Dopamine and cAMP-regulated phosphoprotein 32 kDa (DARPP-32) and survival in breast cancer: a retrospective analysis of protein and mRNA expression

Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population

BACKGROUND

Copy number variations (CNVs) are an important source of genomic variation that play an active role in modulating biological processes by altering gene expression and dosage. These structural variants involve duplications and deletions of segments usually exceeding 1 kilobase in size, dispersed throughout the genome of humans and livestock individuals. We mapped CNVs from high-density single-nucleotide polymorphism (SNP) genotyping array data on 3,601 Holsteins. Following, we explored their association with reported quantitative trait loci (QTLs), genes, and biological pathways, unveiling the potential biological contributions of CNVs to economically important traits in the dairy industry and breeding programs.

RESULTS

We identified 4,113 non-redundant high-confidence CNVs, of which 78% were deletions and 22% duplications, distributed across all bovine autosomal chromosomes (BTA). Out of the 1,184 compiled CNV regions (CNVRs) covering 3.02% of the autosomal genome, 199 novel CNVRs were mapped. QTLs overlapping with CNVRs detected in this study were enriched for 140 economically important traits, such as milk yield, conception and pregnancy rates, susceptibility to diseases and length of productive life, indicating that CNVs likely underlie productive, reproductive and health performance in Holstein dairy cattle. Moreover, detected CNVRs overlapped with 2,788 annotated genes, including those linked to milk production, fertility, and immune response in cattle, such as DGAT1, AFF1, and ADAMTS13 genes. Furthermore, the gene set analysis revealed GO terms related to metabolic processes, immune system, response to stimulus, and cellular binding activities. Notably, enriched GO terms highlighted relevant genes to cattle health and reproduction overlapping CNVRs, such as DEFB4A, GATA3, GNB1, and PPP1R1B.

CONCLUSIONS

We mapped and demonstrated the characteristics of genome-wide distributed CNVs in a large commercial Holstein population genotyped with a high-density SNP array. Collectively, the results emphasize the role of CNVs as a valuable resource of genetic variation and contribute to better understand the genetic architecture of economic complex traits in dairy cattle. Furthermore, these findings may provide opportunities for the development of novel and enhanced genomic selection strategies in Holstein cattle.

Landscape of intrinsically disordered proteins in mental disorder diseases

Disrupted genes linked to mental disorders sometimes exhibit characteristics of Intrinsically Disordered Proteins (IDPs). However, few studies have comprehensively explored the functional associations between protein disorder properties and different psychiatric disorders. In this study, we collected disrupted proteins for seven mental diseases (MDD, SCZ, BP, ID, AD, ADHD, ASD) and a control dataset from normal brains. After calculating the disorder scores for each protein, we thoroughly compared the proportions and functions of IDPs between differentially expressed proteins in each disease and healthy controls. Our findings revealed that disrupted proteins, particularly in ASD and ADHD, contain more IDPs than controls from normal brains. Distinct patterns in disorder properties were observed among different mental disorders. Functional enrichment analysis indicated that IDPs in mental disorders were associated with neurodevelopment, synaptic signaling, and gene expression regulatory pathways. In addition, we analyzed the proportion and function of liquid-phase-separated proteins (LLPS) in psychiatric disorders, finding that LLPS proteins are mainly enriched in pathways related to neurodevelopment and inter-synaptic signaling. Furthermore, to validate our findings, we conducted an analysis of differentially expressed genes in an ASD cohort, revealing that the encoded proteins also exhibit a higher proportion of IDPs. Notably, these IDPs were particularly enriched in pathways related to neurodevelopment, including head development, a process known to be disrupted in ASD. Our study sheds light on the crucial role of IDPs in psychiatric disorders, enhancing our understanding of their molecular mechanisms.

Protein Tyrosine Kinase 7 (PTK7) in Breast Cancer: A Retrospective Analysis of Tumour Expression and Association with Clinical Outcome

Protein tyrosine kinase 7 (PTK7), originally known as colon carcinoma kinase (CCK4), is an evolutionary conserved, catalytically defective transmembrane receptor involved in Wnt signalling. PTK7 has been identified as a potential therapeutic target, and a PTK7 antibody drug conjugate (PF-06647020; cofetuzumab pelidotin) has been investigated in phase I clinical trials for triple-negative breast cancer, ovarian cancer, and non-small cell lung cancer. PTK7 protein expression was evaluated in 1136 early-stage invasive breast tumours by immunohistochemistry. In addition, PTK7 mRNA expression in the METABRIC (n = 1980) and the TCGA breast cancer cohorts (n = 1082) was evaluated. Associations between PTK7 expression and clinicopathological criteria and patient outcome were determined. No association between PTK7 protein expression and breast cancer-specific survival was observed; however, PTK7 mRNA expression in the METABRIC cohort was associated with breast cancer-specific survival (p < 0.001). PTK7 protein and mRNA expression were associated with breast cancer-specific survival of patients with a poor prognostic Nottingham Prognostic Index (NPI) and a moderate prognostic NPI, respectively. Taken together, these data indicate that PTK7 expression is associated with patient outcome in subgroups of breast cancer patients.

Detection of novel PPP1R1B::STARD3 fusion transcript in acute myeloid leukemia: a case report

BACKGROUND

Acute myeloid leukemia (AML) is the second most common type of leukemia in children. Although prognostic and diagnostic tests of AML patients have improved, there is still a great demand for new reliable clinical biomarkers for AML. Read-through fusion transcripts (RTFTs) are complex transcripts of adjacent genes whose molecular mechanisms are poorly understood. This is the first report of the presence of the PPP1R1B::STARD3 fusion transcript in an AML patient. Here, we investigated the presence of PPP1R1B::STARD3 RTFT in a case of AML using paired-end RNA sequencing (RNA-seq).

CASE PRESENTATION

A Persian 12-year-old male was admitted to Dr. Sheikh Hospital of Mashhad, Iran, in September 2019 with the following symptoms, including fever, convulsions, hemorrhage, and bone pain. The patient was diagnosed with AML (non-M3-FAB subtype) based on cell morphologies and immunophenotypical features. Chromosomal analysis using the G-banding technique revealed t (9;22) (q34;q13).

CONCLUSIONS

Single-cell RNA sequencing (scRNA-seq) analysis suggested that the PPP1R1B promoter may be responsible for the PPP1R1B::STARD3 expression. Alterations in the level of lipid metabolites implicate cancer development, and this fusion can play a crucial role in the cholesterol movement in cancer cells. PPP1R1B::STARD3 may be considered a candidate for targeted therapies of the cholesterol metabolic and the PI3K/AKT signaling pathways involved in cancer development and progression.

Evaluation of t-DARPP Expression Alteration in Association with DDR1 Expression in Non-Small Cell Lung Cancer

Background

Discoidin domain receptor 1 (DDR1) signaling plays a critical role in various cellular functions. Increased DDR1 expression has been shown in different human cancers. t-DARPP is a truncated isoform of DARPP-32, and its upregulation promotes cell survival and migration. Most lung cancer patients have non-small cell lung cancer (NSCLC), and their survival rate is low. Therefore, it is necessary to study new and effective targeted therapies. Increased t-DARPP expression in NSCLC patients is associated with patient survival and can act as a prognostic marker correlated with increasing stages of NSCLC. The current study aimed to evaluate alteration in DDR1 expression and its effects on t-DARPP expression in NSCLC.

Methods

Two human lung adenocarcinoma cell lines, A549 and Calu-3, were treated with collagen type I and transfected with DDR1 siRNA. The relative expression of DDR1 and t-DARPP was evaluated using qRT-PCR.

Results

The results indicated that collagen type I could stimulate DDR1 expression in NSCLC cells. Also, DDR1 upregulation resulted in a significant increase in t-DARPP expression. In contrast, suppression of DDR1 expression significantly decreased t-DARPP expression.

Conclusion

Our findings propose that modification in the expression of DDR1, caused by collagen type I and siRNA, might influence the expression of t-DARPP in NSCLC that is linked to NSCLC progression. Moreover, this alteration could potentially serve as an innovative target for therapeutic intervention.

Unravelling transcriptomic complexity in breast cancer through modulation of DARPP-32 expression and signalling pathways

DARPP-32 is a key regulator of protein-phosphatase-1 (PP-1) and protein kinase A (PKA), with its function dependent upon its phosphorylation state. We previously identified DKK1 and GRB7 as genes with linked expression using Artificial Neural Network (ANN) analysis; here, we determine protein expression in a large cohort of early-stage breast cancer patients. Low levels of DARPP-32 Threonine-34 phosphorylation and DKK1 expression were significantly associated with poor patient prognosis, while low levels of GRB7 expression were linked to better survival outcomes. To gain insight into mechanisms underlying these associations, we analysed the transcriptome of T47D breast cancer cells following DARPP-32 knockdown. We identified 202 differentially expressed transcripts and observed that some overlapped with genes implicated in the ANN analysis, including PTK7, TRAF5, and KLK6, amongst others. Furthermore, we found that treatment of DARPP-32 knockdown cells with 17β-estradiol or PKA inhibitor fragment (6-22) amide led to the differential expression of 193 and 181 transcripts respectively. These results underscore the importance of DARPP-32, a central molecular switch, and its downstream targets, DKK1 and GRB7 in breast cancer. The discovery of common genes identified by a combined patient/cell line transcriptomic approach provides insights into the molecular mechanisms underlying differential breast cancer prognosis and highlights potential targets for therapeutic intervention.

DARPP-32 and t-DARPP in the development of resistance to anti-HER2 agents. Pre-clinical evidence from the STEP study

The therapeutic scenario of Human Epidermal Growth Factor Receptor 2 positive advanced breast cancer (ABC) has been recently enriched by a number of innovative agents, which are reshaping treatment sequence. While randomized trials have documented an advantage in terms of efficacy, for the newly available agents we lack effectiveness and tolerability evidence from the real-world setting. Similarly, the identification of predictive biomarkers might improve clinical decision. We herein describe the outline of a prospective/retrospective study which aims to explore the optimal sequence of treatment in HER2+, pertuzumab pre-treated ABC patients treated in II line with anti-HER2 agents in clinical practice. As part of the pre-clinical tasks envisioned by the STEP study, in vitro cell models of resistance were exploited to investigate molecular features associated with reduced efficacy of HER2 targeting agents at the transcript level. The aggressive behavior of resistant cell populations was measured by growth assessment in mouse models. This approach led to the identification of DARPP-32 and t-DARPP proteins as possible predictive biomarkers of efficacy of anti-HER2 agents. Biomarkers validation and the clinical goals will be reached through patients' inclusion into two independent cohorts, i.e., the prospective and retrospective cohorts, whose setup is currently ongoing.

A retrospective analysis of ezrin protein and mRNA expression in breast cancer: Ezrin expression is associated with patient survival and survival of patients with receptor-positive disease

INTRODUCTION

The cytoskeletal protein ezrin is upregulated in many cancer types and is strongly associated with poor patient outcome. While the clinical and prognostic value of ezrin has been previously evaluated in breast cancer, most studies to date have been conducted in smaller cohorts (less than 500 cases) or have focused on specific disease characteristics. The current study is the largest of its kind to evaluate ezrin both at the protein and mRNA levels in early-stage breast cancer patients using the Nottingham (n = 1094) and METABRIC (n = 1980) cohorts, respectively.

RESULTS

High expression of ezrin was significantly associated with larger tumour size (p = 0.027), higher tumour grade (p < 0.001), worse Nottingham Prognostic Index prognostic group (p = 0.011) and HER2-positive status (p = 0.001). High ezrin expression was significantly associated with adverse survival of breast cancer patients (p < 0.001) and remained associated with survival in multivariate Cox-regression analysis (p = 0.018, hazard ratio (HR) = 1.343, 95% confidence interval (CI) = 1.051-1.716) when potentially confounding factors were included. High ezrin expression was significantly associated with adverse survival of patients whose tumours were categorised as receptor (oestrogen receptor (ER), progesterone receptor (PgR) or HER2) positive (p < 0.001) in comparison to those categorised as triple-negative breast cancer (p = 0.889). High expression of ezrin mRNA (VIL2) in the METABRIC cohort was also significantly associated with adverse survival of breast cancer patients (p < 0.001).

CONCLUSION

Retrospective analyses show that ezrin is an independent prognostic marker, with higher expression associated with shortened survival in receptor-positive (ER, PgR or HER2) patients. Ezrin expression is associated with more aggressive disease and may have clinical utility as a biomarker of patient prognosis in early-stage breast cancer.

A highly specific and flexible detection assay using collaborated actions of DNA-processing enzymes for identifying multiple gene expression signatures in breast cancer

Most nucleic acid biosensors employ nucleic acid-processing enzymes to bind, degrade, splice, synthesize, and modify nucleic acids. Utilizing their unique substrate preference, binding mode, and catalytic activity is of great importance in designing nucleic acid biosensors. Combination with DNA-processing enzymes enables them to transform into a new generation of molecular diagnostics tools with enhanced selectivity and sensitivity and reduced reaction time. Here, we report an isothermal amplification strategy by coemploying a structure-specific endonuclease (flap endonuclease 1, FEN1) and a strand-displacing DNA polymerase (Bst DNA polymerase) to detect long RNA targets. This approach couples the FEN1-driven invasive cleavage reaction with toehold-mediated rolling circle amplification (iFEN-tRCA), enabling the highly selective and rapid detection of long RNA targets and offering a detection limit below 10 pM within 1 h. We used two targets, such as human epidermal growth factor receptor 2 (HER2, encoded by ERBB2) and dopamine- and cyclic AMP-regulated phosphoprotein (DARPP, encoded by PPP1R1B), associated with prognosis or response to anticancer therapy. We demonstrated the feasibility and quantitative capability of the iFEN-tRCA assay by assessing the expression of two RNA transcripts (ERBB2 and PPP1R1B) with total RNA extracts purified from human breast cancer cells. Therefore, we envision that the developed assay will provide a suitable prognostic and diagnostic tool for identifying appropriate patients for HER2-targeted therapy and predicting the clinical outcome and occurrence of metastasis relapse in breast cancer.

System analysis based on the ER stress-related genes identifies WFS1 as a novel therapy target for colon cancer

BACKGROUND

Colon cancer (COAD) is the third-largest common malignant tumor and the fourth major cause of cancer death in the world. Endoplasmic reticulum (ER) stress has a great influence on cell growth, migration, proliferation, invasion, angiogenesis, and chemoresistance of massive tumors. Although ER stress is known to play an important role in various types of cancer, the prognostic model based on ER stress-related genes (ERSRGs) in colon cancer has not been constructed yet. In this study, we established an ERSRGs prognostic risk model to assess the survival of COAD patients.

METHODS

The COAD gene expression profile and clinical information data of the training set were obtained from the GEO database (GSE40967) and the test set COAD gene expression profile and clinical informative data were downloaded from the TCGA database. The endoplasmic reticulum stress-related genes (ERSRGs) were obtained from Gene Set Enrichment Analysis (GSEA) website. Differentially expressed ERSRGs between normal samples and COAD samples were identified by R "limma" package. Based on the univariate, lasso, and multivariate Cox regression analysis, we developed an ERSRGs prognostic risk model to predict survival in COAD patients. Finally, we verified the function of WFS1 in COAD through in vitro experiments.

RESULTS

We built a 9-gene prognostic risk model based on the univariate, lasso, and multivariate Cox regression analysis. Kaplan-Meier survival analysis and Receiver operating characteristic (ROC) curve revealed that the prognostic risk model has good predictive performance. Subsequently, we screened 60 compounds with significant differences in the estimated half-maximal inhibitory concentration (IC50) between high-risk and low-risk groups. In addition, we found that the ERSRGs prognostic risk model was related to immune cell infiltration and the expression of immune checkpoint molecules. Finally, we determined that knockdown of the expression of WFS1 inhibits the proliferation of colon cancer cells.

CONCLUSIONS

The prognostic risk model we built may help clinicians accurately predict the survival of patients with COAD. Our findings provide valuable insights into the role of ERSRGs in COAD and may provide new targets for COAD therapy.

A reference-free approach for cell type classification with scRNA-seq

Single-cell RNA sequencing (scRNA-seq) has become a revolutionary technology to characterize cells under different biological conditions. Unlike bulk RNA-seq, gene expression from scRNA-seq is highly sparse due to limited sequencing depth per cell. This is worsened by tossing away a significant portion of reads that attribute to gene quantification. To overcome data sparsity and fully utilize original reads, we propose scSimClassify, a reference-free and alignment-free approach to classify cell types with k-mer level features. The compressed k-mer groups (CKGs), identified by the simhash method, contain k-mers with similar abundance profiles and serve as the cells’ features. Our experiments demonstrate that CKG features lend themselves to better performance than gene expression features in scRNA-seq classification accuracy in the majority of experimental cases. Because CKGs are derived from raw reads without alignment to reference genome, scSimClassify offers an effective alternative to existing methods especially when reference genome is incomplete or insufficient to represent subject genomes.

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Compressed k-mer groups (CKGs) are used to classify cell types without references

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CKGs are competitive to gene expression features for cell type classification

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CKGs are associated with genes sharing gene specific k-mers

Urinary exosomal mRNA detection using novel isothermal gene amplification method based on three-way junction

Exosomal messenger RNA (mRNA) has emerged as a valuable biomarker for liquid biopsy-based disease diagnosis and prognosis due to its stability in body fluids and its biological regulatory function. Here, we report a rapid one-step isothermal gene amplification reaction based on three-way junction (3WJ) formation and the successful detection of urinary exosomal mRNA from tumor-bearing mice. The 3WJ structure can be formed by the association of 3WJ probes (3WJ-template and 3WJ-primer) in the presence of target RNA. After 3WJ structure formation, the 3WJ primer is repeatedly extended and cleaved by a combination of DNA polymerase and nicking endonuclease, producing multiple signal primers. Subsequently, the signal primers promote a specially designed network reaction pathway to produce G-quadruplex probes under isothermal conditions. Finally, G-quadruplex structure produces highly enhanced fluorescence signal upon binding to thioflavin T. This method provides a detection limit of 1.23 pM (24.6 amol) with high selectivity for the target RNA. More importantly, this method can be useful for the sensing of various kinds of mRNA, including breast cancer cellular mRNA, breast cancer exosomal mRNA, and even urinary exosomal mRNA from breast cancer mice. We anticipate that the developed RNA detection assay can be used for various biomedical applications, such as disease diagnosis, prognosis, and treatment monitoring.

Dopamine and cAMP-regulated phosphoprotein 32kDa (DARPP-32), protein phosphatase-1 and cyclin-dependent kinase 5 expression in ovarian cancer

Dopamine and cyclic‐AMP activated phosphoprotein Mr32kDa (DARPP‐32) is a central signalling protein in neurotransmission. Following DARPP‐32 phosphorylation by protein kinase A (PKA), DARPP‐32 becomes a potent protein phosphatase 1 (PP1) inhibitor. DARPP‐32 can itself inhibit PKA following DARPP‐32 phosphorylation by cyclin‐dependent kinase 5 (Cdk5). Increasing evidence indicates a role for DARPP‐32 and its associated signalling pathways in cancer; however, its role in ovarian cancer remains unclear. Using immunohistochemistry, expression of DARPP‐32, PP1 and Cdk5 was determined in a large cohort of primary tumours from ovarian cancer patients (n = 428, 445 and 434 respectively) to evaluate associations between clinical outcome and clinicopathological criteria. Low cytoplasmic and nuclear DARPP‐32 expression was associated with shorter patient overall survival and progression‐free survival (P = .001, .001, .004 and .037 respectively). Low nuclear and cytoplasmic DARPP‐32 expression remained significantly associated with overall survival in multivariate Cox regression (P = .045, hazard ratio (HR) = 0.734, 95% confidence interval (CI) = 0.542‐0.993 and P = .001, HR = 0.494, 95% CI = 0.325‐0.749, respectively). High cytoplasmic and nuclear PP1 expression was associated with shorter patient overall survival and high cytoplasmic PP1 expression with shorter progression‐free survival (P = .005, .033, and .037, respectively). High Cdk5 expression was associated with shorter progression‐free survival (P = .006). These data suggest a role for DARPP‐32 and associated signalling kinases as prognostic markers with clinical utility in ovarian cancer.

Retrospective assessment of cyclin-dependent kinase 5 mRNA and protein expression and its association with patient survival in breast cancer

Cyclin‐dependent kinase 5 (Cdk5) is an atypical member of the cyclin‐dependent kinase family and functions as a serine/threonine kinase that can be activated by non‐cyclin binding activators p35 or p39. Cdk5 expression and activity has been linked with the development and progression of cancer; however, its expression in breast cancer has not been fully described. Protein expression of Cdk5 was determined in a large cohort of early‐stage invasive breast cancer tumours (n = 1110) with long‐term follow‐up data using immunohistochemistry. Expression of CDK5 mRNA was assessed in the METABRIC cohort (n = 1980). Low nuclear and cytoplasmic expression of Cdk5 expression was significantly associated with shorter breast cancer‐specific survival (P = .004 and P = .001, respectively). Importantly, low nuclear and cytoplasmic expression of Cdk5 remained associated with survival in multivariate analysis, including potentially confounding factors (hazard ratio (HR) = 0.612, 95% confidence interval (CI) = 0.418‐0.896, P = .011 and HR = 0.507, 95% CI = 0.318‐0.809, P = .004, respectively). In addition, low nuclear and cytoplasmic expression of Cdk5 was significantly associated with clinicopathological criteria associated with adverse patient prognosis. Low CDK5 mRNA expression was associated with shorter patient survival (P = .005) in the METABRIC cohort; no associations between copy gain or loss and survival were observed. These data suggest that low Cdk5 expression is associated with poor clinical outcome of breast cancer patients and may be of clinical relevance.