Clinical utilities and end-user experience of pharmacogenomics:39 mo of clinical implementation experience in an Australian hospital setting

BACKGROUND Pharmacogenomics(PG)testing is under-utilised in Australia.Our research provides Australia-specific data on the perspectives of patients who have had PG testing and those of the clinicians involved in their care,with the aim to inform wider adoption of PG into routine clinical practice.AIM To investigate the frequency of actionable drug gene interactions and assess the perceived utility of PG among patients and clinicians.METHODS We conducted a retrospective audit of PG undertaken by 100 patients at an Australian public hospital genetics service from 2018 to 2021.Via electronic surveys we compared and contrasted the experience,understanding and usage of results between these patients and their clinicians.RESULTS Of 100 patients who had PG,84% were taking prescription medications,of which 67% were taking medications with actionable drug-gene interactions.Twenty-five out of 81 invited patients and 17 out of 89 invited clinicians completed the surveys.Sixty-eight percent of patients understood their PG results and 48% had medications changed following testing.Paired patient-clinician surveys showed patient-perceived utility and experience was positive,contrasting their clinicians’hesitancy on PG adoption who identified insufficient education/training,lack of clinical support,test turnaround time and cost as barriers to adoption.CONCLUSION Our dichotomous findings between the perspectives of our patient and clinician cohorts suggest the uptake of PG is likely to be driven by patients and clinicians need to be prepared to provide information and guidance to their patients.

2D and 3D refraction-based visualization of breast cancer for early clinical check

Ductal carcinoma in-situ (DCIS) has been visualized by 2D XDFI (X-ray dark-field imaging) and further by a 3D X-ray CT, and the data was acquired by the X-ray optics DEI (diffraction-enhanced imaging). A newly made algorithm was used for CT. Data of 900 projections with interval of 0.2 degrees were used. Ductus lactiferi, microcalci-fication in a 3D form have been clearly visible. The spatial resolution available was approximately 30μm.

Effect of BNT162b2 mRNA COVID-19 vaccine on sperm morphokinetics and DNA integrity: A prospective observational study in Japan

Objective:To assess whether the coronavirus disease 2019(COVID-19)mRNA vaccine affects sperm morphokinetics using a computer-assisted semen analyzer and other semen parameters using a sperm chromatin structure assay.Methods:Healthy male volunteers in two Japanese clinics between May 2021 and December 2021 were prospectively analyzed.Participants donated sperm twice,two days apart,in the following phases:before vaccination,2 weeks after the first vaccine dose,and 2,4,and 12 weeks after the second dose.Basic sperm parameters,sperm motility characteristics,and the percentage of DNA-damaged sperm were compared among the different phases.Results:Ninety-six semen samples from ten volunteers,who were vaccinated with the BNT162b2 mRNA vaccine,were evaluated.There were no significant differences between any phases in basic semen findings and parameters of the sperm chromatin structure assays.Regarding sperm motion characteristics,the average linear velocity,beat-cross frequency,and sperm motility index significantly decreased after the second vaccine dose(P=0.018,P=0.003,and P=0.027,respectively),with no significant differences between any two phases by post-hoc pairwise comparisons.Conclusions:After COVID-19 mRNA vaccination,while sperm motion characteristics might fluctuate,no apparent deterioration of basic sperm parameters or sperm DNA integrity was observed.Given the adverse effects of COVID-19 on sperm,our findings suggest that there might be no reason to refrain from vaccination for healthy individuals.

Pulmonary nocardiosis with bloodstream infection diagnosed by metagenomic next-generation sequencing in a kidney transplant recipient:A case report

BACKGROUND Pulmonary nocardiosis is difficult to diagnose by culture and other conventional testing,and is often associated with lethal disseminated infections.This difficulty poses a great challenge to the timeliness and accuracy of clinical detection,especially in susceptible immunosuppressed individuals.Metagenomic nextgeneration sequencing(mNGS)has transformed the conventional diagnosis pattern by providing a rapid and precise method to assess all microorganisms in a sample.CASE SUMMARY A 45-year-old male was hospitalized for cough,chest tightness and fatigue for 3 consecutive days.He had received a kidney transplant 42 d prior to admission.No pathogens were detected at admission.Chest computed tomography showed nodules,streak shadows and fiber lesions in both lung lobes as well as right pleural effusion.Pulmonary tuberculosis with pleural effusion was highly suspected based on the symptoms,imaging and residence in a high tuberculosisburden area.However,anti-tuberculosis treatment was ineffective,showing no improvement in computed tomography imaging.Pleural effusion and blood samples were subsequently sent for mNGS.The results indicated Nocardia farcinica as the major pathogen.After switching to sulphamethoxazole combined with minocycline for antinocardiosis treatment,the patient gradually improved and was finally discharged.CONCLUSION A case of pulmonary nocardiosis with an accompanying bloodstream infection was diagnosed and promptly treated before the dissemination of the infection.This report emphasizes the value of mNGS in the diagnosis of nocardiosis.mNGS may be an effective method for facilitating early diagnosis and prompt treatment in infectious diseases,which overcomes the shortcomings of conventional testing.

促黄体激素受体突变导致的性器官发育异常(英文)

The Luteinizing hormone/chorionic gonadotropin receptor (LHR) plays a critical role in human male sexual development. Both gain-of-function and loss-of-function mutations of the LHR have been described. Gain-of-function mutations are dominant and cause constitutive activation of the receptor resulting in familial male-limited precocious puberty (FMPP). All activating mutations are single point mutations and are located in the transmembrane domain (TM). TM helix Ⅵ harbors the largest number of activating mutations with the codon of Asp-578 being the hot-spot of mutation. Besides causing abnormal sexual development, constitutively activated LHR may predispose an individual to the development of testicular neoplasia. The anti-thesis of FMPP is Leydig cell hypoplasia (LCH). This is caused by mutations that inactivate the LHR resulting in subnormal male sexual development or male pseudohermaphroditism. Inactivating mutations are recessive. The genetic cause of LCH is variable and there is no mutation hot-spot. Genotype-phenotype correlation can be identified in LCH with the milder form caused by mutated LHR with residual activity and the severe form caused by absence of signal transduction activity of the mutated receptor. Molecular diagnosis of the disorders caused by mutation of the LHR can be achieved by direct sequencing of the LHR gene.

Mucosal-associated invariant T cells and oral microbiome in persistent apical periodontitis

Opportunistic bacteria in apical periodontitis (AP) may pose a risk for systemic dissemination.Mucosal-associated invariant T (MAIT) cells are innate-like T cells with a broad and potent antimicrobial activity important for gut mucosal integrity.It was recently shown that MAIT cells are present in the oral mucosal tissue,but the involvement of MAIT cells in AP is unknown.Here,comparison of surgically resected AP and gingival tissues demonstrated that AP tissues express significantly higher levels of Vα7.2-Jα33,Vα7.2- Jα20,Vα7.2-Jα12,Cα and tumour necrosis factor (TNF),interferon (IFN)-γ and interleukin (IL)-17A transcripts,resembling a MAIT cell signature.Moreover,in AP tissues the MR1-restricted MAIT cells positive for MR1–5-OP-RU tetramer staining appeared to be of similar levels as in peripheral blood but consisted mainly of CD4^+ subset.Unlike gingival tissues,the AP microbiome was quantitatively impacted by factors like fistula and high patient age and had a prominent riboflavin-expressing bacterial feature.When merged in an integrated view,the examined immune and microbiome data in the sparse partial least squares discriminant analysis could identify bacterial relative abundances that negatively correlated with Vα7.2-Jα33,Cα,and IL-17A transcript expressions in AP,implying that MAIT cells could play a role in the local defence at the oral tissue barrier.In conclusion,we describe the presence of MAIT cells at the oral site where translocation of oral microbiota could take place.These findings have implications for understanding the immune sensing of polymicrobial-related oral diseases.

Gallbladder cancer harboring ERBB2 mutation on the primary and metastatic site: A case report

BACKGROUND Bile duct cancer constitutes gallbladder cancer(GBC),intrahepatic cholangiocarcinoma(ICA),and extrahepatic cholangiocarcinoma(ECA).These three entities show morphological and immunohistochemical resemblance so that it is difficult to differentiate between primary ICA and liver metastasis of GBC,which sometimes becomes a point of discussion in clinical practice.Although these cancers demonstrate significant differences in their mutational landscape,several reports demonstrated shared genomic alteration in paired primary and metastatic site aids in distinguishing metastatic recurrence from second primary cancers.CASE SUMMARY We present a 73-year-old female patient who underwent curative resection for GBC harboring epidermal growth factor receptor 2(ERBB2)activating mutation on next-generation sequencing(NGS)-based genomic testing.One year later,a hepatic lesion was observed on follow-up imaging and she underwent surgical resection for a pathological diagnosis.The histological findings of the hepatic lesion were similar to those of the primary lesion.Additionally,using NGS panel testing,the hepatic lesion was found to have ERBB2 activating mutation,which is the identical mutation detected in the sequencing result of the primary site.ERBB2 activating mutation occurs more frequently in GBC than ICA and ECA.Therefore,in the present case,we think this molecular finding potentiated the diagnosis of the liver mass toward a metastatic recurrence.Additionally,this patient underwent HER2-targeted treatment with lapatinib in combination with capecitabin and obtained clinical benefit.CONCLUSION This case illustrated NGS panel usefulness in distinguishing GBC recurrence from second primary cancer and HER2-targeted agent efficacy on ERBB2 mutated GBC.

Endoscopy-based Kyoto classification score of gastritis related to pathological topography of neutrophil activity

BACKGROUND Endoscopy-based Kyoto classification for gastritis and pathological topographic distribution of neutrophil infiltration are correlated with gastric cancer risk.AIM To investigate the association between Kyoto classification and the topographic distribution of neutrophil activity.METHODS Kyoto classification score,ranging from 0 to 8,consisted of atrophy,intestinal metaplasia,enlarged folds,nodularity,and diffuse redness.Neutrophil activity was scored according to the updated Sydney System using biopsy samples obtained from the greater curvature of the corpus and the antrum.The participants were divided into four categories,inactive stomach,antrumpredominant gastritis,pangastritis,and corpus-predominant gastritis,based on the topographic distribution of neutrophil activity.Effects of sex,age,body mass index,drinking habit,smoking habit,family history of gastric cancer,serum Helicobacter pylori(H.pylori)antibody,and Kyoto score on topography of neutrophil infiltration were analyzed.RESULTS A total of 327 patients(comprising 50.7%women,with an average age of 50.2 years)were enrolled in this study.H.pylori infection rate was 82.9%with a mean Kyoto score of 4.63.The Kyoto score was associated with the topographic distribution of neutrophil activity.Kyoto scores were significantly higher in the order of inactive stomach,antrum-predominant gastritis,pangastritis,and corpuspredominant gastritis(3.05,4.57,5.21,and 5.96,respectively).Each individual score of endoscopic findings(i.e.,atrophy,intestinal metaplasia,enlarged folds,nodularity,and diffuse redness)was correlated with the topographic distribution of neutrophil activity.On multivariate analysis,the Kyoto score,age,and serum H.pylori antibody were independently associated with the topographic distribution of neutrophil activity.CONCLUSION The Kyoto classification score was associated with the topographic distribution of neutrophil activity.

The next generation of cancer management

As readers of Cancer Biology and Medicine well know,there has been a seismic shift in human molecular biology over the past few years,as momentous in its own way as the discovery of the double-helical structure of DNA by Watson and Crick 60 years ago,the elucidation of the genetic code shortly thereafter,the advent of recombinant DNA and gene

A novel GPCR mediates pancreatic cancer associated fibroblast-cancer cell interaction

OBJECTIVE Pancreatic ductal adenocarcinoma(PDAC),a lethal cancer in need of new,effective therapies,has a unique tumor microenvironment characterized by a dense fibrotic stroma(desmoplasia)that is generated by pancreatic cancer-associated fibroblasts(PCAFs)derived from pancreatic stellate cells(PSCs)and pancreatic fibroblasts(PFs).METHEDS and RESULTS Hypothesizing that G protein-coupled receptors(GPCRs)may regulate PCAFs,we used an unbiased GPCRomic array approach to compare GPCR expression in PCAFs,PFs and PSCs and identified 82 GPCRs commonly expressed by PCAFs derived from primary tumors of five PDAC patients.We discovered that PCAFs have increased expression of numerous GPCRs,in particular a GPCR with much higher expression in PCAFs compared to both PFs and PSCs.Immunohistochemistry revealed increased expression of this GPCR in PDAC tumors.Co-culture of PSCs with PDAC cells or incubation with TNFαinduced its expression.Activation of the GPCR in PCAF sincreased expression of interleukin-6(IL-6)via a cA MP/PKA/CREB signaling pathway.GPCR knockdown with siR NA diminished IL-6 production and secretionby PCAFs and ability of PCAF conditioned media to enhance proliferation of PDAC cells.CONCLUSION We conclude that PDAC cells induce expression by PCAFs of a novel GPCR,resulting in increased IL-6 production by PCAFs and promotion of PDAC cell proliferation.This PCAF-expressed GPCR thus contributes to PDAC cell-PCAF interaction and as such,may be a novel therapeutic target for PDAC tumors.

Multidisciplinary management of patients diagnosed with von Hippel-Lindau disease: A practical review of the literature for clinicians

Objective:The aim of the current review is to summarize the available evidence to aid clinicians in the surveillance,treatment and follow-up of the different primary tumors developed by patients diagnosed with von Hippel-Lindau(VHL)syndrome.Methods:A non-systematic narrative review of original articles,meta-analyses,and random-ized trials was conducted,including articles in the pre-clinical setting to support relevant find-ings.Results:VHL disease is the most common rare hereditary disorder associated with clear cell renal cell carcinoma.Affected individuals inherit a germline mutation in one VHL allele,and any somatic event that disrupt the other allele can trigger mutations,chromosomal rearrange-ments,or epigenetic regulations leading to oncogenesis.From a clinical perspective,patients continuously develop multiple primary tumors.Conclusion:Because VHL is considered a rare disease,very limited evidence is available for diagnosis,surveillance,active treatment with local or systemic therapy and follow-up.

Artificial intelligence in gastrointestinal diseases

Artificial intelligence(AI)applications are growing in medicine.It is important to understand the current state of the AI applications prior to utilizing in disease research and treatment.In this review,AI application in the diagnosis and treatment of gastrointestinal diseases are studied and summarized.In most cases,AI studies had large amounts of data,including images,to learn to distinguish disease characteristics according to a human’s perspectives.The detailed pros and cons of utilizing AI approaches should be investigated in advance to ensure the safe application of AI in medicine.Evidence suggests that the collaborative usage of AI in both diagnosis and treatment of diseases will increase the precision and effectiveness of medicine.Recent progress in genome technology such as genome editing provides a specific example where AI has revealed the diagnostic and therapeutic possibilities of RNA detection and targeting.

Lack of evidence for germline WWP1 pathogenic variants in gastrointestinal polyposis and other phenotypes suggestive of PTEN-hamartoma-tumor syndrome

Germline activating variants in WWP1,which encodes an E3 ubiquitin ligase that antagonizes PTEN tumor suppressive function,have been proposed as an alternative mechanism of PTEN inactivation in PTEN-hamartoma-tumor syndrome(PHTS)-like patients with wildtype PTEN.1 More specifically,heterozygous,potentially activating wwP1 variants were first identified by Lee et al in patients affected with gastrointestinal oligopolyposis,including adenomatous,hyperplastic/serrated,and hamartomatous polyps,and occasionally with colorectal cancer(Table 1).Subsequently,based on the PHTS phenotypic features,wWP1 mutational screening was performed in patients with thyroid nodules,2 or normocephalic autism spectrum disorder(ASD),3 where germline WWP1 variants were also identified(Table S1).

Identification of telomere maintenance gene variations related to lung adenocarcinoma risk by genome-wide association and whole genome sequencing analyses

Dear editor,Lung carcinoma is responsible for the highest fatal-ity rate among cancer-related deaths globally,with lung adenocarcinoma(LADC)emerging as the prevailing sub-type.

Characterizing and annotating the genome using RNA-seq data

Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts(especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome-guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.

Claudin-11 and occludin are major contributors to Sertoli cell tight junction function, in vitro

The Sertoli cell tight junction （T J） is the key component of the blood-testis barrier, where it sequesters developing germ cells undergoing spermatogenesis within the seminiferous tubules. Hormonally regulated claudin-11 is a critical transmembrane protein involved in barrier function and its murine knockout results in infertility. We aimed to assess quantitatively the significance of the contribution of claudin-11 to TJ function, in vitro, using siRNA-mediated gene silencing. We also conducted an analysis of the contribution of occludin, another intrinsic transmembrane protein of the TJ. Silencing of claudin-11 and/or occludin was conducted using siRNA in an immature rat Sertoli cell culture model. Transepithelial electrical resistance was used to assess quantitatively TJ function throughout the culture. Two days after siRNA treatment, cells were fixed for immunocytochemical localization of junction proteins or lyzed for RT-PCR assessment of mRNA expression. Silencing of claudin-11, occludin, or both resulted in significant decreases in TJ function of 55% （P 〈 0.01）, 51% （P 〈 0.01）, and 62% （P 〈 0.01）, respectively. Data were concomitant with significant decreases in mRNA expression and marked reductions in the localization of targeted proteins to the Sertoli cell TJ. We provide quantitative evidence that claudin-11 contributes significantly （P 〈 0.01） to Sertoli cell TJ function in vitro. Interestingly, occludin, which is hormonally regulated but not implicated in infertility until late adulthood, is also a significant （P 〈 0.01） contributor to barrier function. Our data are consistent with in vivo studies that clearly demonstrate a role for these proteins in maintaining normal TJ barrier structure and function.

Developmental staging of male murine embryonic gonad by SAGE analysis

Despite the identification of key genes such as Sry integral to embryonic gonadal development, the genomic classification and identification of chromosomal activation of this process is still poorly understood. To better understand the genetic regulation of gonadal development, we performed Serial Analysis of Gene Expression （SAGE） to profile the genes and novel transcripts, and an average of 152,000 tags from male embryonic gonads at E10.5 （embryonic day 10.5）, E11.5, E12.5, E13.5, E15.5 and E17.5 were analyzed. A total of 275,583 non-singleton tags that do not map to any annotated sequence were identified in the six gonad libraries, and 47,255 tags were mapped to 24,975 annotated sequences, among which 987 sequences were uncharacterized. Utilizing an unsupervised pattern identification technique, we established molecular staging of male gonadal development. Rather than providing a static descriptive analysis, we developed algorithms to cluster the SAGE data and assign SAGE tags to a corresponding chromosomal position; these data are displayed in chromosome graphic format. A prominent increase in global genomic activity from E10.5 to E17.5 was observed. Important chromosomal regions related to the developmental processes were identified and validated based on established mouse models with developmental disorders. These regions may represent markers for early diagnosis for disorders of male gonad development as well as potential treatment targets.

Identifying and annotating human bifunctional RNAs reveals their versatile functions

Bifunctional RNAs that possess both protein-coding and noncoding functional properties were less explored and poorly understood. Here we systematically explored the characteristics and functions of such human bifunctional RNAs by integrating tandem mass spectrometry and RNA-seq data. We first constructed a pipeline to identify and annotate bifunctional RNAs,leading to the characterization of 132 high-confidence bifunctional RNAs. Our analyses indicate that bifunctional RNAs may be involved in human embryonic development and can be functional in diverse tissues. Moreover, bifunctional RNAs could interact with multiple miRNAs and RNA-binding proteins to exert their corresponding roles. Bifunctional RNAs may also function as competing endogenous RNAs to regulate the expression of many genes by competing for common targeting miRNAs. Finally,somatic mutations of diverse carcinomas may generate harmful effect on corresponding bifunctional RNAs. Collectively,our study not only provides the pipeline for identifying and annotating bifunctional RNAs but also reveals their important gene-regulatory functions.

实践指南：个体基因组筛查的解读和临床应用

研究学者们以飞快的速度找到了常见疾病的遗传相关性。基于大量可用的全基因组关联研究数据，几家全球性营利性公司已经开展了检测服务，对检测者可能患疾病的风险以及一些非医学情况和特质进行了大范围的预测，包括家系分组、耳垢类型和前列腺癌患病的风险。大部分公司直接向检测者提供服务，不需要医生或者其他医疗保健人员的认可。

中国结直肠癌错配修复功能缺陷患病率较低:一项多中心研究

背景:尽管错配修复功能缺陷(dMMR)检测已被推荐用于所有结直肠癌患者,但其用于中国人群中仍缺乏数据支持。因此,我们调查了一个大型中国结直肠癌队列中dMMR的患病率及其临床病理特征。方法:纳入2010年8月至2016年9月间在四家医疗中心就治的7,373例结直肠癌患者,记录其基线资料和病理特征,并比较MLH1/PMS2表达缺失(dMLH1/PMS2)与MSH2/MSH6表达缺失(dMSH2/MSH6)患者的临床病理特征。结果:本组病例中654例(8.9%)被判定为dMMR,其中401例(61.3%)为男性,中位发病年龄55岁(范围:22-87岁);355例(54.3%)为II期肠癌(AJCC 8版)。dMLH1/PMS2和dMSH2/MSH6的出现率分别为51.5%(337/654)和25.1%(164/654)。与dMSH2/MSH6组相比,dMLH1/PMS2组患者年龄较大(57岁vs 52岁,P<0.001),女性占比更高(45.7%vs 31.5,P=0.004),肿瘤更多位于右半结肠(59.0%vs 47.6%,P=0.015),具有肿瘤家族史的比例较低(29.7%vs 43.3%,P=0.003)。结论:中国结直肠癌人群dMMR患病率偏低,尤其是dMLH1/PMS2。不同类型dMMR患者有着不同的临床病理特征。