also a significant difference between patients and controls in haplotype CCA, while haplotype ACA was only significantly associated with nonsmokers and female nonsmokers. CONCLUSIONS: Polymorphisms of CYP19A1 may be related to the increased risk of lung cancer; in particular, haplotype ACA may contribute to lung-cancer progression in nonsmokers. Further validation with larger populations is required.

Clinical analysis of postoperative venous thromboembolism risk factors in lung cancer patients.

BACKGROUND AND OBJECTIVES: The objective of this study is to explore clinical risk factors for venous thromboembolism (VTE) in postoperative lung cancer patients in order to provide a basis for the prevention and treatment of postoperative VTE. METHODS: A total of 1,001 lung cancer patients were retrospectively analyzed. Each patient was confirmed with surgical pathology diagnosis and had a complete clinical and follow-up record. VTE was identified in a combination of spiral computed tomography (CT), pulmonary angiography, and color Doppler ultrasound. We used life table method to create an occurrence frequency curve of thrombosis. We also searched for high risk factors for postoperative VTE with Cox multivariate regression model and created frequency curves of thrombosis against different risk factors using Kaplan-Meier method. RESULTS: As of July 31, 2011, the median follow-up time is 25.73 ± 0.11 months (19.23-31.37). The cumulative frequency of VTE among 1,001 lung cancer patients is 2%, 3%, 4%, 5%, and 5.3% over 1, 3, 6, 12, and 30 months after the surgery. COX regression analysis showed that the hazard ratio of VTE occurrence in patients with incomplete resection relative to ones with complete resection is 9.867 (95% CI: 5.275-18.459, P = 0.000). And the hazard ratio of VTE occurrence is 3.472 (95% CI: 1.761-6.845, P = 0.000) in patients with anti-angiogenesis treatment compared to patients without such treatment. The hazard ratio of VTE occurrence is 2.808 (95% CI: 1.439-5.479, P = 0.002) in patients with EGFR-TKI treatment relative to patients without the treatment, and 7.520 (95% CI: 3.968-14.250, P = 0.000) in patients with an increase in D-dimer level relative to normal ones CONCLUSIONS: The highest incidence of VTE is within 1 month after lung cancer surgery. High risk factors for VTE include incomplete surgical resection, postoperative use of anti-angiogenesis drugs, EGFR-TKI application and an increase in preoperative D-dimer level.

[Effects of recombinant human interleukin 11 on hematological malignancy after allogeneic hematopoietic cell transplantation].

OBJECTIVE: To investigate the effects of recombinant human interleukin 11 (rhIL-11) on hematological malignancy after allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS: A total of 48 patients with hematological malignancy from January 2006 to June 2010 were alternately enrolled into a prospective randomized study. And they were assigned into the control and rhIL-11 injection groups. Later the investigators compared two groups with regards to hematopoietic reconstitution, graft versus host disease (GVHD) classification, clinical recurrence rate and disease-free survival. RESULTS: With the therapy of rhIL-11, the absolute neutrophil counts recovering to 0.5 × 10(9)/L and platelet recovering to 20 × 10(9)/L were (15.1 ± 1.6) and (18.2 ± 3.3) days respectively. And they were significantly lower than those in control group [(16.1 ± 1.6) vs (22.4 ± 5.5) days, P = 0.032, 0.003]. The incidence of acute GVHD was surprisingly low in the study group (26.1% vs 50.0%, P = 0.048). There was no significant difference in chronic GVHD (36.8% vs 38.9%, P = 0.899) or relapse rate (5.1% vs 7.7%, P = 0.662) between two groups during a median follow-up period of 11.7 months. A trend of improved 3-year-disease-free survival was observed in the study group (65.4% vs 50.9%, P = 0.637). CONCLUSION: The application of rhIL-11 after allo-HSCT may accelerate both neutrophil and platelet engraftment and lower the occurrence of acute GVHD.

Discrepancy of biologic behavior influenced by bone marrow derived cells in lung cancer.

Disseminated cancer cells may initially require local nutrients and growth factors to thrive and survive in bone marrow. However, data on the influence of bone marrow derived cells (BMDC, also called bone stromal cells in some publications) on lung cancer cells is largely unexplored. This study explored the mechanism of how bone stromal factors contribute to the bone tropism in lung cancer. The difference among lung cancer cell lines in their abilities to metastasize to bone was found using the SCID animal model. Supernatant of bone marrow aspiration (BM) and condition medium from human bone stromal cells (BSC) were used to study the activity of bone stromal factors. We found bone stromal factors significantly increased the proliferation, invasion, adhesion and expression of angiogenosis-related factors, and inhibited the apoptosis for high bone metastasis H460 lung cancer cells. These biologic effects were not seen in SPC-A1 or A549 cells, which are low bone metastasis lung cancer cells. Adhesion of H460 cells to surface coated with bone stromal cells can activate some signal transduction pathways, and alter the expression of adhesion associated factors, including integrin ß 3 and ADAMTS-1, two potential targets related with bone metastasis. We concluded that bone marrow derived cells had a profound effect on biological behavior of lung cancers, therefore favoring the growth of lung cancer cells in bone.