Immunotherapy, especially anti-PD-1, is becoming a pillar of modern muscle-invasive bladder cancer (MIBC) treatment. However, the objective response rates (ORR) are relatively low due to the lack of precise biomarkers to select patients. Herein, the molecular subtype, tumor mutation burden (TMB), and CD8+ T cells were calculated by the gene expression and mutation profiles of MIBC patients. MIBC immunotypes were constructed using clustering analysis based on tumor mutation burden, CD8+ T cells, and molecular subtypes. Mutated genes, enriched functional KEGG pathways and GO terms, and co-expressed network-specific hub genes have been identified. We demonstrated that ORR of immunotype A patients identified by molecular subtype, CD8+ T cells, and TMB is about 36% predictable. PIK3CA, RB1, FGFR3, KMT2C, MACF1, RYR2, and EP300 are differentially mutated among three immunotypes. Pathways such as ECM-receptor interaction, PI3K-Akt signaling pathway, and TGF-beta signaling pathway are top-ranked in enrichment analysis. Low expression of ACTA2 was associated with the MIBC survival benefit. The current study constructs a model that could identify suitable MIBC patients for immunotherapy, and it is an important step forward to the personalized treatment of bladder cancers.

Introduction: Newborn screening (NBS) by quantifying T cell receptor excision circles (TRECs) and Kappa re-ceptor excision circles in neonatal dried blood spots (DBS) enables early diagnosis of different types of primary immune deficiencies. Global newborn screening for PID, using an assay to detect T-cell receptor excision circles (TREC) in dried blood spots (DBS), is now being performed in all states in the United States. In this review, we discuss the development and outcomes of TREC, TREC/KREC combines screening, and continued challenges to implementation. Objective: To review the diagnostic performance of published articles for TREC and TREC/ KREC based NBS for PID and its different types. Methods: Different research resources were used to get an approach for the published data of TREС and KREC based NBS for PID like PubMed, Scopus, Google Scholar, Research gate EMBASE. We extracted TREC and KREC screening Publisher with years of publication, content and cut-off values, and a number of retests, repeat DBS, and referrals from the different published pilot, pilot cohort, Case series, and cohort studies. Results: We included the results of TREC, combine TREC/KREC system based NBS screening from different research articles,and divided these results between the Pilot studies, case series, and cohort. For each of these studies, different parameter data are excluded from different articles. Thirteen studies were included, re-confirming 89 known SCID cases in case series and reporting 53 new SCID cases in 3.15 million newborns. Individual TREC contents in all SCID patients were <25 TRECs/μl (except in those evaluated with the New York State assay). Conclusion: TREC and KREC sensitivity for typical SCID and other types of PID was100 %. It shows its importance and anticipating the significance of implementation in different undeveloped and developed countries in the NBS program in upcoming years. Data adapting the screening algorithm for pre-term/ill infants reduce the amount of false-positive test re-sults.

Hennekam lymphangiectasia-lymphedema syndrome has been linked to single-nucleotide polymorphisms in the CCBE1 (collagen and calcium-binding EGF domains 1) gene. Several bioinformatics methods were used to find the most dangerous nsSNPs that could affect CCBE1 structure and function. Using state-of-the-art in silico tools, this study examined the most pathogenic nonsynonymous single-nucleotide polymorphisms (nsSNPs) that disrupt the CCBE1 protein and extracellular matrix remodeling and migration. Our results indicate that seven nsSNPs, rs115982879, rs149792489, rs374941368, rs121908254, rs149531418, rs121908251, and rs372499913, are deleterious in the CCBE1 gene, four (G330E, C102S, C174R, and G107D) of which are the highly deleterious, two of them (G330E and G107D) have never been seen reported in the context of Hennekam syndrome. Twelve missense SNPs, rs199902030, rs267605221, rs37517418, rs80008675, rs116596858, rs116675104, rs121908252, rs147974432, rs147681552, rs192224843, rs139059968, and rs148498685, are found to revert into stop codons. Structural homology-based methods and sequence homology-based tools revealed that 8.8% of the nsSNPs are pathogenic. SIFT, PolyPhen2, M-CAP, CADD, FATHMM-MKL, DANN, PANTHER, Mutation Taster, LRT, and SNAP2 had a significant score for identifying deleterious nsSNPs. The importance of rs374941368 and rs200149541 in the prediction of post-translation changes was highlighted because it impacts a possible phosphorylation site. Gene-gene interactions revealed CCBE1’s association with other genes, showing its role in a number of pathways and coexpressions. The top 16 deleterious nsSNPs found in this research should be investigated further in the future while researching diseases caused CCBE1 gene specifically HS. The FT web server predicted amino acid residues involved in the ligand-binding site of the CCBE1 protein, and two of the substitutions (R167W and T153N) were found to be involved. These highly deleterious nsSNPs can be used as marker pathogenic variants in the mutational diagnosis of the HS syndrome, and this research also offers potential insights that will aid in the development of precision medicines. CCBE1 proteins from Hennekam syndrome patients should be tested in animal models for this purpose.

Autism spectrum disorder (ASD) has become a critical public health issue that affects more than 78 million people. In many recent studies, the authors have demonstrated that equine-assisted activities and therapies (EAATs) can substantially improve the social and behavioral skills of children with ASD. However, the qualities of the studies differ, and some authors reached opposite conclusions. In this review, we systematically and objectively examined the effectiveness of EAATs for people with ASD, combining both qualitative and quantitative methods. We searched five databases (PubMed, Scopus, ERIC, ProQuest, and MEDLINE) and added relevant references, and we identified 25 articles for data extraction and analysis. According to our results, EAAT programs can substantially improve the social and behavioral functioning and language abilities of children with ASD. However, among the subdomains, the results were inconsistent. According to the meta-analyses, there were considerable improvements in the social cognition, communication, irritability, and hyperactivity domains, but not in the domains of social awareness, mannerisms, motivation, lethargy, stereotypy, or inappropriate speech. Moreover, there was a lack of sufficient comparative data to conclude that EAAT programs lead to substantial improvements in motor and sensory functioning. In addition, among the included studies, we noted the indicator of whether EAAT programs decreased parental stress and improved family functioning, and although there were four articles in which the researchers considered this aspect, we were unable to draw any conclusions because of the insufficient data and conflicting descriptive evidence. However, we need to consider the improvement in parental mental health as a factor in the effectiveness of this complementary intervention. We hope that in future studies, researchers will focus on family functioning and conduct more randomized controlled trials (RCTs) with blinded assessments using different scales and measures.

Single-nucleotide polymorphisms in the ELANE (Elastase, Neutrophil Expressed) gene are associated with severe congenital neutropenia, while the ELANE gene provides instructions for making a protein called neutrophil elastase. We identified disease susceptibility single-nucleotide polymorphisms (SNPs) in the ELANE gene using several computational tools. We used cutting-edge computational techniques to investigate the effects of ELANE mutations on the sequence and structure of the protein. Our study suggested that eight nsSNPs (rs28931611, rs57246956, rs137854448, rs193141883, rs201723157, rs201139487, rs137854451, and rs200384291) are the most deleterious in ELANE gene and disturb protein structure and function. The mutants F218L, R34W, G203S, R193W, and T175M have not yet been identified in patients suffering from SCN and cyclic hematopoiesis, while C71Y, P139R, C151Y, G214R, and G203C reported in our study are already associated with both of the disorders. These mutations are shown to destabilize structure and disrupt ELANE protein activation, splicing, and folding and might diminish trypsin-like serine protease efficiency. Prediction of posttranslation modifications highlighted the significance of deleterious nsSNPs because some of nsSNPs affect potential phosphorylation sites. Gene-gene interactions showed the relation of ELANE with other genes depicting its importance in numerous pathways and coexpressions. We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking. This research sheds light on how ELANE failure upon mutation results in disease progression, including congenital neutropenia, and validation of these novel predicted nsSNPs is required through the wet lab.

This article is a Letter to the Editor and does not include an Abstract.

RBCK1 deficiency is a rare congenital autoinflammatory disease that causes inflammatory disruption on the molecular level. This deficiency has three major clinical manifestations: increased sensitivity to bacterial infections, autoinflammation syndrome, and the accumulation of amylopectin in skeletal muscle. The amylopectinosis causes myopathy and cardiomyopathy. The pathogenesis of the disease is poorly investigated and may include unnoticed relationships. We performed gene expression analysis on patients with RBCK1 deficiency and three other autoinflammatory diseases. The identification of differentially expressed genes revealed a large number of downregulated genes that are involved in the activation of essential metabolic and immune pathways, including NF-kB and Pi3k-Akt-mTOR. Signaling pathways were analysed using the KEGG (Kyoto Encyclopedia of Genes and Genomes) and Gene Ontology resource. Predicted protein-protein interactions were retrieved from the STRING (Search Tool for the Retrieval of Interacting proteins database). Besides the primary involvement of RBCK1 in disease pathology, several downregulated pathways aggravate symptoms of myopathy, cardiomyopathy, and bacterial disease. The studied pathways may serve as new targets for the development of compensatory therapies for patients with RBCK1 deficiency.

Background: Congenital neutropenia (CN) is a primary immunodeficiency disease (PID), which is associated with recurrent bacterial infections, autoimmunity, hematological malignancies, and neuropsychiatric symptoms. Understanding the protein-protein interaction (PPI) network of CN genes and finding candidate CN genes is crucial for early CN diagnosis. The purpose of current study was to investigate the PPI network of CN genes and use computational techniques to identify candidate CN genes.Methods: PPI data for CN and PID genes provided from the STRING database were examined using network density and biological distance. Gene expression data of patients with CN were obtained from the Gene Expression Omnibus, and then Pearson’s correlation coefficient, a PPI database, and Kyoto Encyclopedia of Genes and Genomes were used to identify candidate CN genes. We then assessed our hypotheses and discovered CN genes that were differently expressed. Results: Characterization of the majority of CN genes were done by high network density and low biological distance whereas low network density and large biological distance were used to characterize most PID genes. The CN genes are functionally relative to each other compared to PID genes. It showed that they are similar and closely related. Next, we found 15 candidate CN genes with biological functions comparable to known CN genes, and other genes have subsequently been identified as CN-related genes. The SRC gene reported in our study may be a good candidate gene for Heneekem syndrome. The candidate gene “STAT3” was downregulated in peripheral blood neutrophils and B cells in CN patients compared to healthy controls (HC), whereas in blood sample the level was up regulated in CN patients relative to HC. Conclusion: Our findings will contribute in the early diagnosis of CN by providing a better understanding of the CN gene complexity.