Nuclear Matrix Protein Research Articles

Iodide-Enhanced Perovskite Nanozyme-Based Colorimetric Platform for Detection of Urinary Nuclear Matrix Protein 22.

In the last decade, perovskite nanocrystals (PNCs) have brought extensive thinking owing to their excellent optical properties. Recently, we have uncovered the peroxidase-like activity of PNCs and used this for detecting many small molecules; however, the low enzymatic activity makes them unsuitable for fluorescence analysis, which is easily disturbed by the autofluorescence of biological media. This greatly limits their application in bioanalysis. Thus, the development of a method to facilely modulate the activity of PNCs for the instrument-free colorimetric detection is highly desirable. Herein, we demonstrated an iodide-enhanced perovskite nanozyme-based colorimetric platform for the visual assay of urinary nuclear matrix protein 22 (NMP22), a typical biomarker for the diagnosis of bladder cancer. We discovered that halogen could regulate the activity of perovskite nanozymes through a simple anion replacement reaction. Experimental analysis suggested that CsPbI3 nanocrystals (NCs) displayed 24-fold higher catalytic efficiency than classical CsPbBr3 NCs. As a proof-of-concept assay, the CsPbI3 NCs could be explored into an immunoassay for the detection of NMP22 in clinical urine specimens, resulting in a low detection limit of 0.03 U/mL. This iodide-enhanced immunoassay deepens our understanding of perovskite nanozymes and also provides great potential for bioanalysis.

Dual inhibition of phosphoinositide 3-kinases delta and gamma reduces chronic B cell activation and autoantibody production in a mouse model of lupus.

Phosphoinositide 3-kinase delta (PI3Kδ) plays key roles in normal B cell activation and is chronically activated in malignant B cells. Targeting of PI3Kδ using FDA-approved drugs Idelalisib or Umbralisib has shown efficacy in treatment of multiple B cell malignancies. Duvelisib, an inhibitor targeting both PI3Kδ and PI3Kγ (PI3Kδγi) has also been used for treatment of several leukemias and lymphomas and was suggested to offer potential additional benefits in supressing T cell and inflammatory responses. Transcriptomics analyses indicated that while most B cell subsets predominantly express PI3Kδ, plasma cells upregulate PI3Kγ. We thus assessed whether PI3Kδγi treatment can impact chronic B cell activation in the context of an autoantibody-mediated disease. Using the TAPP1R218LxTAPP2R211L (TAPP KI) mouse model of lupus-like disease driven by dysregulated PI3K pathway activity, we performed 4 week PI3Kδγi treatments and found significant reduction in CD86+ B cells, germinal center B cells, follicular helper T cells and plasma cells in multiple tissues. This treatment also significantly attenuated the abnormally elevated serum levels of IgG isotypes observed in this model. The profile of autoantibodies generated was markedly altered by PI3Kδγi treatment, with significant reductions in IgM and IgG targeting nuclear antigens, matrix proteins and other autoantigens. Kidney pathology was also impacted, with reduced IgG deposition and glomerulonephritis. These results indicate that dual inhibition of PI3Kδ and PI3Kγ can target autoreactive B cells and may have therapeutic benefits in autoantibody-mediated disease.

The role of MATRIN3 (MATR3) in innate immune response

Abstract MATR3, one of the most abundant inner nuclear matrix proteins, is implicated in amyotrophic lateral sclerosis (ALS) and distal myopathy. MATR3 has been reported to have both DNA- and RNA-binding abilities. However, it is not understood mechanistically how mutation of MATR3 leads to ALS pathogenesis. To understand its loss of function effects, we mutated MATR3 in the human HAP1 cell line using CRISPR/Cas9 technology. Using two different RNA sequencing methods, Oxford Nanopore Technologies and Illumina, we discovered the upregulation of many interferon-stimulated genes (ISGs) in MATR3-deficient HAP1 cells. Furthermore, we have validated these results by Nanostring technology. Next, we hypothesized that HAP1 cells may be responding to endogenous double-stranded RNAs. Interestingly, we observed similar amounts of dsRNA in both MATR3 knock-out (KO) and wildtype (WT) cells which suggests that indeed intracellular dsRNAs are present and could be stimulating HAP1 cells; however, it is not the case that MATR3 KO cells are stimulated because they are producing significantly more dsRNAs. Currently, we are investigating whether and which RNA sensors are activated in MATR3 KO cells. Also, we are investigating whether MATR3’s DNA- and/or RNA-binding abilities are responsible for the innate immune response. Accordingly, we plan to perform CUT & RUN and photoactivatable ribonucleoside enhanced crosslinking and immunoprecipitation (PAR-CLIP) respectively, in HAP1 cells. Altogether, our results illustrate that MATR3 is a novel negative regulator of the innate immune response. This work was supported by the Intramural Research Program of NIAID, NIH. This work was supported by the Intramural Research Program of NIAID, NIH.

Study on Early Prostate Cancer Antigen (EPCA) and existent risk factors of prostate cancer, Sudan: A case-control study

Background: Early prostate cancer antigen (EPCA), a nuclear matrix protein, has recently been recommended as a hopeful biomarker for early prostate carcinogenesis. Objectives: To evaluate the validity of serum early prostate cancer antigen (EPCA) in the early detection of prostate cancer (PCa) and the characteristics of Sudanese patients diagnosed with prostate cancer. Method: In this study, seventy men were considered as a case subject, who were diagnosed as cancer prostate at Gezira Hospital for Renal Disease and Surgery (GHRDS), Sudan during the period February 2018 to July 2019. Randomly selected sixty patients of BPH patients and forty-five apparently healthy men as controls group. EPCA, and PSA estimations were performed from serum samples using the principle of Enzyme Linked Immunosorbent Assay (ELISA). Results: There was significant association between age, family history, residence, unhealthy habits, education, BMI, occupations and prostate cancer, results also revealed a significant elevation between the means of the serum levels of both early prostate cancer antigen and prostate specific antigen of the patients with prostate cancer when compared with the control groups. EPCA biomarker offered the best performance statically (P= 0.00) and highest specificity (81%) and sensitivity (94%) in prostate cancer detection in Sudanese males over PSA biomarker. Conclusions: Cases of studied prostate cancer linked to many risk factors. Serum levels of early prostate cancer antigen and prostate specific antigen were significantly increased in patients with prostate cancer, however, our data proposed that EPCA has higher power statistical value, so could be utilized as a prostate cancer specific and sensitive biomarker for early detection of prostate cancer.

Noninvasive Detection of Bladder Cancer Markers Based on Gold Nanomushrooms and Sandwich Immunoassays

Bladder cancer is one of the most common malignancies in the urinary system. Cystoscopy is the traditional standard diagnostic method for bladder cancer with subsequent biopsy or surgery. However, this method is uncomfortable for most patients because it requires anesthesia and possibly causes infections. Because of the high recurrence rate of bladder cancer, a rapid, low-cost, high-sensitivity, and noninvasive sensing method is needed. This study employed gold nanomushroom (AuNM) chips for bladder cancer biomarker detection, combining the benefits of sandwich immunoassay and localized surface plasmon resonance (LSPR) sensing. With a metal nanotransfer printing technique, which is cheap and straightforward, the AuNMs were patterned on flexible polycarbonate (PC) sheets. The gold caps stood above PC stems and provided ample spatial areas for capturing the biomarkers to be sensed. Three biomarkers served as the antigens and analytes, including human complement factor H (CFH), hyaluronic acid (HA), and nuclear matrix protein 22 (NMP22). Different antibodies, against the same biomarker, were covalently conjugated to AuNMs or gold nanoparticles, respectively. When the antibody–antigen–antibody sandwich structure formed, the plasmonic coupling between the AuNM surface and the gold nanoparticles significantly enhanced LSPR signals. The LSPR red shifts correlated quantitatively with the concentrations of the biomarkers. The limits of detection were 6.5, 8.3, and 7.0 pg/mL for CFH, HA, and NMP22, respectively. The chip’s specificity was tested and confirmed, excluding the nonspecific binding and false-positive possibility. The sensing performance of this sandwich immunoassay-based AuNM chip was better than that of the commercialized enzyme-linked immunosorbent assay. It provided a rapid, label-free, and easy operating platform for diagnosing and monitoring bladder cancer.

The Clinical Significance of Septin 9 and Colon Cancer Specific Antigen-2 (CCSA-2) in Colorectal Cancer.

Colorectal cancer (CRC) is a major health problem Worldwide, Egypt shows a high rate of early CRC in the world as 35% of 1,600 Egyptian CRC patients were under 40 with threefold increased risk of death within 5 years. DNA methylation-based biomarkers as methylated Septin9 (mSEPT9) has a promising role for detecting CRC. As well as set of nuclear matrix proteins associated with changes in the nuclear structure/architecture. detection of these nuclear proteins resulted in identification of biomarkers that are specific for colon cancer. Particular interest has been placed on colon cancer specific antigen-2(CCSA-2). A total of 30 newly diagnosed CRC patients, 7 colonic adenoma patients, and 15 age- and sex-matched control subjects were recruited in this study. Plasma mSEPT9was assayed by Epi procolon kit, CCSA-2 by ELISA and, Occult blood in stool by Guaiac-based fecal occult blood test. The level of Colon Cancer mSEPT9 and CCSA-2 were carried on CRC patients both preoperatively and three months postoperatively. mSEPT9 has 96.7% sensitivity and 95.5% specificity in differentiating colorectal cancer patients from non-malignant cases. Also, our study showed a highly statistically significant difference between the pre and three months postoperative expression of mSEPT9 in colorectal cancer as there was a dramatically decrease in the expression of mSEPT9 postoperatively (p value < 0.001). The CCSA-2 at the cutoff level of >1.43 would provide 93.3% sensitivity and 90.9% specificity in differentiation between malignant and non-malignant cases. Also, the study showed that there is a statistically significant difference between colorectal cancer patients preoperatively and postoperatively according to CCSA-2 with dramatic decrease in its level postoperatively (p value > 0.001). The plasma SEPT9 DNA methylation level and Serum CCSA-2 could be used as promising non-invasive methods for observing the CRC patients postsurgical response to predict the occurrence of complete remission or relapses.

Role of C-Terminal Phosphorylation of Lamin A in DNA Damage and Cellular Senescence.

The nuclear matrix protein lamin A is a multifunctional protein with roles in DNA replication and repair, gene activation, transcriptional regulation, and maintenance of higher-order chromatin structure. Phosphorylation is the main determinant of lamin A mobility in the nucleus and nuclear membrane dissolution during mitosis. However, little is known about the regulation of lamin A phosphorylation during interphase. Interestingly, C-terminal lamin A mutations trigger cellular senescence. Recently, we showed that the C-terminal region of lamin A interacts with casein kinase II (CK2). In the present study, we have expanded on our previous research to further investigate lamin A phosphorylation and elucidate the mechanisms underlying the effect of C-terminal mutations on cellular senescence. Our results indicate that glycogen synthase kinase 3β (GSK3β) and CK2 jointly mediate the phosphorylation of lamin A at C-terminal Ser628 and Ser636 residues. Furthermore, a loss of phosphorylation at either of these two sites affects the nuclear distribution of lamin A, leading to an impaired DNA damage response as well as cellular senescence. Thus, phosphorylation at C-terminal sites in lamin A appears to be important for maintaining genomic stability and preventing cellular senescence. These findings provide insight into how loss of the C-terminal region of lamin A may induce premature aging. Furthermore, enhancement of GSK3β and CK2 activity may represent a possible therapeutic approach for the treatment of aging-related diseases.

Low Expression of MATR3 Is Associated with Poor Survival in Clear Cell Renal Cell Carcinoma

Matrin 3 (MATR3) is one of the most abundant inner nuclear matrix proteins involved in multiple nuclear processes. However, to date, the biological role and prognostic relevance of MATR3 in human cancers still need to be explored. Therefore, the present study aimed to examine the expression levels and prognostic significance of MATR3 in clear cell renal cell carcinoma (ccRCC) patients. We assessed MATR3 immunohistochemical staining and RNA-seq data from publicly available data sets, and the results were analyzed with reference to clinicopathological characteristics and the overall survival of patients. Furthermore, the protein-protein interaction (PPI) network for MATR3 and its neighbors was constructed, functionally annotated, and screened for survival-related genes. MATR3 protein and mRNA levels were lower in tumor tissues compared to control tissues. Lower MATR3 protein (HR 2.36, 95%CI 1.41-3.97; p = 0.001) and mRNA (HR 2.01, 95%CI 1.46-2.75; p < 0.0001) expression levels were found to be a significant independent adverse prognostic factor for the patient's overall survival (OS). Moreover, of the candidate genes, the MRPL23 gene was identified as being the most predictive of OS, and combined MRPL23/MATR3 expression status predicted patient survival better than looking at each marker individually (HR 3.15, 95%CI 2.05-4.83; p < 0.0001). In conclusion, the results from the present investigation warrant further research into the biological and prognostic value of MATR3 and MRPL23 in ccRCC patients.

MATR3 P154S knock-in mice do not exhibit motor, muscle or neuropathologic features of ALS

Matrin 3 is a nuclear matrix protein that has many roles in RNA processing including splicing and transport of mRNA. Many missense mutations in the Matrin 3 gene (MATR3) have been linked to familial forms of amyotrophic lateral sclerosis (ALS) and distal myopathy. However, the exact role of MATR3 mutations in ALS and myopathy pathogenesis is not understood. To demonstrate a role of MATR3 mutations in vivo, we generated a novel CRISPR/Cas9 mediated knock-in mouse model harboring the MATR3 P154S mutation expressed under the control of the endogenous promoter. The P154S variant of the MATR3 gene has been linked to familial forms of ALS. Heterozygous and homozygous MATR3 P154S knock-in mice did not develop progressive motor deficits compared to wild-type mice. In addition, ALS-like pathology did not develop in nervous or muscle tissue in either heterozygous or homozygous mice. Our results suggest that the MATR3 P154S variant is not sufficient to produce ALS-like pathology in vivo.

Atomic Force Microscopy-Based Measurements of Retinal Microvessel Stiffness in Mice with Endothelial-Specific Deletion of CCN1.

Vascular stiffness is an independent predictor of human vascular diseases and is linked to ischemia, diabetes, high blood pressure, hyperlipidemia, and/or aging. Blood vessel stiffening increases owing to changes in the microscale architecture and/or content of extracellular, cytoskeletal, and nuclear matrix proteins. These alterations, while best appreciated in large blood vessels, also gradually occur in the microvasculature and play an important role in the initiation and progression of numerous microangiopathies including diabetic retinopathy. Although macroscopic measurements of arterial stiffness by pulse wave velocity are often used for clinical diagnosis, stiffness changes of intact microvessels and their causative factors have not been characterized. Herein, we describe the use of atomic force microscopy (AFM) to determine stiffness of mouse retinal capillaries and assess its regulation by the cellular communication network (CCN) 1, a stiffness-sensitive gene-encoded matricellular protein. AFM yields reproducible measurements of retinal capillary stiffness in lightly fixed freshly isolated retinal flat mounts. AFM measurements also show significant changes in compliance properties of the retinal microvasculature of mice with endothelial-specific deletion of CCN1, indicating that CCN1 expression, or lack thereof, affects the mechanical properties of microvascular cells in vivo. Thus, AFM has the force sensitivity and the spatial resolution necessary to measure the local modulus of retinal capillaries in situ and eventually to investigate microvascular compliance heterogeneities as key components of disease pathogenesis.

Panniculitis, an uncommon skin manifestation in adult dermatomyositis

This case-cohort study was performed to investigate the skin manifestations of 205 adult inpatients with dermatomyositis (DM). We then analysed the association between the clinical characteristics and panniculitis in adult patients with DM. This study was conducted at the First Medical Centre of PLA General Hospital, Beijing, China from 1 March 2016 to 30 December 2020 with follow-up until 31 December 2021. This case-cohort study involved 205 eligible participants with DM who met the criteria for idiopathic inflammatory myopathy. Clinical data, cutaneous manifestations, and lesion locations were screened and analysed. Serum samples were collected, and immunoblotting was used to detect 16 types of myositis-specific antibodies and myositis-associated antibodies. The results showed that 16 (7.8%) of the 205 adult patients with DM had panniculitis. The panniculitis was mainly distributed in the subcutaneous fat of the abdomen, buttocks, and thighs. This condition was often accompanied by skin ulcers, atrophic scars, and calcinosis. Moreover, 9 (72.7%) of the 16 patients with panniculitis were positive for antibodies to nuclear matrix protein 2 (anti-NXP2 antibodies). In conclusion, our data showed that panniculitis is an uncommon skin manifestation in adult patients with DM, with a positivity rate of 7.8%. The appearance of panniculitis is likely associated with anti-NXP2 antibodies.

Clinical value of urine nuclear matrix protein 22 (NMP22) quantitative test in the diagnosis of bladder cancer in a schistosoma endemic region

Background: Bladder cancer is the ninth commonest cancer and the 13th most common cause of mortality worldwide. Its early diagnosis poses a great challenge therefore the need to identify biomarkers which may improve the current diagnostic practice.Methods: This is a prospective study of patients managed for bladder cancer at the urology unit, department of surgery, Usmanu Danfodiyo University Teaching Hospital, Sokoto, Nigeria between April 2019 to June 2020. Urine cytology, urine nuclear matrix protein 22 (NMP22) quantitative test and histology of the bladder biopsy specimens were done at the Histopathology and Chemical Pathology laboratory respectively of the Usmanu Danfodiyo University Teaching Hospital, Sokoto. Data was collected using a structured proforma and analyzed using statistical package for social sciences (SPSS) version 20.0.Results: Eighty-three patients enrolled in the study however 46 of them with features of bladder carcinoma participating in the study group and 37 in the control group. The study and control groups' mean age and age range are (49.70±11.45,18-69) and (51.84±13.75,18-78) years, respectively. The sensitivity, specificity, PPV, NPV and AUC of urine NMP22 and urine cytology in the study were (78.3% vs. 58.7%), (32.4% vs. 100.0%), (59.0% vs. 100.0%), (54.6% vs. 66.1%), (0.207 vs. 0.538) respectively for the diagnosis of bladder cancer.Conclusions: Urine NMP22 quantitative test shows high sensitivity, low specificity and a low AUC compared to urine cytology and thus of poor clinical value in the diagnosis of bladder cancer in our region.

Clinical evaluation of urine laminin-γ2 monomer as a potent biomarker for non-muscle invasive bladder cancer.

To evaluate whether urine laminin-γ2 monomer (Ln-γ2m) offers a useful biomarker for patients with non-muscle-invasive bladder cancer (NMIBC). Participants comprised 297 patients, including 111 patients with NMIBC, 136 patients with benign genitourinary disease (BD) and 50 healthy donors (HD). Urine Ln-γ2m was prospectively measured and accuracy was analyzed. Receiver operating characteristic (ROC) curves were determined and area under the ROC curve (AUC) was calculated for urine Ln-γ2m, and compared to those of traditional urine tumor markers such as nuclear matrix protein 22 (NMP22), bladder tumor antigen (BTA) and cytology. The net benefits of combining urine markers were analyzed by decision curve analysis. Mean urine Ln-γ2m was significantly higher in NMIBC than in BD or HD. The AUC for urine Ln-γ2m was significantly higher than those for urine NMP22, BTA or cytology when comparing NMIBC with HD. In patients with low-grade NMIBC, the AUC for urine Ln-γ2m was higher than the AUCs for NMP22, BTA or cytology. A net benefit of combined examination using urine Ln-γ2m/uCRN with NMP22 was demonstrated. These results suggest urine Ln-γ2m as a potentially useful biomarker for NMIBC, particularly in cases of low-grade cancer.

Comparison of urinary telomerase, CD44, and NMP22 assays for detection of bladder squamous cell carcinoma.

BackgroundSquamous cell carcinoma (SCC) of the bladder is common in many regions around the world. Prognosis is very poor, as most cases are diagnosed at an advanced stage due to a lack of affordable and valid screening markers for this type of cancer. The diagnostic accuracy of urinary nuclear matrix protein-22 (NMP22), telomerase activity, and CD44 were evaluated in urine samples of patients with bladder SCC.Materials and methodsWe conducted a case-control study comprised of 60 consecutive newly diagnosed bladder SCC patients diagnosed by cystoscopy and histopathological examination, and controls were 60 outpatients with benign urologic conditions and healthy clinic visitors. Urine samples collected from each subject underwent testing for NMP22, telomerase activity, and CD44. Descriptive and correlational statistical analysis of cases and controls were carried out and receiver operating characteristic curve analysis was used to determine optimal cut-off points for the three assays.ResultsArea under the curve was calculated at 0.96, 0.93, and 0.62 for NMP22, telomerase, and CD44, respectively. Urine levels of NMP22 and telomerase activity were significantly higher in the SCC group compared to controls (p < 0.001). Urine CD44 levels were not significantly higher in the SCC group compared to controls (p = 0.111). The overall sensitivity of NMP22, telomerase, and CD44 was 96.7%, 87%, and 45%, respectively, while the specificity was 85%, 88.6%, and 86.7%, respectively.ConclusionsUrinary telomerase activity, followed by NMP22 urine levels, showed high diagnostic yield and could hold potential promise as urinary biomarkers for the diagnosis of bladder SCC.

Prognostic significance of MATR3 in stage I and II non-small cell lung cancer patients.

Matrin 3 (MATR3) is a nuclear matrix protein involved in mRNA stabilization, nuclear retention of hyper-edited RNAs, and RNA splicing. The role of MATR3 in cancer is still unclear. The present study aimed to investigate expression levels and prognostic significance of MATR3 in stage I and II non-small cell lung cancer (NSCLC) patients. We examined MATR3 protein immunohistochemically in tumoral and non-tumoral tissue sections from n = 67 NSCLC patients treated at hospital, and MATR3 mRNA from The Cancer Genome Atlas (TCGA) cohort with respect to valid prognostic and predictive features, as well as treatment outcome. Significantly higher immunohistochemical levels of MATR3 protein were found in tumor-adjacent tissue compared to cancer (p = 0.049). A decrease in MATR3 protein expression was found to be a significant independent adverse prognostic factor for patients overall survival (p = 0.007). By contrast, we observed higher MATR3 mRNA levels in tumoral tissue compared to control lung tissues (p < 0.001). Based on the TCGA dataset, we reported that high MATR3 mRNA level was significantly associated with worse OS of NSCLC patients (p < 0.001); however, it was not an independent prognostic marker (p = 0.156). The discrepancies in prognostic significance of MATR3 gene mRNA and protein levels imply a need for further investigation. In conclusion, the present study warrants further investigation into the biological and prognostic value of MATR3 as a potential prognostic marker in early-stage NSCLC patients.

A multianalyte assay for the detection of dermatomyositis-related autoantibodies based on immunoprecipitation combined with immunoblotting.

To develop a multianalyte assay for the detection of dermatomyositis (DM)-related autoantibodies using immunoprecipitation (IP) combined with immunoblotting (IB). Sera from 116 DM patients were subjected to RNA and protein immunoprecipitation assays as well as commercial enzyme-linked immunosorbent assays (ELISAs) for anti-aminoacyl transfer RNA synthetase, anti-melanoma differentiation antigen 5 (MDA5), anti-Mi-2, anti-transcriptional intermediary factor-1γ (TIF-1γ), and anti-U1 ribonucleoprotein antibodies. The IP/IB assay was developed by immunoprecipitation of autoantigens from HeLa cell extracts using patient sera, followed by immunoblotting with an antibody against Mi-2, TIF-1γ, OJ, nuclear matrix protein (NXP)-2, MDA5, PM/Scl, small ubiquitin-like modifier activating enzyme (SAE), or Ku. A multianalyte assay was designed by mixing primary antibodies in the IP/IB assay. IP assays identified any DM-related autoantibodies in 100 patients (86%), of which 82% were covered by commercial ELISAs, with a false-positive result in two sera and a false-negative result in one serum. The results obtained from the multianalyte IP/IB assay and 'gold-standard' IP assays were concordant in terms of the presence or absence of anti-MDA5, anti-TIF-1γ, anti-OJ, anti-NXP-2, anti-PM/Scl, anti-SAE, anti-Mi-2, and anti-Ku antibodies. This multianalyte IP/IB assay combined with commercial ELISAs is an alternative to 'gold-standard' IP assays for the detection of DM-related autoantibodies.

SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs.

Regulation of chromatin structure and accessibility determines the transcription activities of genes, which endows the host with function-specific patterns of gene expression. Upon viral infection, the innate immune responses provide the first line of defense, allowing rapid production of variegated antiviral cytokines. Knowledge on how chromatin accessibility is regulated during host defense against viral infection remains limited. Our previous work found that the nuclear matrix protein SAFA surveilled viral RNA and regulated antiviral immune genes expression. However, how SAFA regulates the specific induction of antiviral immune genes remains unknown. Here, through integration of RNA-seq, ATAC-seq and ChIP-seq assays, we found that the depletion of SAFA specifically decreased the chromatin accessibility, activation and expression of virus induced genes. And mutation assays suggested that the RNA-binding ability of SAFA was essential for its function in regulating antiviral chromatin accessibility. RIP-seq results showed that SAFA exclusively bound with antiviral related RNAs following viral infection. Further, we combined the CRISPR-Cas13d mediated RNA knockdown system with ATAC-qPCR, and demonstrated that the binding between SAFA and according antiviral RNAs specifically mediated the openness of the corresponding chromatin and following robust transcription of antiviral genes. Moreover, knockdown of these associated RNAs dampened the accessibility of related genes in an extranuclear signaling pathway dependent manner. Interestingly, VSV infection cleaved SAFA protein at the C-terminus which deprived its RNA binding ability for immune evasion. Thus, our results demonstrated that SAFA and the interacting RNA products collaborated and remodeled chromatin accessibility to facilitate antiviral innate immune responses.

Autoantibodies and Cancer Association: the Case of Systemic Sclerosis and Dermatomyositis.

Several rheumatic diseases have a perplexing association with cancer. Unraveling this mysterious connection is likely to provide deeper understanding regarding mechanisms governing the onset of both autoimmunity and cancer immunity, in addition to providing clinicians much needed guidance around whom and when to screen for occult malignancy. Systemic sclerosis (scleroderma) and dermatomyositis are two diseases in which the association with internal malignancy is well-described and can be considered as models from which to gain important insights that likely have broader applicability. The past 15 years have witnessed a striking acceleration in understanding how these two diseases are related to cancer emergence-an important crack in this inscrutable armor has been the discovery and characterization of disease-specific autoantigens that are closely tied with risk of cancer emergence. The best-described examples of this are antibodies against anti-RNA polymerase III (anti-POL3) and transcription intermediary factor 1-gamma (anti-TIF1γ). Patients with systemic sclerosis and cancer that are diagnosed within a short time interval of each other frequently have anti-POL3 antibodies. Antibodies against the minor spliceosome protein RNA-Binding Region Containing 3 (RNPC3) are also associated with increased cancer incidence in systemic sclerosis. Similarly, in the dermatomyositis spectrum, the majority of anti-TIF1γ-associated cancers are detected around the time of DM onset (most often within 1 year). Antibodies against Nuclear Matrix Protein 2 are also potentially associated with increased cancer emergence in dermatomyositis. The systemic sclerosis/anti-POL3 connection with close cancer onset led to the first experiments directly supporting the concept that rheumatic disease may in fact be a manifestation of cancer. It is now clear that studying these diseases through the lens of autoantibodies can reveal relationships and insights that would otherwise remain obscured. Extending these studies, new findings show that antibodies against RNA polymerase I large subunit are associated with protection against short interval cancers in anti-POL3-positive systemic sclerosis patients. These insights highlight the fact that autoantigen discovery related to cancer emergence remains an important priority; such new tools will enable the testing of specific hypotheses regarding mechanisms governing disease emergence and development of effective anti-tumor responses. Autoantibody phenotype will likely play an important role in the development of cancer screening guidelines that are critically needed by clinicians taking care of these patients. In this review, we will summarize the current state of knowledge regarding the different ways in which autoantibodies are connected with systemic sclerosis/dermatomyositis and malignancy and highlight potential paths forward.

The Role of NMP22 and CSTB Levels in Predicting Postoperative Recurrence of Bladder Cancer

Objective To investigate the value of preoperative urinary nuclear matrix protein 22 (NMP22) and Cystatin B (CSTB) expressions in evaluating the postoperative recurrence of bladder cancer. Methods The clinical case data of 102 patients with bladder cancer who underwent surgical treatment from January 2017 to January 2022 were collected, and the patients were divided into a recurrence group (n = 54) and nonrecurrence group (n = 48) according to whether the patients recurred after surgery, and the preoperative NMP22 and CSTB expression levels between the two groups were compared. Receiver operating curve (ROC) was used to analyze the evaluation value of preoperative NMP22 and CSTB expression in patients with bladder cancer postoperative recurrence. Logistic multivariate regression method was used to analyze the correlation between preoperative NMP22 and CSTB expression and postoperative bladder cancer recurrence. The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of NMP22 and CSTB single detection and combined detection were evaluated for postoperative recurrence of bladder cancer. Results The preoperative expression levels of NMP22 and CSTB in the recurrence group were significantly higher than those in the nonrecurrence group (P < 0.05). The results of ROC curve analysis showed that the AUC of preoperative NMP22 and CSTB expression levels to assess postoperative recurrence of bladder cancer was 0.696 and 0.659, respectively (P < 0.05). Logistic multivariate regression analysis showed that preoperative NMP22 and CSTB overexpression was an independent risk factor for postoperative recurrence of bladder cancer (OR = 1.042, 2.307, P < 0.05). The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of preoperative NMP22 combined with CSTB in evaluating bladder cancer recurrence after surgery were higher than those of preoperative NMP22 and CSTB alone, and the differences were statistically significant (P < 0.05). Conclusion Preoperative NMP22 and CSTB conveying is hardly interrelated to postoperative recurrence of bladder carcinoma and has certain appraisal worth for postoperative recurrence of bladder carcinoma, and the combined testing of the two has a taller appraisal worth. NMP22 combined with CSTB detection will help to detect postoperative recurrence of bladder cancer and formulate effective treatment measures in time.

Abstract A033: Identification of cancer-specific alterations in expression of nuclear matrix proteins through proteomic and RNAsequencing analyses of ductal carcinoma in situ

Abstract Background and Objectives: In 2021 breast cancer (BC) was the most common cancer affecting women and the second deadliest cancer in the U.S. Ductal Carcinoma In Situ (DCIS) is the earliest identifiable pre-invasive breast cancer lesion. Approximately 20-25% of diagnosed breast cancer cases are ductal carcinoma in situ (DCIS). Estimates show that 14 to 50% of DCIS cases progress to invasive breast cancer. We used a novel tissue-engineering system established in the Latimer laboratory to generate model systems representative of different molecular and histological subtypes of all stages of BC, including DCIS. Using a mass spectrometry (MS)-based relative quantitative methodology, we analyzed one novel DCIS cell line, the matching isogenic contralateral cell line and the non-tumor adjacent cell line, as well as two non-diseased breast reduction mammoplasty cell lines and the established stage IV BC cell lines MCF7 and MDA MB231. RNA sequencing analysis included additional cell lines from stages I, II and III. In order to limit the number of proteins for proteomic assessment, nuclear matrix proteins (NMPs) were targeted for analysis. NMPs have previously been linked with cancers of the prostate, colon, and breast. Maldi-TOF/TOF-MS analysis identified 270 NMPs with high confidence. Our objective was to identify NMPs with specifically altered expression in DCIS and later stages of BC compared to non-diseased breast and contralateral breast. Such markers may help to accurately identify invasive DCIS and improve early detection of BC. Results: We identified two nuclear matrix proteins that are significantly downregulated in DCIS and all other stages of BC in our collection. This downregulation was also apparent through mRNA expression analysis. These proteins are upregulated in non-diseased breast reduction tissue and contra-lateral DCIS derived from the same patient. We also identified four NMPs that were significantly upregulated in DCIS and all other BC stages compared to non-diseased breast reduction tissue and contralateral DCIS. Gene expression analyses showed that these four genes were upregulated with BC progression. Finally, we identified nine NMPS with significant differences in expression between DCIS and all stages of BC versus non-diseased breast reduction tissue and contralateral DCIS where gene expression did not follow the same trend as proteomic analysis. Conclusion: Our findings suggest that the changes that occur in the nuclear matrix of DCIS vs. normal breast epithelium could provide a basis for the development of prognostic biomarkers for DCIS and allow for targeted prevention of progression to invasive disease. This work was supported by grant W81XWH-0701-0660 from the DOD CDMRP BC program. Citation Format: Ali Almutairy, Abdullah Alhamed, Stephen G. Grant, Miranda Sarachine Falso, Billy W. Day, Jean J. Latimer. Identification of cancer-specific alterations in expression of nuclear matrix proteins through proteomic and RNAsequencing analyses of ductal carcinoma in situ [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A033.