bluuebunny/crossref_metadata_2025 huggingface dataset:
Preclinical anti-tumor activity of small-molecule oral PD-L1 checkpoint inhibitors.
Authors: Thi Emily P. , Cole Andrew G. , Heffernan Gavin , Iott Christina L. , Ozturk Seyma , Ganchua Sharie C. , Nguyen Dan , Graves Ingrid , Quintero Jorge G. , Stever Kim , Fan Kristi , Ahuja Vijay , Kultgen Steven G. , Shubina Maria , Liu Boya , Tang Sunny , Harasym Troy , Lam Angela M. , Sofia Michael J.
Published: June 2022

e14558

Background: The PD-1/PD-L1 checkpoint axis is a validated target in oncology, and immunotherapy with antibody approaches have proven efficacy across various tumor types. Oral small-molecule inhibitors of PD-L1 may offer advantages over antibody approaches by enabling tunable on-target engagement and the potential for better tissue penetration and improved efficacy. Here we report the preclinical in vitro activity of small-molecule inhibitors of PD-L1 possessing a novel mechanism of action, favorable pharmacokinetics, and demonstrated in vivo efficacy in a mouse colon adenocarcinoma model. Methods: In vitro activity was assessed in a Jurkat T cell NFAT reporter assay and PD-L1 reduction was confirmed in CHO-K1 cells expressing human PD-L1 (CHO-K1-hPD-L1) and in peripheral blood mononuclear cells (PBMCs) from healthy donors. T cell activation assays were conducted with PBMCs from healthy donors. Non-specific cytokine release was evaluated in human whole blood. Pharmacokinetic (PK) evaluations were conducted in rodents and non-human primates (NHP). In vivo efficacy was evaluated in an MC38 tumor humanized PD-L1 and PD-1 mouse model. Results: Small-molecule inhibitors of PD-L1 were able to disrupt PD-1:PD-L1 and PD-L1:CD80 interactions through the reduction of PD-L1 expression on the cell surface via a novel internalization mechanism, resulting in PD-L1 degradation (EC50s ranged from 1.9 – 24 nM in CHO-K1-hPD-L1 and primary human myeloid cells). Lead PD-L1 inhibitors mediated potent activation of T cells in a NFAT reporter assay (EC50s of 13 and 18 nM) as well as dose responsive elevations in IL-2 production in human PBMCs stimulated with staphylococcal enterotoxin B. Compound treatment did not elicit non-specific cytokine release in human whole blood, supportive of favorable immune safety. PK profiles showed low systemic clearance in rodents and NHP. In an MC38 tumor model, once daily oral administration of compounds at 3, 10, and 30 mg/kg resulted in dose responsive tumor reduction that was associated with T cell activation and infiltration into tumors. Conclusions: Oral small-molecule PD-L1 inhibitors possessing a novel mechanism of action and the ability to mediate T cell activation in primary human immune cell types were identified. These compounds display in vivo anti-tumor efficacy comparable to anti-PD-L1 antibody and possess favorable preclinical profiles for further development, with the potential for all-oral treatment regimens for oncology.
HDAC inhibitor Chidamide, but not romidepsin, synergizes with humanized PD1 antibody to enhance T-cell chemokine expression and augment IFN-gamma response in NK-T-cell related lymphoma: A preclinical study.
Authors: Wen Tingyu , Ma Fei , Liu Peng
Published: June 2022

e14568

Background: The incidence of NK-T cell lymphoma (NKTL) in Asia is significantly higher than that in European and American countries. The median survival time of EKTL is only 8-12 months, and the 5-year overall survival rate is still less than 30%. New therapies or combinations are warranted. Methods: The murine NKTL cell line EL4 and RMA were used to establish cell line xenograft models in transgenic humanized PD1 mice. Different dosages or sequential HDAC inhibitors were combined with humanized PD1 antibody in vivo to test whether the synergistic effect is existing. RNA-seq, qPCR, and IHC were performed to illustrate the potential mechanisms. Three NTKL patients who were treated with hPD1 and Chidamide in clinical were recorded in this study. Results: Romidepsin combined with hPD1 antibody is superior to hPD1 antibody alone in the treatment of two NKTL CDX models (EL4 and RMA), but it is similar with romidepsin single agent, either in different dosages or sequence. However, Chidamide combined with hPD1 antibody significantly inhibits the tumor growth compared to single agents in these two pre-clinical models. RNA-seq reveals Chidamide synergizes with humanized PD1 antibody to enhance T-cell chemokine expression, augment IFN-gamma response and increase CD8 T cell infiltration. String PPI analysis and ingenuity pathway analysis suggest IFN-gamma is the hub upstream regulator in the combination. On the contrary, the romidepsin combinations decrease the activity of T cell immune responses and the function of immune cell migration. The expression of IFN-gamma gene set signatures is decreased in the romidepsin combination. Three NKTL patients who received PD1 antibody and Chidamide are showed promising efficacy, and the progression-free survival is 26+ months, 8 months, and 9+ months respectively. Conclusions: Different HDAC inhibitor shows different combination effects with immunotherapy. Chidamide combination shows a synergistic effect with immunotherapy by enhancing INF-gamma response, but romidepsin combination antagonizes this effect significantly.
A pan-cancer analysis of the granzyme family based on the TCGA database and single-cell RNA sequencing data.
Authors: Xu Bin , He Junju , Li Jing , Wu Jie , Zhang Huibo , Jin Yan , Yao Yi , Song Qibin
Published: June 2022

e14580

Background: Human Granzymes (GZMs) are mainly regarded as protective cytotoxic proteases that block the development of cancer. This study aimed to systematically analyze the expression signature, immune infiltration pattern, predictive values of prognosis and immune response, and the biological process associated with GZMs in different cancers. Methods: We estimated the predictive values of GZMs in prognosis and drug sensitivities by Cox regression analysis, immunophenoscore (IPS) algorithm, etc. We identified potential factors associated with the expression of GZMs, involving the somatic mutation and copy number variation of driver genes. We further investigate the distributions of GZMs and their discrepancy in single-cell resolution. The package CellChat and SCENIC were used for cell-cell communications and regulatory network reconstruction respectively. The ssGSEA algorithm was used to calculate the GZMs score for a gene set of five granzymes and the enrichment score (ES) of regulons based on the bulk-seq data. We chose the specific regulons to cluster patients in pan-cancer. Results: In the immunotherapy context, the higher GZMs score was associated with better overall survival (OS) in urothelial carcinoma (HR = 0.31, p< 0.01). In melanoma, the pooled HR value calculated by meta-analysis assay was 0.33 (95%CI: 0.189-0.58). In the single-cell resolution, we found the three patterns of GZMs expression in CD8+T/NK cells. Furthermore, we analyzed the discrepancy among different GZMs subtype cells in functions, cell-cell communications, and cell-type-specific regulons. In CD8+ Effector memory T cells, cluster 1 (GZMB+) and cluster 2 (GZMK+) exhibited different enriched pathways in adhesion, anti-bacteria, chemotaxis, migration, and metabolism. In the cell-cell communications analysis, the IFNG − (IFNGR1+IFNGR2) between CD8+ T cells and malignant cells was only significant in the C1 and C2 clusters. Pan-cancer patients were divided into five regulons clusters based on the regulons. Cluster 5 had the worst OS (HR = 8.49, 95%CI = 6.67-10.81, p< 0.01) compared to cluster 1 which had the best prognosis. Cluster 5 had higher ES of regulons including Myb, Hmgb2, E2f7, E2f8, and lower ES of Egr3. Conclusions: In conclusion, the expressions of GZMs, GZMs score, and the specific regulons identified in this study were associated with the prognosis in pan-cancer patients. GZMs score was a valuable biomarker that can predict the response to immunotherapy. The patients who belong to different regulons subtypes have specific transcription factors, which may be potential targets for the precision medicine of anti-tumor strategies in pan-cancer.
Structure-based prediction of neoantigens paired with T cell receptors on pre-existing CD8+ tumor-infiltrating lymphocytes.
Authors: Lee Bo Ryeong , Kim Sungsik , Kim Sung-min , Park Keunchil , Park Woong-Yang
Published: June 2022

e14583

Background: Tumor neoantigens have ability to expand tumor-specific T cell immunity, which could be boosted by anti-PD-1 immunotherapy. Therapeutically relevant neoantigens should be presented on patient HLAs and recognized by tumor-reactive T cells. Despite tumor-infiltrating lymphocytes (TILs) have enriched tumor-reactive T cell populations, most tumor-specific TILs exhibit exhausted phenotype and have limitations to in vitro screening. Here, we developed in silico structure-based prediction of neoantigen discovery pipeline by pairing with T cell receptors (TCRs) on pre-existing CD8+ exhausted tumor-infiltrating lymphocytes. Methods: Tumor resections from patients with liver, stomach, colorectal, and lung cancers are subject to whole exome and transcriptome. In addition, TILs from the patients are subject to scRNA/TCRseq to select TCRs of exhausted T cells, which are mostly thought to have tumor-reactivity. Neoantigen epitopes are prioritized from our in silico pipeline including HLA binding and TCR-peptide-HLA structure-based pairing score. To evaluate the immunogenicity of selected neoantigens, the neoantigens are tested for in vitro IFNg ELISPOT assay using peripheral blood mononuclear cells (PBMCs) from the same patients, which sensitively detects antigen-experienced T cells. Results: For 5 patients with T cell-reactive neoantigens, among 23 neoantigens selected by our in silico pipeline and tested in vitro, 10 neoantigens showed positive pre-existing T cell responses by matched patients. Then, we analyzed gene expression profiles of TILs paired in silico with in vitro T cell response-positive or negative neoantigens (pTILs and nTILs, respectively) combined with TILs from 23 solid cancer patients. Interestingly, pTILs were mostly mapped to the clusters which highly expressed markers of exhaustion and cytotoxicity, while nTILs showed random distribution across all the clusters. Conclusions: Neoantigen prediction using structure-based pairing of neoantigens and phenotype-selected TILs showed promising potential to better select therapeutically-relevant cancer vaccines. This data supports further investigation of our in silico pipeline into more patient samples and preclinical studies in mouse tumor models.
Validity of mutations as a cancer chronometer.
Authors: Kawsar Farhan , Safar Ahmad Mazen , Chen Jim Zhongning
Published: June 2022

e15015

Background: Staging is devised to assess prognosis, and ultimately direct the management of cancer. Though staging systems don't necessarily confirm chronological progression from stage I to IV, there is near consensus that advanced stages are 'later' versions of a given cancer. This is reflected in the philosophy and efforts to identify 'early' cancer in screening programs. Tumor Mutational Burden (TMB) is one measure of the degree of proliferation, thus can be utilized as a molecular clock (Vogelstein), a surrogate for chronology. Since TMB is currently a clinical metric provided to oncologists in routine practice, proper interpretation of TMB is critical. We hypothesized that (i) metastatic disease is a ‘different’, rather than 'later' manifestation of a given cancer. Furthermore, we hypothesized that (ii) proliferation rates would be mirrored by the TMB, and lastly, that (iii) TMB will correlate with clinical virulence. Methods: (i) We mined the publicly-available TCGA database (cbioportal.org) for TMB from 558 samples spanning 5 whole genome & whole exome neoplasm datasets (Breast, Colon, Renal cell, Pancreatic, Cervical cancers). (ii) We compared the TMB in Burkitt's lymphoma, a highly proliferative neoplasm, with follicular lymphoma, a classically quiescent malignancy. (iii) We compared the TMB in skin squamous cell carcinoma (SSCC), a cancer with negligible impact on survival, with Acute Myelogenous Leukemia (AML), a highly lethal malignancy despite aggressive therapy. Results: (i) The 95% Confidence Intervals (CI) surrounding the median TMB were overlapping without statistical significance across ALL stages within EVERY histology examined. (ii) To our surprise, the TMB 95% CI were overlapping between the 2 subsets of B-cell lymphoma examined. (iii) TMB was substantially higher in SSCC (median of ̃800) compared to a mere 8 in AML. Conclusions: Assuming validity of Vogelstein’s molecular clock model, mutational probing does not support the concept that a stage IV malignancy is a chronologically delayed manifestation of a given neoplasm. Rather, we suggest an alternative approach where aggressive/metastatic cancers are inherently 'different' with unique abilities rather than a ‘later’ edition of a monodirectional succession. We also posit that cells that live for years (follicular lymphoma) can accumulate comparable levels of TMB as Burkitt's because the limited life span in Burkitt's (days to weeks) precludes the accumulation of high TMB. Finally, the clinical outcome cannot be discerned from the degree or mutability— which is rationally a predictor of immune susceptibility. It's noteworthy that the observed levels of mutations in SSCC, reflective of the sun mutagenicity, is more than 3-fold of that reported for melanoma (̃274) but this fact is rarely presented in cancer genomic landscapes, and may explain the rarity of metastatic SSCC owing to the immune clearance of metastases unlike the skin surface devoid of such immune access.
Dexamethasone and brain metastasis-infiltrating CD8+ T cells.
Authors: Sudmeier Lisa , Hoang Kimberly B. , Nduom Edjah , Goyal Subir , Liu Yuan , Olson Jeffrey J. , Ramalingam Suresh S. , Ahmed Rafi
Published: June 2022

e15075

Background: Nearly all patients who develop large and/or symptomatic brain metastases receive corticosteroids such as dexamethasone (Dex) to treat or prevent symptoms like nausea, headaches, or focal neurologic deficits. Dex has immunosuppressive effects such as induction of T cell apoptosis, so it’s possible that this treatment may impair the anti-tumor immune response. To address this question, we performed a secondary analysis of our in-press data describing the phenotype of brain metastasis-infiltrating CD8+ T cells to determine whether the duration of Dex therapy prior to surgical resection correlated with phenotypes we described our cohort. Methods: Fresh brain metastases specimens were weighed, and immune cells were isolated. CD45+ and CD8+ lymphocytes were counted via flow cytometry from 35 and 34 samples, respectively. A subset of samples were analyzed by high-parameter spectral flow cytometry to gain phenotypic information. Dex treatment was later extracted from the electronic medical record, and Spearman’s correlation coefficients (CC) were calculated to evaluate the association between duration of Dex therapy and brain metastasis-infiltrating lymphocyte density or phenotype. Results: Patients were on Dex for a median of 3 days (4mg q6 hours) prior to surgery. On univariate analysis, the CC between CD45+ lymphocytes or CD8+ T cells per gram of tumor and duration of Dex treatment was -0.185 (P=0.288) and -0.122 (P=0.49), respectively. The CC between frequency of PD-1+ CD8+ T cells and duration of Dex was -0.064 (p=0.784, 21 patients). In our previous work, we used the FLOWSOM algorithm to identify distinct populations of CD8+ T cells that were enriched in brain metastases compared to blood. We described two such populations, one with a tissue residence phenotype, and the other with terminally-differentiated phenotype. The CC between frequency of these populations and duration of Dex was 0.043 (p=0.889) and 0.238 (p=0.433), respectively (13 patients). We also tested for correlation between frequency of individual PD-1+ CD8+ T cell populations and duration of Dex treatment (13-18 patients). The CC for Tim3+, CD39+, CTLA4+, CD127+, Tcf-1+, CD28+, and GZMB+ populations of PD-1+ CD8+ T cells were 0.037 (p=0.891), 0.096 (p=0.705), -0.094 (p=0.738), 0.011 (p=0.971), -0.026 (p=0.918), 0.384 (p=0.128), and 0.236 (p=0.358), respectively. Conclusions: Within this cohort of patients who were on Dex for a median of 3 days prior to surgery, duration of pre-surgery Dex did not significantly affect density of brain metastasis-infiltrating CD45+ lymphocytes or CD8+ T cells or frequency of PD-1+ CD8+ T cells.
Development of PLM-102, a novel dual inhibitor of FLT3 and RET as a new therapeutic option for acute myeloid leukemia.
Authors: Kim Myungjin , Oh Su-jin , Kim WooChan , Choi Yong June , Lee Jae-Seon , Lee So-Deok , Park Jin-Hee , Lee Eun Ji , Kang Keon Wook , Jang Soo Yeon , Kim Yong-Chul
Published: June 2022

e15103

Background: Mutations of the FMS-like tyrosine kinase 3 (FLT3) gene occur in approximately 30% of all acute myeloid leukemia (AML) cases, with the internal tandem duplication (ITD) representing the most common type of FLT3 mutation (FLT3-ITD; approximately 25% of all AML cases). Although several FLT3 inhibitors have been developed, occurrence of secondary TKD mutations of FLT3 such as FLT3/D835Y and FLT3/F691L causes the acquired resistance to the current FLT3 inhibitors and eventually become a key area of unmet medical needs. Here, we have revealed that PLM-102, a novel, orally active FLT3 and RET dual inhibitor, has a potential to overcome the acquired resistance to current FLT3 inhibitors. Methods: 1. Kinase assay- Biochemical assays for FLT3 (WT and D835Y) and RET (WT and Mutants) were performed according to ADP-Glo kinase assay protocol(Promega). 2. Cell proliferation and Apoptosis- Human leukemia cell line MV4-11 and MOLM-14 were purchased from ATCC and DSMZ. Cells were seeded at a density of 2 X 103 cells per well and treated with the indicated concentrations of inhibitors for 72 hours at 37°C. Cell viability was determined by an Alamar Blue assay (Bio-Rad). Caspase-3/7 activity was measured by using the Caspase-Glo 3/7 assay (Promega). 3. Western blot analysis- Immunoblotting using MOLM-14 cells was performed using anti-phospho-FLT3 (Cell Signaling Technology #3461) and anti-FLT3 antibody (Cell Signaling Technology #3462). 4. In vivo mouse models- The MV4-11 and MOLM-14 cells are implanted into the subcutaneous space of the left flank of the mice. Resulting tumors are monitored by calipering twice weekly. Treatment started after randomization when tumor volumes had reached a size of approximately 100-150 mm3. For statistical analysis, analysis of variance (ANOVA) was performed using Prism 9.0 to examine statistical differences. Results: In compared to FDA-approved Gilteritinib, PLM-102 showed stronger sub-nanomolar IC50 values in FLT3 kinases regardless of wild-type, ITD, TKD and ITD/TKD mutants in both kinase- and cell-based assays. PLM-102 inhibited phosphorylation of FLT3 and its downstream signaling pathways, and induced apoptosis as evidenced by PARP-cleavage and caspase-3 activation. Moreover, PLM-102 showed an excellent anti-tumor activity in mouse xenograft models implanted with MV4-11 and MOLM-14 AML cells. Conclusions: Taken together, PLM-102 showing potent anti-cancer activity against various in vitro and in vivo AML models could be developed as a valuable agent overcoming the acquired resistance to the current FLT3 inhibitor.
Clinical pharmacokinetic/pharmacodynamic relationship of DZD2269, a potent and selective A2aR antagonist designed to overcome high levels of adenosine induced immunosuppression.
Authors: Liu Ziyi , Bai Yu , Hu Dongdong , Zhang Lin , Yong Tanyada , Yang Zhenfan
Published: June 2022

e15106

Background: Extracellular adenosine suppresses immune cells’ function through binding to its receptor A2aR. In the tumor microenvironment, adenosine concentration could be several hundred-fold higher than in blood. DZD2269 was designed to fully block A2aR in a wide range of adenosine concentrations. In preclinical studies, DZD2269 could most effectively restore immune cell function inhibited by high levels of adenosine among A2aR antagonists currently in clinical studies. In mouse syngeneic prostate cancer model, DZD2269 could significantly enhance the antitumor activity of anti-PD1 antibody as well as radiotherapy. Two ongoing clinical studies of DZD2269 in healthy volunteers (PAN-GU 2, NCT04932005) and patients with metastatic castration resistant prostate cancer (PAN-GU 1, NCT04634344) are being conducted to characterize its safety, PK, PD and to assess its preliminary anti-tumor efficacy. Here, we report clinical data from the PAN-GU 2 study. Methods: The phase 1 healthy volunteer study is a double-blind, placebo-controlled study to evaluate safety, PK, and effect on biomarkers. It consists of three parts: single ascending dose (SAD): 5, 10, 20, 40, 80 and 160 mg; multiple ascending dose (MAD): from 10 mg BID for 7 consecutive days; and food effect (FE): fasted, low-fat or high-fat meal condition. A2aR pathway blockade by DZD2269 is evaluated by analyzing pCREB inhibition on whole blood T cells following ex vivo stimulation with 10 µM NECA. Results: In SAD part of the healthy volunteer study, a total of 48 subjects received a single oral dose of DZD2269 (n = 36) from 5 mg to 160 mg or placebo (n = 12). There were 7 TEAEs reported by 4 subjects and no ≥ grade 3 TEAE or SAE. After a single oral dose, the rate of absorption of DZD2269 was moderate (median tmax: 1.0 to 2.75 hr). DZD2269 exhibited low to moderate clearance (averaged value: 16.1 to 45.3 L/h) and extensive volume of distribution (averaged value: 209 to 738 L), resulting in a mean t1/2 of 7 ̃ 10 hr; a trend of increased t1/2 was observed at higher dose levels. Systemic exposure of DZD2269 (AUC and Cmax) increased in an approximately dose-dependent manner. Based on PK/PD analysis, approximately 90% pCREB inhibition could be achieved by a single dose of 80mg for 24 hours. Conclusions: Single oral dose of DZD2269 ranging from 5 mg to 160 mg was safe and well tolerated. Good PK/PD correlation was demonstrated in the study. DZD2269 could effectively reverse high adenosine induced immunosuppression. A phase1/2 study evaluating safety and efficacy of DZD2269 in patients is ongoing. Clinical trial information: NCT04932005.
A potential mechanism of ferroptosis modulation for immunotherapy in LUAD: ceRNAs networks of OTUD6B-AS1 modulate the balance of ubiquitination.
Authors: Yao Lintong , Zhou HaiYu
Published: June 2022

e15111

Background: Ferroptosis plays a pivotal role in cancer progression and therapeutic response of immunotherapy in lung adenocarcinoma (LUAD). Recent studies on ferroptosis regulation by lncRNAs were conducted sporadically. Our study explored FrlncRNAs in LUAD comprehensively, exploring functional mechanisms and verified the correlation between ferroptosis and ubiquitination. Methods: Data of LUAD samples were download from GEO and TCGA databases. Annotated ferroptosis-related genes were retrieved from FerrDb and GeneCards databases. Ferroptosis-related lncRNA (FrlncRNAs) was identified by correlation analysis. The LASSO analysis and cox regression analysis were performed to filtrate significant prognostic FrlncRNAs, followed with model construction and patient stratification. Tumor immune microenvironment, functional pathways were investigated. Subcellular location and potential competing endogenous RNAs (ceRNAs) mechanisms were predicted by GDCRNATools algorithm. Results: Ferroptosis-related prognostic model constructed by 14 FrlncRNAs signature showed high prognostic efficacy with significant survival difference and robust area under the curve (AUC for 5 years survival: 0.89 in training cohort and 0.87 in validation cohort). Higher proportion of myeloid-derived suppressor cells were detected in high-risk group, of which ferroptotic status were supressed. Ferroptosis-enhanced samples harboured higher expression of immune checkpoints such as PD-L1, CTLA-4, TIM3 and CD47 and immune-recruiting interleukins such as IL2, IL4, IL7. Reasonably, more potential responders to immunotherapy were predicted in ferroptosis-enhanced samples. Considering the subcellular location, potential mechanism of ceRNA network was predicted that OTUD6B-AS1 may compete with mir-144 to regulate or modify NUDCD1 and MARCH7 through miRNA sponge. OTUD6B-AS1 encodes the protein of ovarian tumor domain deubiquitinase 6B, while MARCH7 contributes to a RING domain of membrane bound E3 ubiquitin ligases. GO, KEGG and GSEA pathway analyses focused on ubiquitin-protein transferase activity, polyubiquitination, mTOR, Hippo and NOTCH pathways. Protein-protein interaction identified hub genes in ferroptotic regulation such as NEDD8 and HERC2, which were coding genes of ubiquitin ligase E3 as well. Hence, the balance of ubiquitination and deubiquitination induced by the interplay of ceRNA network could be pivotal process in ferroptosis modulation in LUAD. Conclusions: In summary, we reveal potential mechanisms that OTUD6B-AS1 may compete with mir-144 to regulate the expression NUDCD1 and MARCH7 through miRNA sponge or modifying protein structures, modulating ferroptosis by balance of ubiquitination and deubiquitination. Ferroptosis may participate in the recruitment of immune system and portrait of tumor immune microenvironment.
The landscape of STK11 mutations and hotspots in Chinese patients with solid tumors.
Authors: Han Yun , Su Junyan
Published: June 2022

e15112

Background: STK11 is a tumor suppressor gene, and loss-of-function mutations are oncogenic, due to loss of AMPK regulation of mTOR and HIF-1-α. STK11 has been identified as a tumor suppressor in several types of cancers. Emerging evidence suggests that STK11 mutations may influence clinical outcome and response to immunotherapy in cancer. However, the genomic features of STK11 are obscured in Chinese solid tumors. In this study, we investigated the landscape of STK11 in Chinese patients with solid tumors. Methods: Next-generation targeted sequencing of major cancer-related 599 genes in a large cohort of 5420 Chinese solid tumors. Results: STK11 mutations were identified in 184 (3.39%, 184/5420) Chinese solid tumors patients. Although STK11 mutations are negligible in solid tumors, endometrial cancer patients (15.79%), esophagus and esophagogastric junction cancer (9.09%), ovarian cancer (4.92%), and lung cancer (4.92%) possess relatively high rates of STK11 mutation. However, STK11 alterations were not found in head and neck cancer, kidney cancer, and CNS tumor cases. A total of 194 mutation sites have been identified in STK11, including 43 pathogenic/ likely pathogenic mutations, the most prominent mutational hotspots are P281fs, D194Y, W308C, S216F, D53fs, and Y60, occupying almost 48.84% of all mutations in STK11. A total of 17 patients harbored copy number variations (CNV) of STK11 in Chinese solid tumors, mainly occurring in the neuroendocrine tumor, breast cancer, and gastric cancer. Conclusions: We found a unique genomic feature of STK11 in Chinese solid tumor patients. Our results show that STK11 may be a potential therapeutic target.
Pan-cancer analysis of IDH1 and IDH2 genomic alterations to reveal a complex molecular landscape.
Authors: Zhou Houjun , He Zhe
Published: June 2022

e15116

Background: As a crucial enzyme involved in cell aerobic metabolism of the tricarboxylic acid cycle, IDH also plays important role in cancer biology. Somatic point mutations in IDH1/2 contribute to oncogenesis by promoting the production and secretion of an oncometabolite, the D-2-hydroxybutyrate, which could alter cellular metabolism and epigenetic regulation. However, data regarding the status and prevalence of IDH1 and IDH2 mutations in pan-cancer from Chinese cancer patients is limited. Methods: Ranging from Jan 14, 2020, to Oct 25, 2021, genomic DNA extracted from 5419 blood or tissue samples involving more than 22 solid tumors types were analyzed by NGS assay to investigate the landscape of IDH1/2 mutations and hotspots. Results: IDH mutations were identified in 205 cases (3.78%), of which 145 cases (2.68%) were from the IDH1 mutations group and 63 cases (1.16%) from the IDH2 mutations group. IDH1 mutations predominantly occurred in CNS tumors, melanoma, and endometrial cancer (with mutation frequencies of 26.09%, 7.41%, 5.26%, respectively), whereas IDH2 mutations occurred commonly in endometrial cancer (5.26%) and gastric cancer (2.90%). Among the 56 mutation sites found in IDH1, Y208(19.46%), R132(16.11%), and R20(12.08%) were the three major IDH1 mutations. M397, which accounts for 33.33% of all IDH2 mutation sites, was the most significantly mutated subtypes, followed by T146(4.76%). Conclusions: Compared with IDH2, IDH1 is more frequently mutated in terms of cancer species as well as shows higher mutation frequency, and our findings implicate mutations in IDH in the pathogenesis of cancers, especially CNS tumors.
Integration of molecular cancer classification and NGS to identify patients with metastatic cancer eligible for BRAF inhibitors.
Authors: Fuentes Bayne Harry E. , Ma Li , Wong Jenna , Treuner Kai , Halfdanarson Thorvardur Ragnar
Published: June 2022

e15118

Background: Melanoma, non-small cell lung cancer (NSCLC), colorectal adenocarcinoma and thyroid tumors frequently harbor BRAF mutations and are tumor types eligible for treatment with FDA-approved BRAF inhibitors. Although there are many ongoing clinical trials with BRAF inhibitors in various advanced tumor types, currently eligibility requires both tumor type identification and BRAF mutation confirmation. The 92-gene assay (CancerTYPE ID) is a gene expression-based classifier of 50 tumor types and subtypes for metastatic patients with diagnostic ambiguity. Multimodal biomarker testing, including NGS, IHC and FISH, enables identification of actionable biomarkers to guide targeted therapy selection. Here, a database of metastatic cases integrating tumor type with biomarker analysis was used to identify patients eligible for BRAF inhibitor treatment. Methods: MOSAIC (Molecular Synergy to Advance Individualized Cancer Care) is an IRB-approved, de-identified database of diagnostically ambiguous cases submitted for CancerTYPE ID testing with tumor type-guided multimodal biomarker testing (Neogenomics). In this study, metastatic cancers of various tumor types with BRAF mutations were identified. Results: CancerTYPE ID determined 27 different tumor types in 2929 (92.5%) of 3168 cases. BRAF mutations were identified in 87 cases across 18 tumor types and subtypes. Out of the 87 cases, 22 (25.3%) had BRAF mutations in a tumor type eligible for FDA-approved BRAF inhibitor treatment, including melanoma, NSCLC, colorectal adenocarcinoma and thyroid cancer. Another 26 (29.9%) BRAF-mutated cases were detected in a tumor type with ongoing BRAF inhibitor clinical trials, including lymphoma, pancreaticobiliary and ovarian cancer (Table). Conclusions: This analysis identified patients with metastatic cancer with actionable BRAF mutations eligible for FDA-approved therapy, and patients who may be eligible for investigational BRAF inhibitors based on tumor type and mutation status. Notably, cancer type identification is critical given that FDA-approved BRAF inhibitor treatment regimens vary based on the tumor-specific indication. These findings support the clinical utility of molecular tumor type classification by CancerTYPE ID combined with biomarker profiling to identify additional treatment options for patients with metastatic cancer.[Table: see text]
Clinical and prognostic features of BRAF V600E-mutant resectable colorectal cancer: A single-center retrospective analysis of Chinese patients.
Authors: Liu Mengling , Xu Xiaojing , Yu Yiyi , Liu Tianshu
Published: June 2022

e15505

Background: Molecular subtyping provides a fundamental basis for the selection of strategies for colorectal cancer treatment. Unresectable metastatic colorectal cancer (CRC) with BRAF V600E mutation have received great attentions due to the poor prognosis. Nevertheless, clinical characteristics and prognosis of Chinese patients with BRAF V600E-mutant (BM) resectable CRC remain poorly reported. Methods: Patients with BM resectable CRC were included according to the following criteria: 1) Diagnosed with colorectal adenocarcinoma at Zhongshan Hospital Fudan University from June 2015 to December 2018. 2) Underwent surgery for the primary tumor of CRC without any anti-tumor treatment before surgery. 3) With BRAF V600E mutation confirmed by the genetic test of the primary tumor tissue. 4) No other primary malignant tumors or inherited tumor history. 5) Written informed consent was obtained. Clinical information was collected by consulting electronic medical records with the approval of the Ethics Committee of Zhongshan Hospital Fudan University (Approval code: B2021-739). KRAS exon2 mutant (KM) and KRAS/BRAF wildtype (WT) patients were selected in a 1:1 ratio by matching gender, age, location and the year of surgery with the BM group. Overall survival was defined as the time from surgery to death for any reason or last follow-up (September, 2021). Categorical data were assessed by chi-square test. Survival analysis was performed using Kaplan-Meier survival curve with log-rank test, univariate and multivariate Cox regression analyses. Results: A total of 214 patients with BM resectable CRC met the inclusion criteria. Among them, 111 (51.9%) patients were females and 103 (48.1%) were males, 114 (53.3%) patients were younger than age 65 years while 100 (46.7%) were > = 65 years old, 108 (50.5%) patients’ primary lesions sited on the left side and 106 (49.5%) on the right side. Numbers of patients with resectable metastasis and with mismatch-repair- deficient (dMMR) were both 48 (22.4%). 171 KM patients and 165 WT patients were matched with BM patients and the three groups were balanced in gender, age, and location by matching. The BM group had the worst overall survival ( P < 0.001) with significant higher proportions of stage IIĨIV ( P = 0.002) and dMMR patients ( P < 0.001). Survival analysis in subgroups suggested that the inferior prognosis of the BM group was more pronounced in patients with pMMR or Stage IV CRC. Conclusions: BRAF V600E-mutant resectable CRC presented a higher incidence of dMMR but a worse prognosis than KRAS exon2 mutant or KRAS/BRAF wildtype patients.
FAT1 mutations in colorectal cancer patients are associated with the therapeutic benefit of immunotherapy.
Authors: Liang Tingbo , He Junjun , Zhu Wei , Yang Lan , Gao Yu , Zhou Yi , Shi Yuqian , Liu Kaihua , Yu Ruoying , Shao Yang , Zhang Wentong , Zhang Qi , Wu Guosheng
Published: June 2022

e15523

Background: Immunotherapy is one of the main treatment modalities for advanced colorectal cancer. Although microsatellite instability (MSI) is widely applied as an effective immune efficacy prediction biomarker in clinical practice, the majority of the colorectal patients are microsatellite stable (MSS). This study is designed to identify new biomarkers for immune efficacy in colorectal cancer. Methods: Targeted sequencing with a 425 gene panel was performed with the tumor tissues from a total of 161 colorectal cancer (CRC) patients (discovery cohort) for mutation analysis. The association between FAT1 mutations and immunotherapy markers MSI and TMB was investigated using an external database of 727 CRC patients from cBioportal (validation cohort). Results: The discovery cohort consisted of 95(59%) males and 66(41%) females with a median age of 59 years old. There were 2(1.2%) stage II, 5(3.1%) stage III, 24(14.9%) stage IV, and 130(80.8%) unknown stage patients. The majority of the discovery cohort was MSS (154, 95.7%), which was similar to the validation cohort (518, 71.2%). FAT1 mutations were present around similar ratios in both discovery cohort (12.4%) and validation cohort (11.6%). In both cohorts, the co-occurrence analysis revealed that MSI events were often co-occurred with FAT1 mutations and patients with FAT1 mutations had a higher mutational load compared to the FAT1 wild-type patients. Analysis with survival data from the validation cohort showed that OS was significantly higher in patients with FAT1-mutated tumors than in ones with FAT1 wild-type. Compared to the FAT1 wild-type tumors, the higher infiltration rate of immune cell identified in the colorectal tumors with FAT1 mutation may also explain the good immune efficacy of patients with FAT1 mutation. Conclusions: Colorectal cancer patients with FAT1 mutations may benefit from immunotherapy. The increased immunogenicity in patients with FAT1 mutations may be due to increased immune cell infiltration.
PD-1 blockade combined chemotherapy and bevacizumab in DNA mismatch repair-proficient/microsatellite stable colorectal liver metastases.
Authors: Men Qianqian , Huang Jun , Duan Yinghua , Pei Fengyun , He Wan , Hu Huabin , Zhao Yandong , Shi Lishuo , Xie Peiyi , Liu GuangJian , Huang Meijin
Published: June 2022

e15547

Background: Although PD-1 blockade has been recommended as the first line treatment in DNA mismatch repair-deficient/microsatellite instability-high (dMMR/MSI-H) metastatic colorectal cancer (mCRC), it is worthwhile to investigate whether mCRC with DNA mismatch repair-proficient/microsatellite stable(pMMR/MSS) tumors benefit from a combination treatment with PD-1 blockade. Methods: In this cohort, ten patients with pMMR/MSS colorectal liver metastases (CRLM) treated in the 6th Affiliated Hospital of Sun Yat-sen University were enrolled. All the patients were exploratively treated with at least four doses of PD-1 monoclonal antibody combined with chemotherapy and bevacizumab as neoadjuvant/adjuvant therapy. The aim of the study was to evaluate the short-term efficacy and safety of this combined strategy. Results: All the 10 patients were confirmed pMMR/MSS by IHC or next generation sequencing (NGS). Eight of the 10 patients accepted the combined therapies before primary tumor resections, disease control rate (DCR) was 100% (8/8) and objective response rate (ORR) was 62.5% (5/8). The ORR of liver metastases was 70% (7/10) after this treatment. Pathologic complete response (pCR) was achieved in one patient’s primary tumor and was also achieved in another patient’s hepatic lesion. Four patients underwent simultaneous resection of primary tumor and liver metastases. Nine patients underwent microwave ablation for liver metastases. Five patients were assessed no evidence of disease (NED) with a median progress-free survival (PFS) of 5.0 (4.2-9.9) months after multimodality treatments for both primary and metastatic lesions. No immunotherapeutic associated sever adverse event (SAE) or operational complications were found in this cohort. Conclusions: PD-1 blockade combined chemotherapy and bevacizumab was safe and effective for patients with pMMR/MSS CRLM, which might lead to better tumor regression as well as more chances of NED. Further clinical phase II studies of evaluation of long-term efficacy of this combined strategy was needed.
Nivolumab with ipilimumab for MSI-H colorectal cancer with liver metastases.
Authors: Michalaki Vasiliki , Theodosopoulos Theodosios , Frangoulidis George , Dafnios Nikolaos , Papakonstantinou Ioannis , Vezakis Antonios , Papadimitriou Christos
Published: June 2022

e15556

Background: Immune checkpoint inhibitor (ICI) therapy has recently demonstrated durable clinical benefit in patients with advanced mismatch repair deficient (dMMR) colorectal cancer. The aim of this study was to test the combination of nivolumab and ipilimumab in microsatellite instability-high (MSI-H) colorectal cancer patients with oligometastatic liver disease. Methods: Twelve patients with MSI-H mCRC and one prior line of treatment for metastatic disease received nivolumab 3 mg/kg plus ipilimumab 1 mg/kg once every 3 weeks (four doses) followed by nivolumab 3 mg/kg once every 2 weeks until disease progression or discontinuation. The primary endpoint was objective response rate (ORR). Results: At baseline, the patients’ median age was 58 years (range, 51-67 years), and 40.7 % of patients were women. Sites of metastases included liver (89.8%), distant lymph nodes (43.6%), and lungs (9.2%). For all 12 patients (median follow-up was 8.2 months), ORR was 71% (95% CI 46.3–78.6). Of 12 patients enrolled, 4 patients (33%) achieved a partial response, and 5 patients (41%) achieved stable disease. Responses were consistent with the overall population across subgroups including age, Eastern Cooperative Oncology Group (ECOG) performance status, prior adjuvant/neoadjuvant therapy, and mutation status. Two patients (16%) had grade 3–4 treatment-related adverse events. Conclusions: Nivolumab plus ipilimumab demonstrated significant clinical benefit and was well tolerated in patients with MSI-H mCRC. Clinical evaluation of ICIs in first-line metastatic, adjuvant and neoadjuvant settings and in combination with other therapies are ongoing.
An observational study of dose-optimization for fruquintinib in elderly patients (pts) with metastatic colorectal cancer (mCRC) who had failed standard therapy.
Authors: Gou Hongfeng , Yu Jing , Cai Xiaohong , Li Qiu
Published: June 2022

e15560

Background: As one of the third-line standard treatment regimens for advanced colorectal cancer, fruquintinib is widely used in clinical practice, but there are limited data on safety and efficacy of fruquintinib in elderly pts. Multiple studies have shown improved tolerability, reduced grade 3-4 adverse events, and comparable efficacy in pts treated with regorafenib through a first-cycle flexible dose optimization regimen. This method of drug administration is more practical especially in elderly pts, and is worthy of clinical adoption. This observational study aims to investigate the safety, tolerability, and efficacy of a dose-optimized regimen of fruquintinib in elderly mCRC pts who had failed previous standard therapy. Methods: Pts ≥65 years with mCRC refractory to fluoropyrimidine-based chemotherapy ± anti-VEGF/EGFR were enrolled. The primary endpoint was progression-free survival (PFS) (RECIST v1.1). All pts were administered with fruquintinib 3mg (po, qd) for one week. If tolerable, fruquintinib 4mg would be administered in the second week. In the third week, fruquintinib 5mg would be administered if 4mg is tolerable, followed by a week’s rest. The maximum tolerated dose (MTD) of fruquintinib confirmed in the first cycle would be administered from the second cycle. Adverse events were evaluated using CTCAE 5.0. Results: As of February 9, 2022, 29 pts were identified, with an median age of 69.59 (65-77) years and 16 males (55.2%) included. Of the 29 pts, the MTD was 3mg in 31% (9/29) pts, 4mg in 58.6% (17/29) pts and 5mg in 10.3% (3/29) pts. Among the 24 pts available for efficacy evaluation, 14 had stable disease (SD) and 10 had progressive disease (PD) as the best response. Disease control rate (DCR) of 3mg group, 4mg group and 5mg group were 33.33% (2/6), 68.75% (11/16) and 50.00% (1/2), respectively. At a median 4.93 months follow-up, the median (m) PFS was 3.73 months [95% CI, 2.32-5.14] and the mOS was 7.97 months [95% CI, 5.05-10.89]. In addition, the median PFS of 3mg group and 4mg group were 1.87 months and 3.73 months, respectively. And the median OS of 3mg group and 4mg group was 7.97 months and 11.0 months, respectively. Treatment-related adverse events (TRAEs) were observed in all 29 pts (100%). Common TRAEs (> 40%) included fatigue (79.3%), anorexia (58.6%) and hand-foot syndrome (44.8%). The most common (> 10%) grade≥3TRAEs were hand-foot syndrome (20.7%), hypertension (17.2%) and diarrhea (10.3%). No grade 5 TRAEs were observed. There were no correlations with efficacy, toxicity, and geriatric assessment scores. Conclusions: The dose-optimized strategy of fruquintinib in pts aged ≥ 65 years showed acceptable toxicities and anti-tumor activities consistent with the overall population in FRESCO study. The dose-optimized strategy of fruquintinib is a viable alternative in older pts with mCRC. Clinical trial information: NCT05025631.
Real-world treatment outcomes from nationwide Onco-colon Turkey registry in RAS wi̇ld-type patients treated with biologics second-line mCRC.
Authors: Yildirim Mahmut Emre , Karaca Mustafa , Artac Mehmet , Cicin Irfan , Geredeli Caglayan , Alacacioglu Ahmet , Tanrikulu Simsek Eda , Bilici Ahmet , Harputluoglu Hakan , Ozcelik Melike , Bozkurt Oktay , Yuksel Sinemis , Tural Deniz , Sakin Abdullah , Cil Timucin , Oven Basak Bala , Dane Faysal , Cevik Duygu , Gumus Mahmut , Isikdogan Abdurrahman
Published: June 2022

e15562

Background: Varieties of systemic treatments in second-line treatment for metastatic colorectal cancer (mCRC) patients have showed an improvement on survival. In this context, most of mCRC patients are likely to progress and to change from first line to second line treatment when they develop resistance to first-line treatment options. Therefore, we aimed to investigate second-line treatment selection in patients with RAS-wild type mCRC. Methods: Medical records from 28 centers were collected for patients diagnosed with RAS wild-type and were included into the study. Histopathological, molecular and clinical characteristics of the patients were recorded. The treatment duration, response rate, progression-free survival and safety results were determined. Patients were compared according to the second-line biological treatments as anti-EGFR group (Group A and B; panitumumab and cetuximab) and anti-VEGF group (group C; bevacizumab or aflibercept). Results: A total of 1064 patients with documented RAS wild-type status were evaluated. Fifty-six percent of all first line patients were treated with regimen including biologics received second line treatment. Median age was 60 years. 34,7 percent of the patients were female. Nineteen percent of the patients had a right-sided colon tumor. 16,3 %, 22,5% and 61,2 % of all second-line patients were treated with regimen including panitumumab, cetuximab and anti-VEGF, respectively. Patients received median 5 (1-21) cycles of treatment. Also, responded patients received median 4 (1-23) cycles of treatment as maintenance treatment with biologics plus fluoropyrimidine. Overall response rate was 28,5 % for all patients. Disease control rate also was 70,6 %. The median OS was 15,7, 14,3, and 14,7 months in A, B and C group respectively (p = 0.764). The median PFS of the patients in second-line setting that received panitumumab, cetuximab and bevacizumab/ aflibercept were 7,8, 6,6 and 7,4 months respectively (p = 0.848). There was not found as independent prognostic factors in multivariate analysis. Conclusions: According to the results of our real-life data study, there is no significant difference in efficacy between the combinations of biological agent and chemotherapy used in the second-line treatments. Therefore, the results of the first-line treatment become important and the use of the most effective agent at this setting also increases survival.