Targets For Precision Medicine Research Articles

The role of IL-35 and IL-37 in breast cancer - potential therapeutic targets for precision medicine.

Breast cancer is still a major concern due to its relatively poor prognosis in women, although there are many approaches being developed for the management of breast cancer. Extensive studies demonstrate that the development of breast cancer is determined by pro versus anti tumorigenesis factors, which are closely related to host immunity. IL-35 and IL-37, anti-inflammatory cytokines, play an important role in the maintenance of immune homeostasis. The current review focuses on the correlation between clinical presentations and the expression of IL-35 and IL-37, as well as the potential underlying mechanism during the development of breast cancer in vitro and in vivo. IL-35 is inversely correlated the differentiation and prognosis in breast cancer patients; whereas IL-37 shows dual roles during the development of breast cancer, and may be breast cancer stage dependent. Such information might be useful for both basic scientists and medical practitioners in the management of breast cancer patients.

The Mydrug Platform Trial: Efficacy and Safety of Daratumumab, Ixazomib, Pomalidomide, and Dexamethasone in Patients with Functionally High-Risk Multiple Myeloma

Background: Multiple myeloma (MM) is an incurable malignant neoplasm with a 5-year relative survival rate of 57.9%. Many new agents have improved overall survival; however, some patients rapidly relapse and develop multidrug resistance, which requires the use of new approaches and drug mechanisms to treat. Precision medicine targeting specific genetic abnormalities has the potential to overcome related inherent and/or acquired resistance in patients with MM, but studying this approach has several limitations. Many different mutations occur in MM, and mutation frequency increases with disease progression and relapse, making it difficult to determine dominant genetic abnormalities and assess their relevance to a particular patient. This is a critical factor, as mutations in certain cancer-associated genes (actionable mutations) are targeted by approved drugs for other cancers. Some mutations are found in only a small number of patients. In addition, a substantial subset of patients appear to lack actionable mutations or have low allelic burden, making recruitment to clinical trials studying one specific mutation operationally difficult. To overcome these challenges and understand the role of novel therapies in precision medicine, the MMRF launched MyDRUG, a platform trial of patients with select actionable genetic mutations. Methods: MyDrug (NCT03732703) is an open-label, multicenter, phase 1/2 platform study of adult patients with functionally high-risk MM (defined as early relapse after initial MM treatment), who have received 1-3 prior therapies. Through different subprotocols, patients received targeted agents or immunotherapy/novel agents in combination with a backbone regimen of ixazomib, pomalidomide, and dexamethasone (IPd). Each subprotocol planned to enroll up to 38 patients, and treatment assignment was based on individual genetic sequencing results as determined by Next-Generation Sequencing assay performed in a CLIA-certified Molecular Characterization Laboratory. Approximately 75% of subjects were expected to have actionable mutations (BRAF, NRAS, KRAS, FGFR3, IDH2, CDK activating) or t(11;14) based on historic data, although not all of these would have the necessary allelic burden of ≥30% to qualify for the targeted subprotocols. Patients with no actionable mutation or mutations with allelic burden below 30% were assigned to the Y1 arm and received daratumumab at the standard dose and schedule in combination with IPd. The primary objective of the Y1 sub-protocol was to evaluate the overall response rate (ORR) according to the International Myeloma Working Group consensus criteria. Secondary objectives included assessment of adverse events (AEs). Confidence intervals were computed using the Clopper-Pearson (exact) method. Results: Thirty-eight patients were enrolled to the Y1 daratumumab arm with a median (range) age of 63 (46-79) years, with 16 (42.1%) patients of ages 65-74 and 2 (5.3%) patients ≥75 years. Thirteen (34.2%) patients were female, and 8 (21.1%) patients were Black or African American. The ORR for patients receiving daratumumab plus IPd was 92.1%, and 19 (50%) patients had a very good partial response. Thirty-seven (97.4%) patients experienced treatment-related AEs, 35 (92.1%) of which were related to daratumumab. Among patients receiving treatment, 22 (57.9%) experienced a serious AE; 3 (7.9%) experienced an AE leading to discontinuation; and 2 (5.3%) had fatal AEs. Conclusions: In this platform study of adult patients with treatment refractory, functionally high-risk MM, patients who received daratumumab plus IPd exhibited significant efficacy and a manageable AE profile.

Abstract 13724: Development of VS-041 as a Precision Medicine Targeting Cardiac-Relevant Matrix Metalloproteases (MMPs) in Heart Failure With Preserved Ejection Fraction (HFpEF)

Introduction. HFpEF is a heterogeneous syndrome, with several underlying etiologic and pathophysiologic factors. As “one size fits all” therapies are not equally efficacious across various HFpEF comorbidities, a precision medicine approach can offer a disease modifying treatment for HFpEF subpopulation stratified for specific molecular targets. Expression of MMP2, 9, and 13 in heart is elevated in HFpEF patients with hypertension, diabetes or coronary disease, and their levels in plasma correlate with survival, suggesting utility as predictive biomarkers. Genetic ablation of MMP2, 9, and 13 leads to a robust antifibrotic effect in the myocardium. Inhibition of MMP2, 9, and 13 directly regulates of Ca 2+ transients and protects sarcomere function. Hypothesis. We present preclinical profile of VS-041, a novel and narrow-spectrum MMP inhibitor, as a drug candidate for HFpEF patients with elevated levels of MMP2, 9, and 13. Methods and Results. VS-041, optimized with computer-aided drug design methods, shows single-digit IC 50 against MMP2 (1nM), MMP9 (2nM) and MMP13 (1nM), and maintains >300-fold selectivity against MMP1 and TACE. In isolated cardiomyocytes VS-041 reduces contractility deficit due to fast pacing. With high predicted metabolic bioavailability (MF%=90), >80% target occupancy by VS-041 is estimated after 50 mg/kg PO dose in rats. VS-041 demonstrated robust efficacy in Dahl Salt Sensitive rat model of hypertension and HFpEF after dosing at 25 or 50 mg/kg PO for 5 wks in a therapeutic mode (after 1-wk of high salt lead-in). VS-041 had no effect on blood pressure or ejection fraction confirming a direct effect on diastolic function. In Doppler mitral inflow, analysis of the isovolumic relaxation time and the E/A ratio of peak velocity of filling waves revealed 40% improvement in diastolic function. LV fibrosis was dose-proportionally decreased based on PSR morphometry. No adverse effects were observed after 5 weeks of dosing. Conclusions. Preclinical pharmacology and safety profile of VS-041 support its nomination as clinical candidate and initiation of IND-enabling studies. VS-041 has potential to be first-in-class precision medicine treatment for HFPEF patients with elevated levels of cardiac-relevant MMP2, 9 and 13.

40. Clonal evolution of Cutaneous T Cell Lymphoma (CTCL) revealed at single cell resolution

Patients with CTCL subtypes Mycosis Fungoides and Sézary Syndrome (MF/SS) frequently progress to advanced stage disease, which has a 20% 5-year survival. The molecular factors that drive MF/SS progression remain undefined. To address this, we subjected 41 longitudinal tumor samples (peripheral blood, skin and lymph node biopsies, 49-1050 days apart) and matched, purified non-malignant cells from 10 MF/SS patients to single-cell (sc)RNA-seq and exome+whole genome sequencing (eWGS). and patient-specific TCR clonotype assignment (scRepertoire). Clustering and cell type inference of scRNAseq (UMAP/Seurat/singleR) showed canonical CTCL marker genes and high clonal proportions (1-100%) of patient-specific TCR clonotypes. Somatic genome copy number variants (CNV) from scRNAseq (copykat) and eWGS (cnvkit), and deleterious/damaging single nucleotide variants (SNV) (eWGS, GATK/Mutect2) were identified in CTCL versus matched, non-malignant cells. To segregate early genomic events from progression-associated, we developed an integrative analysis pipeline to prioritize somatic CNV/SNV in genes with altered expression in >=30% of patients. This novel approach revealed alterations in NF-KB and T-cell receptor pathways (NFKB2, STAT3/5, TOX) as early events that were maintained in subsequent CTCL samples. We demonstrate gain-of-function activity in a novel-to-CTCL mutation in STAT3. Losses of some chromatin-modifying enzymes (DNMT3A, KDM6B) are early events, while gains of others (EZH2) are acquired with progression. Strikingly, progression-associated mutations were enriched in cell metabolism, growth, and motility genes, some of which are new to MF/SS: HIF1A, ITPR3, GTPase/RAS (IQGAP1/2, RASA1), and PI kinase (AKT1, MTOR, PIK3R1). These findings represent new insights into MF/SS progression and identify new precision medicine targets for currently available therapies.

Classification and Prognosis Analysis of Pancreatic Cancer Based on DNA Methylation Profile and Clinical Information.

Pancreatic adenocarcinoma (PAAD) has a poor prognosis with high individual variation in the treatment response among patients; however, there is no standard molecular typing method for PAAD prognosis in clinical practice. We analyzed DNA methylation data from The Cancer Genome Atlas database, which identified 1235 differentially methylated DNA genes between PAAD and adjacent tissue samples. Among these, 78 methylation markers independently affecting PAAD prognosis were identified after adjusting for significant clinical factors. Based on these genes, two subtypes of PAAD were identified through consistent clustering. Fourteen specifically methylated genes were further identified to be associated with survival. Further analyses of the transcriptome data identified 301 differentially expressed cancer driver genes between the two PAAD subtypes and the degree of immune cell infiltration differed significantly between the subtypes. The 14 specific genes characterizing the unique methylation patterns of the subtypes were used to construct a Bayesian network-based prognostic prediction model for typing that showed good predictive value (area under the curve value of 0.937). This study provides new insight into the heterogeneity of pancreatic tumors from an epigenetic perspective, offering new strategies and targets for personalized treatment plan evaluation and precision medicine for patients with PAAD.

Evolutionary conservation of motifs within vanA and vanB of vancomycin-resistant enterococci.

Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. This study aimed to identify conserved genetic sequences and their evolutionary pathways among vancomycin-resistant Enterococcus species such as Enterococcus faecium and Enterococcus faecalis. We retrieved a total of 26 complete amino acid and nucleotide sequences of resistance determinant genes against vancomycin (vanA and vanB), streptomycin (aac-aah), and penicillin (pbp5) from the publicly available genetic sequence database, GenBank. The sequences were comprised of bacteria classified under the genera of Enterococcus, Staphylococcus, Amycolatopsis, Ruminococcus, and Clostridium. Sequences were aligned with Clustal Omega Multiple Sequence Alignment program and Percent Identity Matrices were derived. Phylogenetic analyses to elucidate evolutionary relationships between sequences were conducted with the neighbor-end joining method through the Molecular Evolutionary Genetics Analysis (MEGAX) software, developed by the Institute of Molecular Evolutionary Genetics at Pennsylvania State University. Subsequent network analyses of the resistance gene, vanB, within E. faecium were derived from ScanProsite and InterPro. We observed the highest nucleotide sequence similarity of vanA regions within strains of E. faecium (100%) and E. faecalis (100%). Between Enterococcus genera, we continued to observe high sequence conservation for vanA and vanB, up to 99.9% similarity. Phylogenetic tree analyses suggest rapid acquisition of these determinants between strains within vanA and vanB, particularly between strains of Enterococcus genera, which may be indicative of horizontal gene transfer. Within E. faecium, Adenosine 5'-Triphosphate (ATP)-Grasp and D-ala-D-ala ligase (Ddl) were found as conserved domains of vanA and vanB. We additionally found that there is notable sequence conservation, up to 66.67%, between resistomes against vancomycin and streptomycin among E. faecium. Resistance genes against vancomycin have highly conserved sequences between strains of Enterococcus bacteria. These conserved sequences within vanA and vanB encode for ATP-Grasp and Ddl motifs, which have functional properties for maintaining cell wall integrity. High sequence conservation is also observed among resistance genes against penicillin and streptomycin, which can inform future drug targets for broader spectrum therapies.

Serine protease inhibitor Kazal type 1 (SPINK1) promotes proliferation, migration, invasion and radiation resistance in rectal cancer patients receiving concurrent chemoradiotherapy: a potential target for precision medicine

Serine peptidase inhibitor Kazal type-1 (SPINK1), a trypsin kinase inhibitor, is known to be associated with inflammation and pathogenesis. The aim in this study was to demonstrate the clinicopathological role and progression of SPINK1 in rectal cancer (RC) patients undergoing concurrent chemoradiotherapy (CCRT). Immunohistochemical staining for SPINK1 protein expression in 111 RC cases revealed high SPINK1 expression was significantly associated with perineural invasion and poor CCRT response in pre-CCRT specimens. In addition, multivariable analyses showed that pre-CCRT SPINK1 expression was a significant prognostic marker of both overall and disease-free survival in RC patients receiving pre-operative CCRT; furthermore, in vitro studies demonstrated SPINK1 interacted with EGFR to promote the abilities of proliferation, migration and invasion attenuated by SPINK1 si-RNA via ERK, p38, and JNK pathways. SPINK1 was also found to regulate radio-resistance in CRC cell lines. In conclusion, SPINK1 expression is an independent prognostic marker in patients receiving pre-operative CCRT, and SPINK1 regulates proliferation, migration and invasion via EGFR-downstream ERK, p38 and JNK pathways. The phenotypes of radiosensitivity that could be reversed with attenuation of SPINK1 levels suggest that targeting SPINK1 might offer a strategy for optimal precision medicine.

DEPDC1B promotes colorectal cancer via facilitating cell proliferation and migration while inhibiting apoptosis

ABSTRACT Colorectal cancer (CRC) is a common malignant tumor with strong invasiveness. Given the reported involvement of DEP domain-containing protein 1B (DEPDC1B) in the progression of some cancers, its role in CRC was explored in this study. DEPDC1B expression in CRC was assessed based on database and tissue microarray (TMA). In addition, the knockdown and overexpression of DEPDC1B in CRC cell lines were constructed using small hairpin RNA (shRNA) interference. The biological function of DEPDC1B in CRC was evaluated in vitro and in vivo through loss/gain-of-function assays. The results demonstrated that DEPDC1B was highly expressed in CRC. Furthermore, DEPDC1B had the ability to promote CRC proliferation and migration coupled by cell apoptosis. In vivo results showed that DEPDC1B knockdown significantly inhibited the growth of xenograft tumors. Additionally, the results of antibody array indicated increased apoptosis-promoting proteins and decreased apoptosis-inhibiting proteins in DEPDC1B-knockdown CRC cells. In conclusion, DEPDC1B played a key driver role in CRC progression, and inhibition of its expression may be a potential target for precision medicine in CRC.

Precision Medicine of Hepatobiliary and Pancreatic Cancers: Focusing on Clinical Trial Outcomes.

Simple SummaryRecently, tumor-agnostic precision medicine employing comprehensive genome profiling (CGP) and using next-generation sequencing (NGS) has been progressing. This review focuses on the recent progress in precision medicine for advanced unresectable hepatobiliary and pancreatic cancers. We highlight therapies that target several regulators of cancer cell growth and tumor-agnostic therapies that effectively treat biliary and pancreatic cancers. We also discuss our current understanding of precision medicine methods developed using NGS of circulating tumor DNA (ctDNA) as a liquid biopsy technique.Tumor-agnostic precision medicine employing comprehensive genome profiling (CGP) and using next-generation sequencing (NGS) has been progressing recently. This review focuses on precision medicine for advanced unresectable hepatobiliary and pancreatic cancers. In this paper, for biliary tract cancer (BTC), therapies that target several regulators of cancer cell growth, including isocitrate dehydrogenase 1 (IDH1), fibroblast growth factor receptor 2 (FGFR2) fusion, proto-oncogene B-Raf (BRAF), and human epidermal growth factor receptor 2 (HER2) alterations, are reviewed. For pancreatic ductal adenocarcinoma (PDAC), therapies for Kirsten rat sarcoma virus (KRAS) gene mutation G12C, neuregulin (NRG)1, and breast cancer type 1 and 2 susceptibility (BRCA1/2), gene alterations are summarized. On the other hand, precision medicine targets were not established for hepatocellular carcinoma (HCC), although telomerase reverse transcriptase (TERT), tumor protein P53 (TP53), and Wnt/β catenin signaling alterations have been recognized as HCC driver oncogenes. Tumor-agnostic therapies for microsatellite instability-high (MSI-H) and neurotropic tyrosine receptor kinase (NTRK) fusion cancers effectively treat biliary and pancreatic cancers. Precision medicine methods developed using NGS of circulating tumor DNA (ctDNA) and utilizing a liquid biopsy technique are discussed.

Update of Key Clinical, Histological and Molecular Features of Malignant Bone Tumours Arising in the Craniofacial Skeleton.

The craniofacial skeleton is a highly complex and specialized anatomic region containing and protecting the brain and sensory organs. Bone sarcomas arising here comprise a heterogeneous group of tumours, some of which differ in their biological behaviour compared to their peripheral counterparts. The reasons for this seem to lie, at least partially, in the embryonal development of the craniofacial bones. For reaching the correct diagnosis as the cornerstone of optimal personalised treatment planning, a multidisciplinary team of specialists, including pathologists, radiologists, oncologists, and head and neck surgeons needs to be involved. The most common tumours arising in the craniofacial bones are bone-forming tumours, cartilage-forming tumours, fibro-osseous lesions, giant cell-rich lesions, and notochordal tumours. While morphology remains the backbone for the diagnosis, the last decade has witnessed tremendous advances in the molecular characterization of tumours, and molecular testing is increasingly becoming a part of the diagnostic process. The integration of these new molecular markers into the diagnostic approach has undoubtedly increased the diagnostic accuracy and objectivity, and holds great promise to also identify new therapeutic targets for precision medicine in the future. Examples include HEY1-NCOA2 in mesenchymal chondrosarcoma, IDH1/2 mutations in chondrosarcoma and TFCP2 rearrangements in rhabdomyosarcoma. In this article, key clinical, histological and molecular features of malignant bone tumours arising in the craniofacial region are discussed, with a special focus on the differential diagnosis and prognostic considerations.

Identification of growth hormone receptor as a relevant target for precision medicine in low-EGFR expressing glioblastoma.

ObjectiveNew therapeutic approaches are needed to improve the prognosis of glioblastoma (GBM) patients.MethodsWith the objective of identifying alternative oncogenic mechanisms to abnormally activated epidermal growth factor receptor (EGFR) signalling, one of the most common oncogenic mechanisms in GBM, we performed a comparative analysis of gene expression profiles in a series of 54 human GBM samples. We then conducted gain of function as well as genetic and pharmocological inhibition assays in GBM patient‐derived cell lines to functionnally validate our finding.ResultsWe identified that growth hormone receptor (GHR) signalling defines a distinct molecular subset of GBMs devoid of EGFR overexpression. GHR overexpression was detected in one third of patients and was associated with low levels of suppressor of cytokine signalling 2 (SOCS2) expression due to SOCS2 promoter hypermethylation. In GBM patient‐derived cell lines, GHR signalling modulates the expression of proteins involved in cellular movement, promotes cell migration, invasion and proliferation in vitro and promotes tumourigenesis, tumour growth, and tumour invasion in vivo. GHR genetic and pharmacological inhibition reduced cell proliferation and migration in vitro.ConclusionThis study pioneers a new field of investigation to improve the prognosis of GBM patients.

Abstract 2276: High frequency of pathogenic germline variants in patients with malignant mesothelioma

Abstract Background: Malignant mesothelioma (MM) is associated with asbestos exposure, tumor heterogeneity and aggressive clinical behavior. Identification and characterization of germline variants in malignant mesothelioma is relevant for identifying potential actionable targets and genetic counseling of family members. Methods: Patients referred to the Phase I Unit at Rigshospitalet were prospectively enrolled into the Copenhagen Prospective Personalized Oncology trial and underwent whole exome sequencing for somatic and germline variants. Between January 2014 and September 2021, 45 patients with MM were identified and 40 patients underwent whole exome sequencing. Germline variants were selected according to association to inherited cancer using a 168-gene panel and variants were classified according to ACMG/AMP classification as pathological (class 5) or likely pathogenic (class 4). Results: 34 males (85%) and 6 females (15%) with a median age of 64 years (range: 43-77) were available for analysis. The majority (85%) had malignant pleural mesothelioma whilst the rest (15%) had malignant peritoneal mesothelioma. Histological subtypes were distributed between epithelioid type (N=24, 60%), biphasic type (N=12, 30%) and the sarcomatoid type (N=4, 10%). A pathogenic or likely pathogenic variant was found in 16 patients (40%). In total 13 different germline variants were identified (ATM, BAP1, BRCA2, CDKN2A, FANCA, FANCC, FANCD2, FANCM, MUTYH, NBN, RAD51B, SDHA and XPC). The variants included five frameshifts (33%), four missenses (25%), four nonsenses (25%), one splice site (6%), one start loss (6%) and one synonymous (6%). The pathogenic germline variants were found in DNA repair pathways, including homologous recombination repair (69%), nucleotide excision repair (13%), cell cycle regulatory (6%), DNA damage checkpoint control (6%) and hypoxic pathway (6%). Three (19%) of the patients with a germline variant had a second cancer. A previously undiagnosed BRCA2 germline mutation was found in 2 patients. A potential treatment target based on the pathogenic germline variant could be suggested in four patients (10%). Conclusion: The current analysis revealed a high frequency of pathogenic germline variants in patients with malignant mesothelioma. These data support germline testing in these patients and provide a rationale for additional investigation of the homologous recombination pathway as a potential target for precision medicine. Citation Format: Laila Belcaid, Birgitte Bertelsen, Karin A. Wadt, Ida V. Tuxen, Iben Spanggaard, Martin Højgaard, Jens B. Sørensen, Ulrik Lassen, Finn C. Nielsen, Kristoffer Rohrberg, Christina W. Yde. High frequency of pathogenic germline variants in patients with malignant mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2276.

VEGF Overexpression Significantly Increases Nanoparticle-Mediated siRNA Delivery and Target-Gene Downregulation.

The availability of nanoparticles (NPs) to deliver small interfering RNA (siRNA) has significantly expanded the specificity and range of ‘druggable’ targets for precision medicine in cancer. This is especially important for cancers such as triple negative breast cancer (TNBC) for which there are no targeted treatments. Our purpose here was to understand the role of tumor vasculature and vascular endothelial growth factor (VEGF) overexpression in a TNBC xenograft in improving the delivery and function of siRNA NPs using in vivo as well as ex vivo imaging. We used triple negative MDA-MB-231 human breast cancer xenografts derived from cells engineered to overexpress VEGF to understand the role of VEGF and vascularization in NP delivery and function. We used polyethylene glycol (PEG) conjugated polyethylenimine (PEI) NPs to deliver siRNA that downregulates choline kinase alpha (Chkα), an enzyme that is associated with malignant transformation and tumor progression. Because Chkα converts choline to phosphocholine, effective delivery of Chkα siRNA NPs resulted in functional changes of a significant decrease in phosphocholine and total choline that was detected with 1H magnetic resonance spectroscopy (MRS). We observed a significant increase in NP delivery and a significant decrease in Chkα and phosphocholine in VEGF overexpressing xenografts. Our results demonstrated the importance of tumor vascularization in achieving effective siRNA delivery and downregulation of the target gene Chkα and its function.

G9a inhibition by CM-272: Developing a novel anti-tumoral strategy for castration-resistant prostate cancer using 2D and 3D in vitro models.

Castration-resistant prostate cancer (CRPC) is an incurable form of prostate cancer (PCa), with DNMT1and G9a being reported as overexpressed, rendering them highly attractive targets for precision medicine. CM-272 is a dual inhibitor of both methyltransferases' activity. Herein, we assessed the response of different PCa cell lines to CM-272, in both 2D and 3D models, and explored the molecular mechanisms underlying CM-272 inhibitory effects. CRPC tissues displayed significantly higher DNMT1, G9a and H3K9me2 expression than localized PCa. In vitro, CM-272 caused a significant decrease in PCa cell viability and proliferation alongside with increased apoptotic levels. We disclose that, under the evaluated dose, CM-272 led to G9a activity inhibition, while not significantly affecting DNMT1 activity. Upon G9a knockdown, DU145 and PC3 showed decreased cell viability. Remarkably, DU145 cells treated with CM-272 or with G9a knockdown displayed no differences in viability, suggesting a SET-dependent mechanism. Contrarily, PC3 cell viability impact was higher in G9a knockdown, compared with CM-272 treatment, suggesting an additional G9a function. Moreover, DU145 cells overexpressing catalytically functional G9a disclosed higher resistance to CM-272 treatment, reinforcing that the drug mechanism of action is dependent on G9a catalytic function. Importantly, we successfully assembled spheroids from several prostate cell lines. Our results showed that CM-272 retained its anti-tumoral effects in 3D PCa models, leading to a clear reduction in cancer cell survival. We concluded that inhibition of G9a methyltransferase activity by CM-272 has anti-tumor effect in PCa cells, holding therapeutic potential against CRPC.

Posttranslational modifications in GPCR internalization.

G protein-coupled receptors (GPCRs) are the largest family of membrane receptors that serve as the most important drug targets. Classically, GPCR internalization has been considered to lead to receptor desensitization. However, many studies over the past decade have reported that internalized membrane receptors can trigger distinct signal activation. The "internalized activation" provides a completely new understanding for the receptor internalization, the mechanism of physiology/pathology and novel drug targets for precision medicine. GPCR internalization undergoes a series of strict regulations, especially by posttranslational modifications (PTMs). Here, this review summarizes different PTMs in GPCR internalization and analyzes their significance in GPCR internalization dynamics, internalization routes, postinternalization fates, and related diseases, which will offer new insights into the regulatory mechanism of GPCR signaling and novel drug targets for precision medicine.

Quantitative proteomic analysis of cerebrospinal fluid reveals CD163, A2M and full-length APP as potential diagnostic biomarkers of paediatric bacterial meningitis.

BackgroundBacterial meningitis (BM) is a life-threatening infectious disease of the central nervous system in infants and children. To date, no diagnostic methods for the early and precise diagnosis of paediatric BM have been developed.MethodsA label-free cerebrospinal fluid (CSF) quantitative proteomic analysis of 8 patients with confirmed or suspected BM, 9 patients with confirmed or suspected viral meningitis (VM) and 6 non-CNS-infected hospital patients was performed via high-resolution LC–MS/MS.ResultsOur CSF proteomic analysis allowed the identification of critical differences between the BM and non-BM groups. Compared to the proteomes of the non-BM groups, the proteome of the paediatric BM group was characterized by upregulation of complement and coagulation cascades, regulation of IGF transport, uptake by IGF-binding proteins and acute inflammatory response, downregulation of developmental growth, and metabolism of carbohydrates. Moreover, the levels of CD163, A2M and full-length APP in CSF showed excellent diagnostic performance for paediatric BM, with AUC values of 0.911 (95% CI: 0.839–0.984), 0.908 (95% CI: 0.816–1.000) and 0.944 (95% CI: 0.86, 1.000), respectively. Among them, A2M and full-length APP are reported here for the first time as potential diagnostic biomarkers of BM. The findings imply that peptidase regulator activity plays an important role in BM and provide potential novel targets for precision medicine in paediatric BM.ConclusionsCD163, A2M and full-length APP are validated as potential diagnostic biomarkers of paediatric BM.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12953-022-00191-5.

Investigating Susceptibility of ꞵ‐catenin‐mutated Hepatocellular Carcinoma to Checkpoint Inhibitors

Hepatocellular Carcinoma (HCC) is the 5th most common cause of cancer‐related death in the United States with an estimated 32,000 annual deaths. The standard of care for HCC as established by the IMBrave150 trial is a combination of the PD‐L1 inhibitor, Atezolizumab, and an antiangiogenic, Bevacizumab. While this combination extends overall survival to 19.2 months in unresectable HCC, only 52% of patients survive to 18 months. Furthermore, objective response rates are around 32% and hence clarifying underlying mechanisms regulating the immune response in HCC oncogenesis might strengthen immunotherapy efficacy. Especially important is to identify response rates of these agents in specific molecular subclasses of HCC may help in better patient selection. The oncogene ꞵ‐catenin is consistently mutated and activated among 30% of HCC patients. The Wnt/ꞵ‐catenin pathway has been approached as a target for precision medicine in HCC. We recently modeled HCCs with ꞵ‐catenin mutations in mice up to 69% genetic similarity. Here, we combine hydrodynamic tail vein injections with the Sleeping Beauty Transposase which is a non‐viral method of expressing genes of interest. Our model co‐expresses an S45Y point mutant of ꞵ‐catenin with the tyrosine kinase receptor MET (B+M). This combination represents ~10% of patient HCCs and provides a clinically relevant tool for the investigation of personalized HCC therapeutics.A recent study demonstrated HCCs driven by a Δ90‐truncation mutant of ꞵ‐catenin in combination with the Myc oncogene are shown to lack sufficient immune cell surveillance. These HCCs have poor cytotoxic T cell and dendritic cell recruitment while responding poorly to checkpoint inhibitors. Since activating point mutations in CTNNB1 gene are common in patient HCCs, we asked whether poor immune surveillance extends to HCC models harboring point mutations. We first checked and found the presence of CD45+, F4/80+, and CD11b+ cells both 2 and 4 weeks after B+M tumor induction. This indicates the presence of both adaptive and innate immune cells in the B+M tumor microenvironment. We next asked whether checkpoint inhibition will effectively reduce tumor burden in the B+M model. Therefore, we treated B+M mice with either IgG or anti‐PD1 monoclonal antibodies 4 weeks after tumor induction. Tissues were harvested 3.5 weeks after treatment. We found a modest 20% reduction in liver weight to body weight ratio, a measure of tumor burden, in B+M mice treated with anti‐PD1 compared to IgG controls. Our results demonstrate that HCCs with missense ꞵ‐catenin mutations do respond albeit marginally to checkpoint inhibitors. In the future, combination of checkpoint inhibitors with other inhibitors will be tested in these models to determine their efficacy in treating ꞵ‐catenin‐mutated HCCs.

Cancer Recurrence and Omics: Metabolic Signatures of Cancer Dormancy Revealed by Transcriptome Mapping of Genome-Scale Networks.

A major problem in medicine and oncology is cancer recurrence through the activation of dormant cancer cells. A system scale examination of metabolic dysregulations associated with the cancer dormancy offers promise for the discovery of novel molecular targets for cancer precision medicine, and importantly, for the prevention of cancer recurrence. In this study, we mapped the total mRNA sequencing-based transcriptomic data from dormant cancer cell lines and nondormant cancer controls onto a human genome-scale metabolic network by using a graph-based approach, and two mass balance-based approaches with one based on reaction activity/inactivity and the other one on flux changes. The gene expression datasets were accessed from Gene Expression Omnibus (GSE83142 and GSE114012). This analysis included two diverse cancer types, a liquid and a solid cancer, namely, acute lymphoblastic leukemia and colorectal cancer. For the dormant cancer state, we observed changes in major adenosine triphosphate-producing pathways, including the citric acid cycle, oxidative phosphorylation, and glycolysis/gluconeogenesis, indicating a reprogramming in the metabolism of dormant cells away from Warburg-based energy metabolism. All three computational approaches unanimously predicted that folate metabolism, pyruvate metabolism, and glutamate metabolism, as well as valine/leucine/isoleucine metabolism are likely dysregulated in cancer dormancy. These findings provide new insights and molecular pathway targets on cancer dormancy, comprehensively catalog dormancy-associated metabolic pathways, and inform future research aimed at prevention of cancer recurrence in particular.

Precision Medicine Targeting FGFR2 Genomic Alterations in Advanced Cholangiocarcinoma: Current State and Future Perspectives.

Although a relatively uncommon tumor, cholangiocarcinoma is on the rise globally. Of note, most patients are diagnosed with metastatic disease, and the prognosis is poor with cytotoxic chemotherapy. Strategies targeting specific genomic alterations have demonstrated promising activity in recent years and could represent a new therapeutic avenue for these patients. In this review, we will address the biology and clinical results of FGFR inhibition in intrahepatic cholangiocarcinoma, highlighting limitations associated with treatment and discussing the use of circulating tumor DNA to detect mechanisms of resistance.

Emerging Trends in the Pathological Research of Human Papillomavirus-positive Oropharyngeal Squamous Cell Carcinoma.

Oropharyngeal squamous cell carcinomas (OPSCCs) have shown an alarming rate of increase in incidence over the past several decades, markedly in men. In the United States, transcriptionally-active human papillomavirus (HPV), particularly HPV 16, has become the highest contributive agent of OPSCCs, affecting approximately 16,000 people a year. Compared to patients with HPV-negative OPSCCs, patients with HPV-positive OPSCCs exhibit better health responses to chemoradiotherapy and an overall increase in long-term survival. Despite promising treatment options, many OPSCCs are discovered at an advanced stage, and ~20% of cases will recur after definitive treatment. Therefore, extensive research is ongoing to identify new targets for precision treatment and to stratify tumor prognosis. The aim of this review is to capture the most updated research on HPV-positive OPSCCs, emphasizing their relevance as potential new targets for precision medicine and survival prognosis.