bluuebunny/crossref_metadata_2025_split huggingface dataset:
A phase 2 basket trial of an ERK1/2 inhibitor (LY3214996) in combination with abemaciclib for patients whose tumors harbor pathogenic alterations in BRAF, RAF1, MAP2K1/2 ERK1/2, and NF1.
Authors: Taza Fadi , Durm Greg Andrew , Opyrchal Mateusz , Jalal Shadia Ibrahim , Radovich Milan , Schneider Bryan P. , Turk Anita Ahmed 
Published: June 2023

e15088 Background: LY3214996 (L) is a potent inhibitor of ERK1/2 kinases that can potentially obviate resistance mechanisms in cancers that harbor BRAF, RAS, NF1, MAP2K1/2, and other MAPK alterations. Abemaciclib (A) is a CDK 4/6 inhibitor. Studies have shown that concomitant inhibition of the MAPK pathway exemplified by ERK inhibitors may augment the antitumor activity of CDK4/6 inhibitors. In this biomarker-informed phase 2 study, we assess the clinical efficacy of L in combination with A. Methods: The study enrolled patients with advanced unresectable or metastatic cancer with no other standard of care options available. The malignancy must harbor pathogenic alterations in BRAF, RAF1, MAP2K1/2, ERK1/2, or NF1, in whom standard treatments failed to provide clinical benefit. L was administered at a dose of 200 mg orally QD in combination with A at 150 mg BID hours on Days 1 through 28 of a 28-day cycle until progression, toxicity, or withdrawal. The primary endpoint is the objective response rate. Secondary outcomes include evaluation of safety and tolerability, progression-free survival (PFS), and duration of the overall response. Additionally, tumor samples were collected for organoid development. Results: Between September 1, 2020, and February 1, 2023, 12 patients were enrolled. Primary malignancies included colorectal (6), lung (1), breast (2), pancreas (1), uterus (1), and thyroid (1). The pathogenic alterations included NF1 (4), BRAF (6), and MAP2K1/2 (2). There were no CR or PR observed. Stable disease was achieved in 4 patients (33%) with a median disease control rate of 6.5 months. Pathogenic alterations in patients with stable disease included BRAF, MAP2K1/2, and NF1. Most common treatment-related adverse events of any grade included fatigue (41%), rash (41%), nausea (33%), vomiting (33%), anemia (25%), anorexia (25%), and increased creatinine (25%). There were no grade 4 or 5 adverse events. Conclusions: The combination of L+A is safe and promising in patients whose tumors harbor pathogenic alterations in BRAF, MAP2K1/2, and NF1. Enrollment is ongoing, and efficacy and toxicity outcomes continue to be assessed. (NCT04534283). Clinical trial information: NCT04534283 .
Capturing age-related changes in the tumor microenvironment of luminal breast cancer using the multiplex immunohistochemistry technique, MILAN.
Authors: Lambrechts Yentl , Antoranz Martinez Asier , De Schepper Maxim , Geukens Tatjana , Vos Hanne , Berben Lieze , Messiaen Julie , Marcelis Lukas , Van Herck Yannick , Neven Patrick , Smeets Ann , Punie Kevin , Desmedt Christine , Bosisio Francesca Maria , De Smet Frederik , Hatse Sigrid , Wildiers Hans , Floris Giuseppe 
Published: June 2023

e15089 Background: The ‘immune landscape’ of luminal breast tumors is poorly described to date. We applied the ‘multiple iterative labeling by antibody ‘neodeposition’ (MILAN) technique for in-depth characterization of the tumor microenvironment of luminal-like breast cancer (BC) in relation to age. Methods: Newly diagnosed patients with early luminal BC (grade 2/3, ER+, HER2-, tumor size ≥1,5 cm) were prospectively included in UH Leuven between March 2014 and November 2015 and divided into 3 distinct age categories (young: 35-45 yrs.; middle: 55-65 yrs.; old: ≥70 yrs.). 55 patients (young: n = 12; middle: n = 16; old: n = 27) were included in the cohort. From each patient up to 2 cores from the tumor center (TC) and 2 cores from the invasive front (IF) were sampled from formalin-fixed and paraffin-embedded tumor resection specimens and embedded in tissue microarrays. The MILAN workflow included 20 rounds of three-color indirect immunofluorescence (FITC, TRITC, and Cy5 channel combined with 58 antibodies), image acquisition, and removal/stripping of the antibodies before any other stain. The MILAN data analysis pipeline was applied to study the expression of phenotypic and functional proteins at single-cell level including spatial resolution. These were compared between the different age groups using Wilcoxon's test (FDR correction). Results: We identified 1,5 million cells, of which 59% were epithelial cells (cancer and normal), 29% were immune cells, and the remaining 12% were endothelial or stromal cells. Within the immune cell fraction, T-helper (Th) cells, B-cells, T-cytotoxic (Tcy) cells, and NK-cells significantly decreased with aging while monocytes significantly increased in TC and IF (Table 1). The evaluation of the functional markers in the inflammatory cells revealed a decreased expression with aging of PD-L1 in Tcy cells (p < 0.001 for TC and IF), Th cells (p = 0.003 for IF), T-regulatory (Treg) cells (p = 0.038 for TC), monocytes (p < 0.001 for TC and IF), and B-cells (p = 0.023 for TC). Perforin expression significantly decreased with aging in Th cells (p < 0.05 for TC and IF) and monocytes (p < 0.001 for TC and IF). OX-40 expression significantly decreased with aging in Th cells (p = 0.001 for TC), Treg cells (p = 0.002 for TC), and B-cells (p = 0.012 for TC). Conclusions: Our results suggest important compositional and functional changes in the tumor inflammatory microenvironment during aging in patients with luminal BC. Further analysis on other cell types is warranted. [Table: see text]
Genomics-based screening of novel therapeutic targets and biomarkers for lung cancer.
Authors: Daigo Yataro , Takano Atsushi , Nakamura Yusuke 
Published: June 2023

e15093 Background: Since the number of lung cancer patients who show objective response to standard treatments is still limited, development of new anti-cancer agents with minimum risk of side effects and specific cancer biomarkers is urgently required. Methods: We have been screening new therapeutic targets and their companion biomarkers for lung cancer as follows; i) To identify overexpressed genes in lung cancers by the gene expression profile analysis, ii) To verify the candidate genes for their scarce expression in normal tissues, iii) To validate the clinicopathological importance of their protein expression by tissue microarray covering hundreds of lung cancers, and iv) To characterize their function for the growth and/or survival of lung cancer cells by siRNAs. Results: We identified dozens of candidate oncoproteins and selected a lung cancer cell division-associated protein 1 (LCDAP1). Immunohistochemical analysis showed that LCDAP1 was expressed in 171 of 267 (64%) non-small cell lung cancer (NSCLC) tissues but not in normal lung epithelia. LCDAP1 expression was significantly associated with poor prognosis for NSCLC patients. To investigate its function, we screened LCDAP1-binding protein in lung cancer cells and found an interaction of LCDAP1 with a member of 5'-to-3' DNA helicase that was also up-regulated in lung cancer cells. Knockdown of either of LCDAP1 or its binding partner expression with siRNAs significantly inhibited the growth of cancer cells. Conclusions: Our genomics-based screening could be useful to develop diagnostic and prognostic biomarkers as well as therapeutic targets for small molecules, monoclonal antibodies, and nucleic acid drugs against lung cancer.
A first-in-human, open-label, phase I trial of daily oral PCLX-001, an NMT inhibitor, in patients with relapsed/refractory B-cell lymphomas and advanced solid tumors.
Authors: Sangha Randeep S. , Jamal Rahima , Spratlin Jennifer L. , Kuruvilla John , Sehn Laurie Helen , Weickert Michael , Berthiaume Luc G. , Mackey John Robert 
Published: June 2023

e15094 Background: Myristoylation, the N-terminal modification of proteins with the fatty acid myristate, regulates multiple membrane-bound signal transduction pathways driving cancer cell biology. This modification is catalyzed by two N-myristoyltransferases (NMT), NMT1 and NMT2. Aberrant NMT expression has been identified in cancer cells and inhibition of myristoylation represents a novel anticancer treatment strategy. PCLX-001 is an oral, highly bioavailable, small molecule NMT inhibitor with strong affinity for both NMT1 and NMT2 proteins (IC50 of 5nM and 8nM, respectively). In vitro, hematologic cancer cell lines were exquisitely sensitive to PCLX-001. PCLX-001 regressed subcutaneous tumors in xenograft models derived from lymphoma cell lines, as well as in a refractory DLBCL patient derived xenograft model. PCLX-001 also demonstrated anticancer activity in multiple solid tumor xenograft models. Based on pre-clinical data, we hypothesized that PCLX-001 would be safe, tolerable, and active as a novel oral cancer therapeutic. Methods: Patients with relapsed/refractory B-cell lymphomas and advanced solid tumors are being enrolled in a multicenter, open label, standard phase I dose escalation design to determine feasibility, maximum tolerated dose (MTD), and pharmacokinetics of PCLX-001 monotherapy. Seven dose levels are being studied: 20 mg, 40 mg, 70 mg, 100 mg, 140 mg, 200 mg, and 280 mg. Dose limiting toxicity (DLT) is defined as: grade (Gr) 4 platelets, Gr 3 platelets with bleeding, Gr 4 ANC ≥ 7 days, febrile neutropenia, or clinically significant > Gr 3 non-hematologic toxicity. Results: Eighteen evaluable patients (3 relapsed B-cell lymphoma; 15 advanced solid tumor) have been accrued through dose level six (200 mg cohort) without DLT. No attributable Gr 3 or 4 toxicities have been identified. Noncompartmental pharmacokinetic (PK) analyses demonstrate rapid oral absorption, a terminal half-life of approximately 10 hours, rapid achievement of steady state, and no induction of metabolism. PCLX-001 trough plasma concentrations at higher dose cohorts exceed the EC90 required to inhibit cultured cancer cells. Conclusions: PCLX-001 is safe and well tolerated up to the 200 mg daily dose. Our results support the ongoing development of PCLX-001 as an oral daily therapy for the treatment of patients with cancer. Updated study results will be presented, summarizing the safety, MTD, and PK outcomes in PCLX-001 treated patients. Preliminary clinical activity will be determined in 20 patient dose expansion cohorts of relapsed/refractory B-cell lymphomas, and selected advanced solid tumors following the identification of PCLX-001 MTD. Clinical trial information: NCT04836195 .
PUF: A potential repressor of oncogenes.
Authors: Aslam Hafiz , Muzaffar Mahvish , Lee Myon Hee 
Published: June 2023

e15095 Background: RNA-binding proteins (RBPs) play a crucial role in orchestrating the function of RNAs. The regulation of RBPs is critical in various biological processes, including tumorigenesis. The PUF (Pumilio/FBF) RBPs are of particular interest due to their function in stem cells and tumor-initiating cells. Its has been shown that PUF proteins inhibit the translation of target genes by binding to a regulatory element (PBE) in the 3’ untranslated regions (3’UTRs) of their target mRNA. PUF proteins are required to maintain normal stem cells and potentially inhibit the formation of tumor-initiating cells by repressing the expression of oncogenes. Bioinformatics analysis has identified many oncogenes as potential targets of PUF, and pilot studies have confirmed that ERK, p38, JAK2, RUNX2, and RET mRNAs specifically interact with PUF protein. The objective of this study is to investigate the function of human PUF proteins in the initiation and progression of cancer cells. Methods: In worms (C. elegans), 100 % PUF mutants form tumors. Bioinformatics were performed to identify PUF target genes, it specifically binds UGUAnAUA sequences on target mRNA 3'UTRs. Yeast three-hybrid assay were performed to test the physical interaction between PUF protein and its target mRNA. The novel function of human PUF proteins in the initiation and progression of cancer cells was investigated using CRISPR/Cas9 knockout cancer cell lines and western Blot/IHC was done to determine their expression. Results: The results of the study showed that PUF proteins play a crucial role in inhibiting the formation of tumor-initiating cells. Loss of PUF function and activation of ERK signaling were found to promote the formation of these cells. Bioinformatics analysis revealed that many oncogenes are potential targets for PUF repression. The study also demonstrated that PUF represses the expression of ERK and p38 mRNAs via their 3’UTRs. These findings suggest that PUF may have therapeutic potential as a target for cancer treatment. Conclusions: In worms and human cells, normal PUF proteins promote the cell proliferation of stem cells, however, stem cells begin to differentiate, PUF proteins are required to complete differentiation. Therefore, in the differentiating cells, PUF mutation cannot complete differentiation, instead, return to undifferentiating cells, resulting in tumors. Bioinformatics and biochemical analyses revealed that many PUF repressing targets (~ > 30%) are oncogene and some labs including us found that PUF knockdown enhanced oncogene expression. PUF can be a potential biomarker, as low PUF expression may initiate tumors. Therapeutically, conditional PUF expression in tumor-initiating cells may suppress tumor progression by suppressing oncogene.
Association of cachexia with loss of function mutations in STK11/LKB1 for NSCLC.
Authors: Infante Rodney E. , Ahn Chul , Minna John D. , Iyengar Puneeth 
Published: June 2023

e15099 Background: Cancer cachexia (CC), a wasting syndrome of muscle and adipose tissue resulting in weight loss, occurs in 50% of non-small cell lung cancer (NSCLC) patients. Management of CC is limited by the absence of biomarkers and knowledge of molecules that drive its phenotype. The evolving landscape of increased genomic testing of human tumors and derived cell lines has further given us an opportunity to leverage these findings to identify a genetic biomarker that regulates CC development through a novel in vivo human NSCLC cachexia screen. Methods: To identify such molecules, we injected 54 human non-small cell lung cancer (NSCLC) lines into immunodeficient mice, 17 of which produced an unambiguous phenotype of cachexia (n = 10) or non-cachexia (n = 7). Whole exome sequencing of tumors was conducted to identify candidate cachexia-associated genes and gene variant analysis was conducted to identify gene variants that associated with NSCLC-associated CC. CRISPR/Cas9 targeted gene silencing in human NSCLC and mouse cancer lines verified if target genes conferred the cachexia phenotype. Circulating tumor DNA analysis of a 246 NSCLC patient cohort was used to confirm candidate gene variants association with cancer-related weight loss. Results: Whole exome sequencing revealed that 8 of 10 cachexia lines, but none of the non-cachexia lines, possessed mutations in STK11/LKB1 (p = 2x10-12), a regulator of nutrient sensor AMP kinase. Silencing of STK11/LKB1 in human NSCLC and murine colorectal carcinoma lines conferred a cachexia phenotype after cell transplantation into immunodeficient and immunocompetent models, respectively. This host wasting was associated with an alteration in the immune cell repertoire of the tumor microenvironments that led to increases in local mRNA expression and serum levels of CC-associated cytokines resulting in host adipose and muscle tissue wasting. Mutational analysis of circulating tumor DNA from 246 NSCLC patients identified 89% concordance between STK11/LKB1 mutations and weight loss at cancer diagnosis (OR = 17 ± 1, p = 0.004). Conclusions: The current data provides evidence that tumor STK11/LKB1 loss of function is a driver of CC in NSCLC, simultaneously serving as the first genetic biomarker for this wasting syndrome.
Base-edited live microbiome therapeutics with target-aid -live biotherapeutic products (LBPS) with synergistic effects of anti-PD-1 antibodies in a syngeneic model of mice.
Authors: Okumura Ryo , Mitsunobu Hitoshi , Ishii Chiaki , Miyazaki Shoko , Tamiya Taiga , Bernier Francois 
Published: June 2023

e15104 Background: Base editing without DNA cleaving is a technique that introduces point mutations using enzymes that induce base conversions. Generally, only the point mutation occurs, achieving a high level of precision. Base editing can easily be applied to bacteria, for which DNA cleaving is often lethal. With Bio Palette's core technology of base editing, Target-AID, we can quickly achieve the required therapeutic effects by making pinpoint modifications to bacteria. Immune checkpoint inhibitors (ICIs) targeting CTLA-4, PD-1, or PD-L1 have shown outstanding therapeutic outcomes in various cancers. However, the therapeutic efficacy of ICIs-based immunotherapy has been limited. Recent studies have revealed that the human gut microbiome controls the efficacy of ICIs. Bacterial flagellin derived from Enterococcus spp. has been suggested to enhance immune responses to cancer through activation of TLR5 signaling (1). As a regulatory mechanism of flagellin secretion in Enterococcus spp, FliD, FlgK, FlgN, or FlgM are known as negative regulators. Thus, if the flagellar expression can be enhanced by making the negative regulator functionally deficient, it can be expected to increase the efficacy and response rate of ICIs when combination with a base-edited strain. Methods: As human TLR5 luciferase reporter assay, HEK293T cells were transfected with human TLR5-expression vector. BALB/cAnN mice (6–8 weeks’ old) were injected subcutaneously with 3 x 106 cells for murine colon cancer cell line CT-26. Six days post inoculation, the mice were randomized based on tumor volume into treatment and vehicle control groups (n = 10 per each group). Anti-mouse PD-1 antibody was dosed 5 mg/kg, q3d, iv, for up to 3 weeks either alone or in combination with each of various strains (1 x 109 CFU/mouse, po). Body weight and tumor size were routinely measured until endpoint. Results: To achieve the increased extracellular secretion of Flagellin, we created fliD dysfunctional strain because deletion of the flagellar cap component FliD was expected to promote extracellular secretion of Flagellin monomers. Comparing the wild-type strains we used, E. casseliflavus activated TLR5 compared to E. gallinarum. E. casseliflavus with a stop codon introduced into the fliD gene, BP5040 strain, was found to increase TLR5 activation by approximately 4.9-fold when compared to wild type strain. In vivo experiments indicated that antitumor effect was observed with BP5040 alone. Strikingly, a remarkable antitumor effect was also demonstrated when BP5040 was combined with an anti-PD-1 antibody. Conclusions: To achieve the desired therapeutic effect, we performed base editing without inserting foreign genes. As a result, BP5040 strain is found to be a potential candidate for the treatment of immuno-oncology, which was created using our LBP platform technology.
Identification of a novel class of early exon ALK rearrangements across two pan tumor sequencing databases.
Authors: Leong Matthew , Li Xiaomo Li , Mercer Jacob , Fields Paul A. , Abraham Eden , Nakasaki Manando , Heneidi Saleh , Gayhart Matthew , Khullar Gaurav , Vail Eric 
Published: June 2023

e15105 Background: ALK-rearrangements are a powerful and highly prevalent driver in cancer biology. The advent of potent tyrosine kinase inhibitors has led to the development of numerous laboratory tests and FDA approved therapies for the detection and treatment of ALK-positive cancers. The vast majority of reported ALK rearrangements involve exon 20 with fusions involving exons 17-19 occasionally reported. While less common, ALK-rearrangements occurring earlier in the ALK gene have not been well characterized. This is largely because most clinically available biomarker testing is only optimized for detection of rearrangements involving the common regions. To this end, we aimed to investigate the prevalence of early exon ALK rearrangements (eALKr). Methods: Two pathology databases, including the Tempus deidentified database, were retrospectively queried to characterize eALKr, which were defined as any rearrangement that involved ALK exons 1-16. Demographic information and tumor type were recorded. Identification of eALKr was performed via targeted amplicon-based RNA sequencing, targeted hybrid capture DNA sequencing and whole transcriptome sequencing. Select specimens with early ALK fusions were also evaluated for ALK detection using available FDA-approved methods (immunohistochemistry [IHC] and fluorescent in-situ hybridization [FISH]). Results: Out of the specimens that underwent NGS testing in the two databases, the prevalence of eALKr was 0.05% (73/143,959) across the databases and 10.3% (73/709) for all tumors with ALK rearrangements. Across the 73 rearrangements, there were 58 unique 5’ partner genes of which 46 were only identified once. eALK rearrangements were identified in all exons from exons 1 to 16 except for exon 13, with exon 4 being the most common. Prostatic, breast and ovarian serous carcinoma were the most common tumor types (Table 1). In three cases IHC and FISH were unreliable due to the early rearrangement location (0/3 IHC positive, 1/3 FISH positive). FISH was negative for samples with rearrangements in exon 2 and 4 and showed an atypical (deletion) pattern with a rearrangement involving exon 12. Conclusions: A non-trivial number of eALKr were detected within two database using next generation sequencing (0.05% of total cancer cases; 10.3% of ALK fusion cases). These novel eALK rearrangements were predominantly in tumor types not normally associated with ALK fusions. FDA approved testing modalities are only optimized to detect common ALK rearrangements, which in part may be a reason why eALK-rearrangements are poorly characterized, with limited prevalence and treatment data available. [Table: see text]