bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preclinical evidence for synergistic effects of autophagy inhibitor and alpelisib in PI3KCA mutated non-small cell lung cancer: Implications for future clinical trials.
Authors: Shim Byoung Yong , Lee Sang-Bin , Kim Hyunho , Park Hyung Soon , An Ho Jung 
Published: June 2023

e21022 Background: The PI3K pathway is frequently activated in a variety of cancers including non-small cell lung cancer (NSCLC). PI3K mutation is associated with worse response to chemotherapy and consequently decrease the effectiveness of single administration of anticancer drugs. In this study, we checked the therapeutic efficacy of alpelisib either alone or in combination with an autophagy inhibitor for the treatment of NSCLC. Methods: We treated alpelisib and autophagy inhibitors in human NSCLC cell lines and measured the cell viability and protein expression of autophagy indicators, p62 and LC3B. Co-treatment of alpelisib and autophagy inhibitors significantly decrease the cell viability and proliferation compared to alpelisib alone. Based on the results of the combination experiment of alpelisib and autophagy inhibitors, Chloroquine (CQ) was selected for further study. Co-treatment of alpelisib and CQ significantly increase apoptosis and decrease tumor-related protein expression in in vitro and in vivo. Results: Our data demonstrates that alpelisib and autophagy inhibitor have a synergistic efficacy against NSCLC in vitro and in vivo. Conclusions: Based on these results, a Phase 1 clinical trial is currently being planned.
Effects of different immune microenvironment characteristics on predictive efficacy of PTCH1 mutations in immune checkpoint inhibitor therapy of solid tumors.
Authors: Zhu Guangyu 
Published: June 2023

e21026 Background: The PTCH1 gene encoding the protein corticosteroid receptor, which regulates the activity of the Sonic Hedgehog (SHH) signaling pathway. Mutations in PTCH1 result in disruption of the SHH signaling pathway and are closely related to the development of various solid tumors. Previous research has shown that mutations of the PTCH1 gene may result in decreased of antigen expression on the surface of tumor cells. However, relevant correlation with the efficacy of ICI therapy and immune microenvironment are still lacking. Methods: NGS data from an independent cohort (the MSKCC study cohort) of 1661 patients and Chinese clinical dataset (panel on 381/733-gene) of 35337 patients with pan-cancer to explore the association between PTCH1 mutations and immune biomarkers. TMB was defined as total number of somatic non-synonymous mutations in coding region. MSI was evaluated by NGS of 500 known MSI loci. PD-L1 expression was evaluated using immunohistochemistry (Dako 22C3). Patients from three independent cohorts (OAK, POPLAR and MSKCC study cohort) and were used to analyze the correlation between PTCH1 mutations and the efficacy of immune checkpoint blockade immunotherapies (ICIs). Estimation of immune filtration cells scores were conducted via TIMER2.0 (http://timer.cistrome.org/). Results: In Chinese cohort, there were 1384 (3.91%) patients harboured PTCH1 mutation ( PTCH1mut), slightly more than the MSKCC cohort (2.52%, 42/1661). For the TMB, both Chinese (median, 24.14 Muts/Mb vs 8.52 Muts/Mb, P ＜0.0001) and MSKCC (median, 22.30 Muts/Mb vs 5.90 Muts/Mb, P = 0.0035) cohort were associated with higher TMB than the wild-type. Supplemental analysis of MSI in the Chinese cohort showed significant differences between the PTCH1mut and PTCH1wt groups (P ＜0.0001), but not on PD-L1 levels (P = 0.64). In terms of prognostic effect with ICIs therapy, PTCH1mut were significantly associated with the overall survival (OS) of NSCLC (median, 5 months vs 11 months; HR = 1.61; 95% CI, 1.00-2.60; P = 0.049) and colorectal (median, 11 months vs 8 months; HR = 0.27; 95% CI, 0.08–0.90; P = 0.023). Interestingly, PTCH1mut in NSCLC was inversely associated with ICIs efficacy, as opposed to other solid tumors. Exploring the correlation between PTCH1 and immune microenvironment, it was found that CD4+ T cell (P＜0.001), macrophages (P＜0.001), NK cells (P＜0.001), and CD8+ T cells (P = 0.015) infiltration was significantly positively correlated in colorectal. But the infiltration of most immune cells was negatively correlated with PTCH1mut in NSCLC, that the B cells (P = 0.005), macrophages (P = 0.049), and NK cells (P = 0.022) had a significant difference. Conclusions: The results showed that the PTCH1 had a high correlation in solid tumors with TMB and MSI. The PTCH1 might a potential biomarker for ICIs therapy, and the immune microenvironment may be a factor affecting of it.
Effects of different immune microenvironment characteristics on effect of immune checkpoint inhibitors in solid tumors with TGFBR2 mutation.
Authors: Yao Rongrong 
Published: June 2023

e21027 Background: TGFBR2 is a member of the TGF-β receptor family, the protein encoded by it was involved in the regulation of cell proliferation, apoptosis, differentiation and other biological processes. TGFBR2 mutation can affect the occurrence of tumors. previous research showed that the TGF-β signaling pathway suppresses the tumor immune response, so TGFBR2 mutations may lead to tumor resistance to immunotherapy. However, effect of TGFBR2 mutations on ICIs and its correlation with immune microenvironment are rarely explored. Methods: NGS data from an independent cohort (the MSKCC study cohort) of 1661 patients and Chinese clinical dataset (panel on 733-gene) of 35337 patients with pan-cancer to explore the association between PTCH1 mutations and immune biomarkers. TMB was defined as total number of somatic non-synonymous mutations in coding region. MSI was evaluated by NGS of 500 known MSI loci. PD-L1 expression was evaluated using immunohistochemistry (Dako 22C3). Patients from three independent cohorts (OAK, POPLAR and MSKCC study cohort) and were used to analyze the correlation between PTCH1 mutations and the efficacy of immune checkpoint blockade immunotherapies (ICIs). Estimation of immune filtration cells scores were conducted via TIMER2.0 (http://timer.cistrome.org/). Results: In Chinese cohort, there were 831 (4.32%) patients harboured TGFBR2 mutation ( TGFBR2mut), in which the most number patients with TGFBR2mut were gastric carcinoma (10.53%), followed by colorectal (8.63%) and NSCLC (2.98%). Same as the MSKCC cohort (2.77%). For the TMB, both Chinese (median, 28.64 Muts/Mb vs 8.39 Muts/Mb, P ＜0.001) and MSKCC (median, 28.53 Muts/Mb vs 6.89 Muts/Mb, P = 0.030) cohort were associated with higher TMB than the wild-type. Supplemental analysis of MSI in the Chinese cohort showed significant differences between the TGFBR2mut and TGFBR2wt groups (P ＜0.001), but not on PD-L1 levels (P = 0.50). In terms of prognostic effect with ICIs therapy, TGFBR2mut were significantly associated with the overall survival (OS) of NSCLC (median, 2 months vs 11 months; HR = 3.46; 95% CI, 1.63-7.35; P ＜0.001) in OAK and POPLAR cohort, same as MSKCC cohort (median, 3 months vs 10 months; HR = 2.21; 95% CI, 1.04-4.71; P = 0.034). Interestingly, In the MSKCC cohort, opposite with NSCLC, majority tumors with TGFBR2mut had a longer survival value, showing a trend toward longer survival. Exploring the correlation between TGFBR2 and immune microenvironment. The results showed NK cell (P = 0.042) and CD4+ T cell (P = 0.036) infiltration were significantly negatively correlated in NSCLC. However, other solid tumors such as colorectal and melanoma are opposite. Conclusions: The results showed that the TGFBR2 had a high correlation in solid tumors with TMB and MSI. The TGFBR2 might a potential biomarker for ICIs therapy in NSCLC, and the immune microenvironment may be a factor affecting of it.
Genomic mechanisms of RET inhibitor sensitivity and resistance in RET-fusion positive cancer cells.
Authors: Heymach John , Nilsson Monique B. , Huo Xiaofang , Kumar Ashwani , He Jun , Kittler Ralf 
Published: June 2023

e21029 Background: RET fusions occur in 2-3% of lung cancer cases, and there are currently two FDA-approved RET-specific inhibitors (RETi), selpercatinib and pralsetinib. RET fusions are heterogeneous and the impact of specific fusion partners and their unique breakpoints on drug sensitivity is poorly understood. Moreover, while patients may be initially sensitive to RETi treatment, therapeutic resistance eventually emerges, and studies have shown that RET-dependent mechanisms of resistance include acquired resistance mutations that alter drug binding. We sought to investigate mechanisms of sensitivity and resistance to RET inhibitors in RET-fusion positive lung cancer in effort to improve treatment options and clinical outcomes in this patient population. Methods: We characterized the landscape of RET-fusions and -mutations in non-small cell lung cancer (NSCLC). KIF5B-RET, CCDC6-RET, and NCOA4-RET were the most frequently observed RET fusions in NSCLC. To investigate the drug sensitivity profile of individual RET fusion variants, we generated a panel of Ba/F3 cells expressing various RET fusion variants and evaluated in vitro sensitivity to RETi including selpercatinib, pralsetinib, vandetinib, cabozantinib, TPX-0046, lovatinib, and ponatinib. We observed that unique RET fusions impart differential sensitivities to RET inhibitors. For example, cells expressing KIF-RET (K15, R12) were highly sensitive to selpercatinib, pralsetinib, and ponatinib, whereas cells expressing KIF-RET (K22, R12) were likewise sensitive to selpercatinib and pralsetinib but were less sensitive to ponatinib. We next established a cell line (MDA-L-30) from a patient harboring a RET-fusion (KIF-RET; K15, R12) and observed a RETi sensitivity profile similar to that observed using the BaF3 system. Results: Next, we employed the LentiMutate approach to rapidly identify genomic mechanisms of RETi resistance. In cells expressing the KIF5B-RET (K15, R12) fusion, the G810S mutation was associated with acquired resistance to both selpercatinib and pralsetinib, consistent with prior reports and clinical observations. However, V804M/E and M918T mutations were associated with acquired resistance to selpercatinib but not pralsetinib, and L730I/V and E732K mutations were associated with resistance to pralsetinib but not selpercatinib. Conclusions: Taken together, these data indicate that individual RET fusion variants with diverse fusion partner breakpoints have distinct drug sensitivity profiles and that secondary resistance mutations may be non-overlapping between RETi. These findings support the need to comprehensively characterize RET-dependent mechanisms of resistance in order to provide therapeutic recommendations for treating RET-fusion driven cancers.
Association of docetaxel efficacy with cancer gene mutation status in patients with metastatic non-small-cell lung cancer who progressed on platinum doublets and immunotherapy.
Authors: Qin Kang , Wang Kaiwen , Li Shenduo , Hong Lingzhi , Rinsurongkawong Waree , Hubert Shawna Marie , Le Xiuning , Vokes Natalie I , Altan Mehmet , Gibbons Don Lynn , Heymach John , Lee J. Jack , Lou Yanyan , Zhang Jianjun 
Published: June 2023

e21030 Background: Docetaxel +/- ramucirumab remains the standard of care therapy after progression on platinum doublet and immune checkpoint blockade (ICB) in patients with metastatic non-small cell lung cancer (NSCLC). However, the clinical benefit from docetaxel is short-lived with substantial toxicity. Additionally, whether cancer gene mutation status impacts the benefit from docetaxel has not been systemically studied. In this real-world study, we aim to investigate whether cancer gene mutation status is associated with benefit from docetaxel. We also explored whether IMPOWER150-based regimens (ABCP-atezolizumab + bevacizumab + carboplatin + paclitaxel; ACP-atezolizumab + carboplatin + paclitaxel; BCP-bevacizumab + carboplatin+paclitaxel) may serve as alternative options with better efficacy in this patient population. Methods: We retrospectively queried MD Anderson Cancer Center GEMINI database for patients with metastatic NSCLC who received docetaxel, docetaxel+ramucirumab, or one of the above-mentioned IMPOWER150-based regimens after progression on concomitant or sequential platinum-doublet and ICI. Primary endpoints include progression-free survival (PFS) and overall survival (OS). Results: 274 patients were analyzed (docetaxel n = 99; docetaxel +ramucirumab n = 142; ABCP n = 28; BCP n = 4, ACP n = 1). No significant difference was observed in mPFS (3.00m versus 3.93m, P = 0.156) or mOS (8.40m vs.8.67m, P = 0.737) between patients from docetaxel monotherapy group and docetaxel+ ramucirumab group. Cancer gene mutations in EGFR, KRAS, TP53 or PD-L1 expression (0-1%; 1-49%; ≥50%) were not associated with PFS or OS in the 241 patients treated with docetaxel +/- ramucirumab. Furthermore, there was no difference in mPFS (5.50m versus 3.47m, P = 0.516) or mOS (10.40m versus 8.83m, P = 0.737) in patients who received IMPOWER 150-based regimens compared to those who were treated with docetaxel+/- ramucirumab. The median treatment duration was 1.60m (0.70m-20.23m), 1.90m (0.70m-32.90m), 4.80m(0.70m-33.47m) and 11 patients (11.11%), 20 patients (14.08%), and 3 patients (9.09%) discontinued treatment due to adverse events in the patients treated with docetaxel monotherapy, docetaxel+ramucirumab combined therapy, and the IMPOWER150 regimens, respectively. Conclusions: These results from this real-world study suggested that unlike for ICI therapy, where onco-driver mutations have profound impact on the clinical benefit, the cancer gene mutation status does not impact the benefit from docetaxel +/- ramucirumab in NSCLC patients who progressed on platinum doublets and ICI. Furthermore, the clinical benefit from docetaxel +/- ramucirumab is short-lived. Novel treatment regimens are urgently needed in this clinical setting.
Clinical outcomes of patients with advanced NSCLC with different EGFR exon 19 deletion subtypes treated with first-line tyrosine kinase inhibitors.
Authors: Gu Yangchun , Yu JinYu , Hu Haifeng , Zhang Hua , Cao Baoshan , Liang Li 
Published: June 2023

e21034 Background: Epidermal growth factor receptor (EGFR) exon 19 deletion (Ex19del) in non-small cell lung cancer (NSCLC) consists of many subtypes, and their sensitivity to tyrosine kinase inhibitors (TKIs) has not been clearly defined. This study aimed to investigate the clinical outcomes of advanced NSCLC patients with different EGFR ex19del subtypes treated with different TKIs. Methods: We retrospectively analyzed stage IIIB-IV NSCLC patients with EGFR Ex19del and first-line TKIs therapy. E746_A750del was defined as classic group, and the others as non-classic group, which was further divided into subgroups according to deletion with or without insertion, starting codon or length of deletion. The primary endpoint was progression free survival (PFS). Results: There were 17 Ex19del subtypes identified in 101 patients. The frequency of E746_A750del was 64.4% (65/101), and the top three frequent non-classic subtypes were L747_T751del (6.9%, 7/101), L747_P753delinsS (5.9%, 6/101) and E746_S752delinsV (5.0%, 5/101). In all patients, the median PFS (mPFS) of first-line TKIs in classic and non-classic groups were 14.3 months (m) and 19.3 m ( p > 0.05). In non-classic group, the mPFS in deletion with insertion (delins) and without insertion subgroups were 25.3 m and 11.2 m; in deletion starting with E746 and with other codon subgroups were 29.7 m and 19.3 m; and in deletion length of 15 nucleotides (n) and of other length subgroups were 11.2 m and 25.3 m. The mPFS of these non-classic subgroups were not statistically different with that of classic group ( p > 0.05). In all patients, the mPFS of first-line therapy with the 1st, 2nd and 3rd generation TKIs were 17.4 m, 15.6 m and 20.5 m, respectively ( p＞0.05); in classic group, the mPFS were 14.3 m, 16.9 m and 20.5 m, respectively ( p＞0.05). However, in non-classic delins subgroup (29.7 m, 15.6 m and 11.9 m) and in deletion length of ≥18 n subgroup (25.3 m，12.3 m and 11.9 m), the 1st generation TKIs had an insignificantly longest mPFS ( p＞0.05). When resistant to 1st or 2nd generation TKIs, patients in classic group showed a trend of higher incidence of T790M mutation than non-classic group (72.0% vs 43.8%, p = 0.070). In multivariant analysis, pleural metastasis (PM) had interaction with Ex19del grouping, warranting stratification analysis. In patients without PM, the mPFS of first-line TKIs in classic group was significantly shorter than non-classic group (13.8 m and 29.7 m, p = 0.026). However, in patients with PM, the mPFS of classic group was numerically longer than non-classic group (16.9 m and 11.7 m, p > 0.05), with the shortest mPFS in non-classic without insertion subgroup, and in non-classic with 15 n deletion subgroup. Conclusions: In advanced NSCLC patients with EGFR Ex19del, the efficacy of first-line TKIs therapy was affected by the presence of pleural metastasis, Ex19del subtypes and different generation of TKIs.
Artificial neural network model analysis in T790M detection after failure of first- and second-generation epidermal growth factor receptor tyrosine kinase inhibitors.
Authors: Pluzanski Adam , Świetlik Dariusz , Krzakowski Maciej Jerzy 
Published: June 2023

e21041 Background: Despite osimertinib availability, first or second generation (1st/2nd gen.) epidermal growth factor receptor tyrosine kinase inhibitors (EGFR TKIs) are commonly used in many countries. Clinical factors identified before first line EGFR TKIs treatment that correlate with T790M occurrence are not well-known. In this single center retrospective study we define the artificial intelligence-based model that support T790M detection in daily practice. Methods: In 80 patients (pts) consecutively progressed on 1st/2nd generation EGFR TKIs T790M mutation was assessed. In multivariate logistic regression factors predictive to T790M mutation were identified. Based on clinical and molecular factors present before EGFR TKIs initiation multi-layer perceptron (MLP) neural network was used for building model classifying patients according to T790M status. The artificial neural network consisted of three layers: input, hidden and output layers of 36, 6 (optimally due to the result of the neural network) and 1 neurons, respectively. During the learning process the weight links between the neurons were modified using Broyden-Fletcher-Goldfarb-Shanno algorithm. To calculate the diagnostic quality of the artificial neural network, we divided at random of all patients for two groups: training and testing. The training group contained 65 and testing group 15 cases. Sensitivity and specificity for both models were assessed. TIBCO Software Inc., Statistica (data analysis software system), version 13 software was used for all calculations. Results: In 49/80 pts (61.3%) T790M was present. In logistic regression model: del19 EGFR mutation, chest or liver metastases and 1st gen. TKI treatment correlated with T790M presence. Parameters included in building neural network model were: del19/L858R/other EGFR mutation status, sex, age, 1st/2nd gen. TKI in first line, clinical stage, metastases location, ECOG PS, smoking history. Learning and testing phase models detected T790M with sensitivity-94.7%, specificity – 91.3% and sensitivity-77.8%, specifity-83.3%. In testing set (15 pts) proposed neural network model achieved 80% accuracy in predicting correctly T790M status. Clinical stage, TKI generation in first line, metastases location, EGFR mutation were the most valuable entrance parameters. After conducting a sensitivity analysis for all 8 the analysed variables the observed error quotients were above 1, therefore, they are all significance and should be entered as input to the developed network. Conclusions: The proposed artificial neural network model used parameters identified before start of TKI treatment and achieved high accuracy in T790M status prevalence. Although this model need to be validated in large cohort it can be an useful tool to support clinicians decision.
Impact of SPARC expression on pembrolizumab treatment response and prognostic role in advanced stage non-small cell lung cancer.
Authors: Goktas Aydin Sabin , Bilici Ahmet , Calis Elif , Olmez Omer Fatih , Karci Ebru 
Published: June 2023

e21042 Background: Secreted protein acidic and cysteine-rich (SPARC) was highly expressed in non-small cell lung cancer (NSCLC) tissue. Studies have indicated the association between SPARC expression and immune-cell infiltration and the prognosis of lung cancer. Despite the optimal first-line treatment approach in advanced NSCLC that lacks a driver mutation includes immunotherapy with or without chemotherapy, a well-defined tool or test for predicting response has yet to be created. We aimed to elucidate the influence of SPARC expression terms of clinicopathology, pembrolizumab response and prognosis in metastatic NSCLC patients. Methods: Thirty-six patients diagnosed with advanced-stage NSCLC without actionable driver mutation and recieved pembrolizumab in the first line setting were included in this study. Programmed death ligand-1(PD-L1) and SPARC expression were assessed by means of PD-L1 IHC 22C3 pharmDx and BenchMark ULTRA assay(Ventana Medical Systems, Tucson, AZ) in paraffin-embedded blocks. The expressions were categorised according to the tumor proportion score. Staining intensity of SPARC was graded according to the following criteria: 1+ (weak), 2+ (moderate), and 3+(strong). Results:The median age was 62 (range 45-81). One patient was female, and four patients did not have a smoking history.Twenty-seven of tumor were adenocarcinoma, and six were squamous cell carcinoma. PDL-1 status was < 1% in 4 (11.4%), 1-49% in 12 (34.3%), and > 50% in 20 (54.3%) patients.There was no significant correlation between SPARC expression and smoking status, histologic type of tumour, T and N status, and liver and bone metastasis. Central nervous system (CNS) metastasis and progression was seen in 8 (57.1%), 2 (12.5%), and 1 (16.7%) and in 6 (16.7%), 0, and 6 (37.5%) patients with SPARC 1+,2+, and 3 +, respectively. Controversially, higher SPARC expression was significantly correlated with lower rates of brain metastasis but higher rates of CNS progression (p = 0.022 and p = 0.011, respectively). While PD-L1 and SPARC expression were not significantly correlated, a trend toward low SPARC expression was seen in patients with PD-L1 > 50%. The objective response rate (ORR) trended to be higher in the SPARC 1+ group (85.7%, 43.8%, and 50.0% in SPARC 1+, 2+ and 3+ group, respectively, p = 0.052). Univariate analysis revealed that SPARC expression was not a significant prognostic factor for both PFS (p = 0.7) and OS (p = 0.07). But, low SPARC expression was a significant predictive factor for the first-line pembrolizumab treatment response (p = 0.04, OR:0.11, 95%CI 0.01-0.92) in NSLC patients. Conclusions: Our study lightened a new area in the literature that SPARC expression might predict the pembrolizumab response and might be a marker for CNS progression in NSLC patients. These results should be explored in further studies to address the potential therapeutic implications of SPARC expression.