1
|
ISO 15189 is a sufficient instrument to guarantee high-quality manufacture of laboratory developed tests for in-house-use conform requirements of the European In-Vitro-Diagnostics Regulation. Clin Chem Lab Med 2023; 61:608-626. [PMID: 36716120 DOI: 10.1515/cclm-2023-0045] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 01/31/2023]
Abstract
The EU In-Vitro Diagnostic Device Regulation (IVDR) aims for transparent risk-and purpose-based validation of diagnostic devices, traceability of results to uniquely identified devices, and post-market surveillance. The IVDR regulates design, manufacture and putting into use of devices, but not medical services using these devices. In the absence of suitable commercial devices, the laboratory can resort to laboratory-developed tests (LDT) for in-house use. Documentary obligations (IVDR Art 5.5), the performance and safety specifications of ANNEX I, and development and manufacture under an ISO 15189-equivalent quality system apply. LDTs serve specific clinical needs, often for low volume niche applications, or correspond to the translational phase of new tests and treatments, often extremely relevant for patient care. As some commercial tests may disappear with the IVDR roll-out, many will require urgent LDT replacement. The workload will also depend on which modifications to commercial tests turns them into an LDT, and on how national legislators and competent authorities (CA) will handle new competences and responsibilities. We discuss appropriate interpretation of ISO 15189 to cover IVDR requirements. Selected cases illustrate LDT implementation covering medical needs with commensurate management of risk emanating from intended use and/or design of devices. Unintended collateral damage of the IVDR comprises loss of non-profitable niche applications, increases of costs and wasted resources, and migration of innovative research to more cost-efficient environments. Taking into account local specifics, the legislative framework should reduce the burden on and associated opportunity costs for the health care system, by making diligent use of existing frameworks.
Collapse
Key Words
- AB, accrediting body
- BRCA1/2, breast cancer genes 1 and 2
- CA, competent authority
- CAPA, corrective and preventive actions
- CDx, companion diagnostics
- CGP, comprehensive genomic profile
- CRGA, clinically relevant genomic alterations
- EEA, European economic area
- EFLM, European Federation of Clinical Chemistry and Laboratory Medicine
- EMA, European Medicines Agency
- EU, European Union
- European Regulation 2017/746 on In-Vitro-Diagnostic Devices
- FMEA, failure-mode effects analysis
- GA, genomic alterations
- GDPR, General Data Protection Regulation
- HI, health institution
- HRD, homologous recombination deficiency
- HRR, homologous recombination repair
- ISO 15189:2012
- ISO, International Organization for Standardization
- IVDD, In-Vitro Diagnostic Device Directive
- IVDR, In-Vitro Diagnostic Device Regulation
- LDT, laboratory-developed test
- MDCG, Medical Device Coordination Group
- MSI, micro satellite instability
- MU, measurement uncertainty
- NB, notified body
- NGS, next generation sequencing
- NTRK, neurotrophic tyrosine receptor kinase
- PARPi, poly (ADP-ribose) polymerase inhibitors
- PRRC, person responsible for regulatory compliance
- PT, proficiency testing
- RUO, research use only
- RiliBÄk, Richtlinie der Bundesärztekammer zur Qualitätssicherung Laboratoriums medizinischer Untersuchungen
- SOP, standard operating procedure
- TMB, tumor mutational burden
- UDI, unique device identifier
- VAF, variant allele frequency
- iQC, internal quality control
- laboratory-developed tests for in-house use
- method validation
Collapse
|
2
|
TCR_Explore: A novel webtool for T cell receptor repertoire analysis. Comput Struct Biotechnol J 2023; 21:1272-1282. [PMID: 36814721 PMCID: PMC9939424 DOI: 10.1016/j.csbj.2023.01.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
T cells expressing either alpha-beta or gamma-delta T cell receptors (TCR) are critical sentinels of the adaptive immune system, with receptor diversity being essential for protective immunity against a broad array of pathogens and agents. Programs available to profile TCR clonotypic signatures can be limiting for users with no coding expertise. Current analytical pipelines can be inefficient due to manual processing steps, open to data entry errors and have multiple analytical tools with unique inputs that require coding expertise. Here we present a bespoke webtool designed for users irrespective of coding expertise, coined 'TCR_Explore', enabling analysis either derived via Sanger sequencing or next generation sequencing (NGS) platforms. Further, TCR_Explore incorporates automated quality control steps for Sanger sequencing. The creation of flexible and publication ready figures are enabled for different sequencing platforms following universal conversion to the TCR_Explore file format. TCR_Explore will enhance a user's capacity to undertake in-depth TCR repertoire analysis of both new and pre-existing datasets for identification of T cell clonotypes associated with health and disease. The web application is located at https://tcr-explore.erc.monash.edu for users to interactively explore TCR repertoire datasets.
Collapse
|
3
|
Circulating cell-free DNA as predictor of pathological complete response in locally advanced rectal cancer patients undergoing preoperative chemoradiotherapy. Clin Transl Radiat Oncol 2022; 36:9-15. [PMID: 35733829 PMCID: PMC9207192 DOI: 10.1016/j.ctro.2022.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/28/2022] Open
Abstract
cfDNA could be a biomarker for tailored follow-up in locally advanced rectal cancer. Circulating cell-free DNA can be quantified by a rapid, and feasible DFA method. Low cfDNA levels at end of therapy were related to pathological complete response. ‘cfDNA responders’ with descending levels during therapy were associated with pCR. We propose cfDNA as a complimentary tool for patient selection for a W&W strategy.
Background The watch and wait (W&W) strategy is proposed for patients with locally advanced rectal cancer (LARC) achieving clinical complete response (cCR) after neoadjuvant radiotherapy. cCR is only in partial concordance with pathological complete response (pCR) due to persisting viable tumour cells. The aim was to investigate circulating-free-deoxyribonucleic-acid (cfDNA) as a biomarker for prediction of pCR. Materials and methods Patients treated with neoadjuvant radiotherapy for LARC, were included in a prospective biomarker study in Aarhus, Denmark from 2017 to 2020. Plasma cfDNA levels were analysed by a direct fluorescent assay (DFA). Surgical specimens were reviewed by pathologists to categorize response to cytotoxic therapy. Results In total, 76 patients were included with plasma available at baseline (n = 70), mid therapy (n = 50), and end of therapy (n = 54). Higher cfDNA levels were observed in LARC patients compared with healthy subjects (p < 0.01). By ROC analysis (AUC: 0.87 (95% CI, 0.81–0.92)) the optimal cut-off was 0.71 ng/µL for differentiation between healthy subjects and LARC patients. Thirteen patients obtained pCR with a median cfDNA level of 0.57 ng/µL at end of therapy. Patients with cfDNA levels at end of therapy below the cut-off (p < 0.02) and ‘cfDNA responders’ with descending levels greater than the 75th percentile during therapy had a significantly higher chance of pCR (p < 0.01). Conclusion This hypothesis generating study indicates that low cfDNA levels at end of treatment or ´cfDNA responderś might be associated with pCR. Quantification of cfDNA by the rapid and feasible DFA analysis could potentially facilitate personalized follow-up as a complementary tool to identify candidates for a W&W strategy.
Collapse
Key Words
- CRT, chemoradiotherapy
- DFA, direct fluorescent assay
- IMRT, intensity modulated radiotherapy
- LARC, locally advanced rectal cancer
- NGS, next generation sequencing
- RT, radiotherapy
- VMAT, volumetric modulated arc therapy
- W&W, watch and wait
- cCR, clinical complete response
- cfDNA, circulating cell free deoxyribonucleic acid
- ddPCR, digital droplet polymerase chain reaction
- ng/µL, nanogram per microliter.
- pCR, pathological complete response
- qPCR, quantitative polymerase chain reaction
Collapse
|
4
|
Untreated PKU patients without intellectual disability: SHANK gene family as a candidate modifier. Mol Genet Metab Rep 2021; 29:100822. [PMID: 34900593 PMCID: PMC8639809 DOI: 10.1016/j.ymgmr.2021.100822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/06/2022] Open
Abstract
Phenylketonuria (PKU) is an inborn error of metabolism caused by variants in the phenylalanine hydroxylase (PAH) gene and it is characterized by excessively high levels of phenylalanine in body fluids. PKU is a paradigm for a genetic disease that can be treated and majority of developed countries have a population-based newborn screening. Thus, the combination of early diagnosis and immediate initiation of treatment has resulted in normal intelligence for treated PKU patients. Although PKU is a monogenic disease, decades of research and clinical practice have shown that the correlation between the genotype and corresponding phenotype is not simple at all. Attempts have been made to discover modifier genes for PKU cognitive phenotype but without any success so far. We conducted whole genome sequencing of 4 subjects from unrelated non-consanguineous families who presented with pathogenic mutations in the PAH gene, high blood phenylalanine concentrations and near-normal cognitive development despite no treatment. We used cross sample analysis to select genes common for more than one patient. Thus, the SHANK gene family emerged as the only relevant gene family with variants detected in 3 of 4 analyzed patients. We detected two novel variants, p.Pro1591Ala in SHANK1 and p.Asp18Asn in SHANK2, as well as SHANK2:p.Gly46Ser, SHANK2:p.Pro1388_Phe1389insLeuPro and SHANK3:p.Pro1716Thr variants that were previously described. Computational analysis indicated that the identified variants do not abolish the function of SHANK proteins. However, changes in posttranslational modifications of SHANK proteins could influence functioning of the glutamatergic synapses, cytoskeleton regulation and contribute to maintaining optimal synaptic density and number of dendritic spines. Our findings are linking SHANK gene family and brain plasticity in PKU for the first time. We hypothesize that variant SHANK proteins maintain optimal synaptic density and number of dendritic spines under high concentrations of phenylalanine and could have protective modifying effect on cognitive development of PKU patients.
Collapse
|
5
|
Identification of GPC3 mutation and upregulation in a multidrug resistant osteosarcoma and its spheroids as therapeutic target. J Bone Oncol 2021; 30:100391. [PMID: 34611509 PMCID: PMC8476350 DOI: 10.1016/j.jbo.2021.100391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 11/15/2022] Open
Abstract
GPC3 mutation in primary osteosarcoma becomes abundant in its metastasis. Mutant GPC3 is over-produced in metastatic spheroids with multidrug resistance. Anti-GPC3 antibody effectively commits metastatic spheroids to apoptosis. GPC3 would be a promising therapeutic target of osteosarcomas.
Background Drug resistance and the lack of molecular therapeutic target are the main challenges in the management of osteosarcomas (OSs). Identification of novel genetic alteration(s) related with OS recurrence and chemotherapeutic resistance would be of scientific and clinical significance. Methods To identify potential genetic alterations related with OS recurrence and chemotherapeutic resistance, the biopsies of a 20-year-old male osteosarcoma patient were collected at primary site (p-OS) and from its metastatic tumor (m-OS) formed after 5 months of adjuvant chemotherapy. Both OS specimens were subjected to cancer-targeted next generation sequencing (NGS) and their cell suspensions were cultured under three-dimensional condition to establish spheroid therapeutic model. Transcript-oriented Sanger sequencing for GPC3, the detected mutated gene, was performed on RNA samples of p-OS and m-OS tissues and spheroids. The effects of anti-GPC3 antibody and its combination with cisplatin on m-OS spheroids were elucidated. Results NGS revealed 4 mutations (GPC3, SOX10, MDM4 and MAPK8) and 6 amplifications (MDM2, CDK4, CCND3, RUNX2, GLI1 and FRS2) in p-OS, and 3 mutations (GPC3, SOX10 and EGF) and 10 amplifications (CDK4, CCND3, MDM2, RUNX2, GLI1, FRS2, CARD11, RAC1, SLC16A7 and PMS2) in m-OS. Among those alterations, the mutation abundance of GPC3 was the highest (56.49%) in p-OS and showed 1.54 times increase in m-OS. GPC3 transcript-oriented Sanger sequencing confirmed the mutation at 1046 in Exon 4, and immunohistochemical staining showed increased GPC3 production in m-OS tissues and its spheroids. EdU cell proliferation and Calcein/PI cell viability assays revealed that of the anti-OS first line drugs (doxorubicin, cisplatin, methotrexate, ifosfamide and carboplatin), 10 μM carboplatin exerted the best inhibitory effects on the p-OS but not the m-OS spheroids. 2 μg/mL anti-GPC3 antibody effectively committed m-OS spheroids to death by itself (76.43%) or in combination with cisplatin (92.93%). Conclusion This study demonstrates increased abundance and up-regulated expression of mutant GPC3 in metastatic osteosarcoma and its spheroids with multidrug resistance. As GPC3-targeting therapy has been used to treat hepatocellular carcinomas and it is also effective to OS PDSs, GPC3 would be a novel prognostic parameter and therapeutic target of osteosarcomas.
Collapse
Key Words
- Anti-GPC3 targeted therapy
- CBP, carboplatin
- CDDP, cisplatin
- DOX, doxorubicin
- FFPE, formalin-fixed, paraffin- embedded
- GPC3 mutation
- GPC3-Ab, anti-GPC3 antibody
- Gene upregulation
- H/E, hematoxylin and eosin
- IHC, immunohistochemistry
- MA, mutation abundance
- MSS, microsatellite stable
- MTX, methotrexate
- Multidrug resistance
- NAC, neoadjuvant chemotherapy
- NGS, next generation sequencing
- Next generation sequencing
- OS, osteosarcoma
- Osteosarcoma
- PDS, patient-derived spheroids
- Patient-derived spheroids
- SNV, single-nucleotide variant
- m-OS, metastatic osteosarcoma
- p-OS, primary osteosarcoma
Collapse
|
6
|
Alterations of DNA damage response pathway: Biomarker and therapeutic strategy for cancer immunotherapy. Acta Pharm Sin B 2021; 11:2983-2994. [PMID: 34729299 PMCID: PMC8546664 DOI: 10.1016/j.apsb.2021.01.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/25/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
Genomic instability remains an enabling feature of cancer and promotes malignant transformation. Alterations of DNA damage response (DDR) pathways allow genomic instability, generate neoantigens, upregulate the expression of programmed death ligand 1 (PD-L1) and interact with signaling such as cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling. Here, we review the basic knowledge of DDR pathways, mechanisms of genomic instability induced by DDR alterations, impacts of DDR alterations on immune system, and the potential applications of DDR alterations as biomarkers and therapeutic targets in cancer immunotherapy.
Collapse
Key Words
- ATM, ataxia-telangiectasia mutated
- ATR, ataxia telangiectasia and Rad3 related
- BAP1, BRCA1-associated protein 1
- BER, base excision repair
- BRAF, v-RAF murine sarcoma viral oncogene homologue B
- BRCA, breast cancer susceptibility gene
- CHEK, cell-cycle checkpoint kinase
- CHK1, checkpoint kinase 1
- DAMP, damage-associated molecular patterns
- DDR, DNA damage response
- DNA damage response
- DNA repair
- DR, direct repair
- DSBs, double-strand breaks
- FDA, United State Food and Drug Administration
- GSK3β, glycogen synthase kinase 3β
- Genomic instability
- HMGB1, high mobility group box-1
- HRR, homologous recombination repair
- ICI, immune checkpoint inhibitor
- IFNγ, interferon gamma
- IHC, immunohistochemistry
- IRF1, interferon regulatory factor 1
- Immunotherapy
- JAK, Janus kinase
- MAD1, mitotic arrest deficient-like 1
- MGMT, O6-methylguanine methyltransferase
- MLH1, MutL homolog 1
- MMR, mismatch repair
- MNT, MAX network transcriptional repressor
- MSH2/6, MutS protein homologue-2/6
- MSI, microsatellite instability
- MUTYH, MutY homolog
- MyD88, myeloid differentiation factor 88
- NEK1, NIMA-related kinase 1
- NER, nucleotide excision repair
- NGS, next generation sequencing
- NHEJ, nonhomologous end-joining
- NIMA, never-in-mitosis A
- NSCLC, non-small cell lung cancer
- ORR, objective response rate
- OS, overall survival
- PALB2, partner and localizer of BRCA2
- PARP, poly-ADP ribose polymerase
- PCR, polymerase chain reaction
- PD-1
- PD-1, programmed death 1
- PD-L1
- PD-L1, programmed death ligand 1
- PFS, progression-free survival
- RAD51C, RAD51 homolog C
- RB1, retinoblastoma 1
- RPA, replication protein A
- RSR, replication stress response
- SCNAs, somatic copy number alterations
- STAT, signal transducer and activator of transcription
- STING, stimulator of interferon genes
- TBK1, TANK-binding kinase 1
- TILs, tumor-infiltrating lymphocytes
- TLR4, Toll-like receptor 4
- TMB, tumor mutational burden
- TME, tumor microenvironment
- TP53, tumor protein P53
- TRIF, Toll-interleukin 1 receptor domain-containing adaptor inducing INF-β
- Tumor microenvironment
- XRCC4, X-ray repair cross complementing protein 4
- cGAS, cyclic GMP–AMP synthase
- cGAS–STING
- ssDNA, single-stranded DNA
Collapse
|
7
|
A pooled CRISPR/AsCpf1 screen using paired gRNAs to induce genomic deletions in Chinese hamster ovary cells. ACTA ACUST UNITED AC 2021; 31:e00649. [PMID: 34277363 PMCID: PMC8261548 DOI: 10.1016/j.btre.2021.e00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 06/06/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022]
Abstract
• Development of a small-scale CRISPR/AsCpf1 screen in CHO. • Usage of paired gRNAs enables full deletion of coding or noncoding genomic regions. • Growth perturbing paired gRNAs identified. • Key points for considerations in future screens identified.
Chinese hamster ovary (CHO) cells are the most widely used host for the expression of therapeutic proteins. Recently, significant progress has been made due to advances in genome sequence and annotation quality to unravel the black box CHO. Nevertheless, in many cases the link between genotype and phenotype in the context of suspension cultivated production cell lines is still not fully understood. While frameshift approaches targeting coding genes are frequently used, the non-coding regions of the genome have received less attention with respect to such functional annotation. Importantly, for non-coding regions frameshift knock-out strategies are not feasible. In this study, we developed a CRISPR-mediated screening approach that performs full deletions of genomic regions to enable the functional study of both the translated and untranslated genome. An in silico pipeline for the computational high-throughput design of paired guide RNAs (pgRNAs) directing CRISPR/AsCpf1 was established and used to generate a library tackling process-related genes and long non-coding RNAs. Next generation sequencing analysis of the plasmid library revealed a sufficient, but highly variable pgRNA composition. Recombinase-mediated cassette exchange was applied for pgRNA library integration rather than viral transduction to ensure single copy representation of pgRNAs per cell. After transient AsCpf1 expression, cells were cultivated over two sequential batches to identify pgRNAs which massively affected growth and survival. By comparing pgRNA abundance, depleted candidates were identified and individually validated to verify their effect.
Collapse
Key Words
- AsCpf1, Cpf1 from Acidaminococcus sp BV3L6
- CHO, Chinese hamster ovary
- CPM, counts per million reads mapped
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- CRISPR/AsCpf1
- Cas9, CRISPR-associated protein 9
- Chinese hamster ovary cells
- Cpf1, CRISPR-associated protein in Prevotella and Francisella
- DE, differentially expressed
- DOWN-TTS, downstream transcription termination site
- DR, differentially represented
- EV, empty vector
- EpoFc, Erythropoietin Fc fusion protein
- FACS, fluorescence activated cell sorting
- FC, fold change
- FDR, false discovery rate
- GS, glutamine synthetase
- Genetic screen
- NGS, next generation sequencing
- NTC, no template control
- PAM, protospacer adjacent motif
- PCA, principal component analysis
- Qp, specific productivity
- RMCE, recombinase-mediated cassette exchange
- TMM, trimmed mean of M values
- UP-TSS, upstream transcription start site
- VCD, viable cell density
- dCas9, deactivated Cas9
- gRNA, guide RNA
- genomic deletion
- lncRNA, long non-coding RNA
- ncGene, non-coding gene
- oligo, oligonucleotide
- paired gRNAs
- pgRNA, paired gRNA
- sgRNA, single guide RNA
- µ, growth rate
Collapse
|
8
|
Whole exome sequencing, in silico and functional studies confirm the association of the GJB2 mutation p.Cys169Tyr with deafness and suggest a role for the TMEM59 gene in the hearing process. Saudi J Biol Sci 2021; 28:4421-4429. [PMID: 34354426 PMCID: PMC8324942 DOI: 10.1016/j.sjbs.2021.04.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/25/2022] Open
Abstract
The development of next generation sequencing techniques has facilitated the detection of mutations at an unprecedented rate. These efficient tools have been particularly beneficial for extremely heterogeneous disorders such as autosomal recessive non-syndromic hearing loss, the most common form of genetic deafness. GJB2 mutations are the most common cause of hereditary hearing loss. Amongst them the NM_004004.5: c.506G > A (p.Cys169Tyr) mutation has been associated with varying severity of hearing loss with unclear segregation patterns. In this study, we report a large consanguineous Emirati family with severe to profound hearing loss fully segregating the GJB2 missense mutation p.Cys169Tyr. Whole exome sequencing (WES), in silico, splicing and expression analyses ruled out the implication of any other variants and confirmed the implication of the p.Cys169Tyr mutation in this deafness family. We also show preliminary murine expression analysis that suggests a link between the TMEM59 gene and the hearing process. The present study improves our understanding of the molecular pathogenesis of hearing loss. It also emphasizes the significance of combining next generation sequencing approaches and segregation analyses especially in the diagnosis of disorders characterized by complex genetic heterogeneity.
Collapse
Key Words
- ARNSHL, autosomal recessive non-syndromic hearing loss
- Actb, Actin beta
- BAM, Binary Alignment Map
- BWA, Burrows-Wheeler Aligner
- C1QTNF9, C1q and TNF related 9
- Cx26, Connexin 26
- ESRRAP2, Estrogen-Related Receptor Alpha Pseudogene 2
- GJB2 gene
- GJB2, Gap Junction Protein Beta 2
- HHLA1, HERV-H LTR-Associating 1
- HL, Hearing loss
- KCNQ3, Potassium Voltage-Gated Channel Subfamily Q Member 3
- Missense mutation
- NGS, next generation sequencing
- NSHL, Non-syndromic hearing loss
- Non-syndromic hearing loss
- PROVEAN, Protein Variation Effect Analyzer
- PolyPhen-2, Polymorphism Phenotyping v2
- RFLP, restriction fragment length polymorphism
- ROH, runs of homozygosity
- RT-PCR, reverse transcription PCR
- RT-qPCR, quantitative reverse transcription PCR
- SAM, Sequence Alignment/Map
- SIFT, Sorting Intolerant From Tolerant
- SJL, Swiss Jim Lambert
- SPATA13, Spermatogenesis Associated 13
- ST3GAL1, ST3 Beta-Galactoside Alpha-2,3-Sialyltransferase 1
- TMEM59, Transmembrane Protein 59
- UAE, United Arab Emirates
- VariMAT, Variation and Mutation Annotation Toolkit
- WES, Whole exome sequencing
- Whole exome sequencing
- dpSNP, Single Nucleotide Polymorphism Database
- gEAR, gene Expression Analysis Resource
- gnomAD, genome aggregation database
- qPCR, quantitative PCR
Collapse
|
9
|
Blood gene transcript signature profiling in pregnancies resulting in preterm birth: A systematic review. Eur J Obstet Gynecol Reprod Biol X 2020; 8:100118. [PMID: 33024956 PMCID: PMC7528201 DOI: 10.1016/j.eurox.2020.100118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE To pursue a systematic review and summarise the current evidence for the potential of transcriptome molecular profiling in investigating the preterm phenotype. STUDY DESIGN We systematically reviewed the literature, using readily available electronic databases (i.e. PubMed/Medline, Embase, Scopus and Web of Science) from inception until March 2020 to identify investigations of maternal blood-derived RNA profiling in preterm birth (PTB). Studies were included if circulating coding or non-coding RNA was analysed in maternal blood during pregnancy and/or at delivery. Interventional trials were not included. The primary outcome was the availability of whole genome expression patterns evaluated in pregnancies resulting in preterm deliveries. RESULTS A total of 35 articles were included in the final analysis. Most of the studies were conducted in high-income countries and published in the last decade. Apart from spontaneous PTB, a variety of phenotypes leading to preterm delivery were reported. Differences in sampling methods, target gene selection and laboratory protocols severely limited any quantitative comparisons. Most of the studies revealed that gene expression profiling during pregnancy has high potential for identifying women at risk of spontaneous and/or non-spontaneous PTB as early as in the first trimester. CONCLUSION Assessing maternal blood-derived transcriptional signatures for PTB risk in pregnant women holds promise as a screening approach. However, longitudinally followed, prospective pregnancy cohorts are lacking. These are relevant for identifying causes leading to PTB and whether prediction of spontaneous PTB or co-morbidities associated with PTB is achievable. More emphasis on widely employed standardised protocols is required to ensure comparability of results.
Collapse
Key Words
- ANC, antenatal care
- Antenatal screening
- DNA, deoxyribonucleic acid
- EGA, estimated gestational age
- FGR, fetal growth restriction
- Gene expression profiling
- HIC, high-income country
- LIC, low-income country
- LMP, last menstrual period
- MIC, middle-income country
- NGS, next generation sequencing
- PCR, polymerase chain reaction
- PICo, Population phenomenon of Interest and Context
- PPROM, preterm premature rupture of membranes
- PROSPERO, Prospective Register of Systematic Reviews
- PTB, preterm birth
- PTL, preterm labour
- PoA, proportion of agreement
- Preterm birth
- RIN, RNA integrity number
- RNA, Ribonucleic acid
- SDG, Sustainable Development Goal
- SGA, small for gestational age
- Systematic review
- Transcriptome
- WBC, white blood cells
- WHO, World Health Organization
- mRNA, messenger RNA
- miRNA, microRNA
- sPTB, spontaneous preterm birth
- sPTL, spontaneous preterm labour
Collapse
|
10
|
Diagnosis, genetic characterization and clinical follow up of mitochondrial fatty acid oxidation disorders in the new era of expanded newborn screening: A single centre experience. Mol Genet Metab Rep 2020; 24:100632. [PMID: 32793418 PMCID: PMC7414009 DOI: 10.1016/j.ymgmr.2020.100632] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Introduction Mitochondrial fatty acid oxidation disorders (FAODs) are a heterogeneous group of hereditary autosomal recessive diseases included in newborn screening (NBS) program in Italy. The aim of this study was to analyse FAODs cases, identified either clinically or by NBS,for clinical and genetic characterization and to evaluate a five years' experience of NBS, in the attempt to figure out the complexity of genotype-phenotype correlation and to confirm the clinical impact of NBS in our centre experience. Materials and methods We analysed FAODs patients diagnosed either by NBS or clinically, followed since February 2014 to April 2019 at the Regional Screening Centre and Inherited Metabolic Diseases Unit of Verona. Diagnosis was confirmed by plasma acylcarnitines, urinary organic acids, enzymatic and genetic testing. For not clear genotypes due to the presence of variants of uncertain significance, in silico predictive tools have been used as well as enzymatic activity assays. Patients underwent clinical, nutritional and biochemical follow up. Results We diagnosed 30 patients with FAODs. 20 by NBS: 3 CUD, 6 SCADD, 5 MCADD, 4 VLCADD, 2 MADD. Overall incidence of FAODs diagnosed by NBS was 1:4316 newborns. No one reported complications during the follow up period. 10 patients were diagnosed clinically: 2 CUD, 2 CPT2D, 1 VLCADD, 5 MADD. Mean age at diagnosis was 29.3 years. Within this group, complications or symptoms were reported at diagnosis, but not during follow-up. 12 mutations not previously reported in literature were found, all predicted as pathogenic or likely pathogenic. Discussion and conclusions Our study highlighted the great phenotypic variability and molecular heterogeneity of FAODs and confirmed the importance of a tailored follow up and treatment. Despite the short duration of follow up, early identification by NBS prevented diseases related complications and resulted in normal growth and psycho-motor development as well. Early identification by newborn screening prevents disease related complications. Newborn screening is changing prevalence clinical and molecular heterogeneity of FAODs. Genotype-phenotype correlation helps to achieve personalized follow-up and treatment. Enzymatic assay may be pivotal in predicting phenotype and symptoms severity. Diagnosis on clinical grounds is anyway important to change disease course.
Collapse
Key Words
- ALT, Alanine aminotransferase
- AST, Aspartate aminotransferase
- CACTD, carnitine-acylcarnitine translocase deficiency
- CK, creatine kinase
- CPT1/2 D, carnitine palmitoyl-CoA transferase 1/2 deficiency
- CUD, carnitine uptake defect
- DBS, dried blood spots
- DNA, Deoxyribonucleic acid
- Enzymatic activity
- Expanded newborn screening
- FAODs, fatty acid oxidation disorders
- Fatty acid oxidation defects
- Hypoglycaemia
- LCHADD, Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency
- MADD, multiple acyl-CoA dehydrogenase deficiency
- MCADD, medium-chain acyl-CoA dehydrogenase deficiency
- Myopathy
- NBS, newborn screening
- NGS, next generation sequencing
- PCR, polymerase chain reaction
- SCADD, short chain acyl-CoA dehydrogenase deficiency
- Synergistic heterozygosity
- TFPD, trifunctional protein deficiency
- TMS, tandem mass spectrometry
- VLCADD, very-long-chain acyl-CoA dehydrogenase deficiency
Collapse
|
11
|
Finding new cancer epigenetic and genetic biomarkers from cell-free DNA by combining SALP-seq and machine learning. Comput Struct Biotechnol J 2020; 18:1891-1903. [PMID: 32774784 PMCID: PMC7387736 DOI: 10.1016/j.csbj.2020.06.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
The effective non-invasive diagnosis and prognosis are critical for cancer treatment. The plasma cell-free DNA (cfDNA) provides a good material for cancer liquid biopsy and its worth in this field is increasingly explored. Here we describe a new pipeline for effectively finding new cfDNA-based biomarkers for cancers by combining SALP-seq and machine learning. Using the pipeline, 30 cfDNA samples from 26 esophageal cancer (ESCA) patients and 4 healthy people were analyzed as an example. As a result, 103 epigenetic markers (including 54 genome-wide and 49 promoter markers) and 37 genetic markers were identified for this cancer. These markers provide new biomarkers for ESCA diagnosis, prognosis and therapy. Importantly, these markers, especially epigenetic markers, not only shed important new insights on the regulatory mechanisms of this cancer, but also could be used to classify the cfDNA samples. We therefore developed a new pipeline for effectively finding new cfDNA-based biomarkers for cancers by combining SALP-seq and machine learning. In this study, we also discovered new clinical worth of cfDNA distinct from other reported characters.
Collapse
Key Words
- ATAC-seq, Assay for Transposase-Accessible Chromatin-sequencing and high-throughput sequencing
- AUC, Area Under Curve
- Biomarkers
- CTC, circulating tumor cell
- Cell-free DNA
- ESCA, esophageal cancer
- Esophageal cancer
- NGS, next generation sequencing
- NIPT, noninvasive prenatal testing
- Next generation sequencing
- PCA, principal component analysis
- SALP-seq
- SALP-seq, Single strand Adaptor Library Preparation-sequencing
- SNP, single nucleotide polymorphism
- SNV, single nucleotide variant
- TCGA, The Cancer Genome Atlas
- TF, transcription factor
- TFBS, TF binding site
- TSS, transcription start site
- Ti, transitions
- Tv, transversion
- cfDNA, cell-free DNA
- cfMeDIP-seq, cell-free methylated DNA immunoprecipitation and high-throughput sequencing
- ctDNA, cell-free tumor DNA
- mRNA, messenger RNA
- miRNA, microRNA
Collapse
|
12
|
Molecular based newborn screening in Germany: Follow-up for cystinosis. Mol Genet Metab Rep 2019; 21:100514. [PMID: 31641587 PMCID: PMC6796768 DOI: 10.1016/j.ymgmr.2019.100514] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 08/29/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Newborn screening (NBS) programs for treatable metabolic disorders have been enormously successful, but molecular-based screening has not been broadly implemented so far. METHODS This prospective pilot study was performed within the German NBS framework. DNA, extracted from dried blood cards was collected as part of the regular NBS program. As cystinosis has a prevalence of only 1:100,000-1:200,000, a molecular genetic assay for detection of the SMN1 gene mutation with a higher prevalence was also included in the screening process, a genetic defect that leads to spinal muscular atrophy (SMA). First tier multiplex PCR was employed for both diseases. The cystinosis screening employed assays for the three most common CTNS mutations covering 75% of German patients; in case of heterozygosity for one of these mutations, samples were screened by next generation sequencing (NGS) of the CTNS exons for 101 CTNS mutations. A detection rate of 98.5% is predicted using this approach. RESULTS Between January 15, 2018 and May 31, 2019, 257,734 newborns were screened in Germany for cystinosis. One neonate was diagnosed with cystinosis, consistent with the known incidence of the disease. No false positive or false negatives were detected so far. Screening, communication of findings to parents, and confirmation of diagnosis were accomplished in a multi-disciplinary setting. This program was accomplished with the cooperation of hospitals, physicians, and parents. In the neonate diagnosed with cystinosis, oral cysteamine treatment began on day 18. After 16 months of treatment the child has no clinical signs of renal tubular Fanconi syndrome. CONCLUSIONS This pilot study demonstrates the efficacy of a molecular-based neonatal screening program for cystinosis using an existing national screening framework.
Collapse
|
13
|
Molecular techniques for the personalised management of patients with chronic myeloid leukaemia. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 11:4-20. [PMID: 28331814 PMCID: PMC5348117 DOI: 10.1016/j.bdq.2017.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 12/28/2016] [Accepted: 01/18/2017] [Indexed: 12/25/2022]
Abstract
Chronic myeloid leukemia (CML) is the paradigm for targeted cancer therapy. RT-qPCR is the gold standard for monitoring response to tyrosine kinase-inhibitor (TKI) therapy based on the reduction of blood or bone marrow BCR-ABL1. Some patients with CML and very low or undetectable levels of BCR-ABL1 transcripts can stop TKI-therapy without CML recurrence. However, about 60 percent of patients discontinuing TKI-therapy have rapid leukaemia recurrence. This has increased the need for more sensitive and specific techniques to measure residual CML cells. The clinical challenge is to determine when it is safe to stop TKI-therapy. In this review we describe and critically evaluate the current state of CML clinical management, different technologies used to monitor measurable residual disease (MRD) focus on comparingRT-qPCR and new methods entering clinical practice. We discuss advantages and disadvantages of new methods.
Collapse
Key Words
- ABL1, Abelson murine leukaemia virus
- ALL, acute lymphoblastic leukaemia
- AP, accelerated phase
- ARQ, armored RNA Quant
- ATP, adenosine triphosphate
- BC, blast crisis
- BCR, breakpoint cluster region
- BM, bone marrow
- BMT, bone marrow transplantation
- Bp, base pair
- CAP, College of American Pathology
- CES, capillary electrophoresis sequencing
- CML
- CML, chronic myeloid leukaemia
- CMR, complete molecular response/remission
- CP, chronic phase
- DESTINY, De-Escalation and Stopping Treatment of Imatinib, Nilotinib or sprYcel in Chronic Myeloid Leukaemia
- DNA, deoxyribonucleic acid
- EAC, Europe Against Cancer
- ELN, European Leukaemia Net
- EURO-SKI, European Stop Tyrosine Kinase Inhibitor Study
- GUSB, glucuronidase beta gene
- IC, inhibotory concentration
- IRIS, interferon and cytarabine versus STI571
- IS, International Scale
- InDels, insertions and deletions
- KDa, Kilo Dalton
- Kbp, Kilo Base Pairs
- LPC, leukemic progenitor cells
- LSC, leukemic stem cell
- LoD, limit of detection
- LoQ, limit of quantification
- M-bcr, major-breakpoint cluster region
- MMR, major molecular response/remission
- MR, deep molecular response/remission
- MRD
- MRD, minimal residual disease
- Mbp, mega base pair
- Molecular monitoring
- NCCN, National Comprehensive Cancer Network
- NEQAS, National External Quality Assessement Service
- NGS
- NGS, next generation sequencing
- NTC, No Template Control
- PB, Peripheral Blood
- PCR, Polymerase Chain Reaction
- PFS, Progression Free Survival
- Ph, Philadelpia
- Q-PCR, quantitative polymerase chain reaction
- QC, Quality Control
- RT, reverse transcription
- RT-dPCR, reverse transcription-digital polymerase chain reaction
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- SCT, stem cell transplant
- SMRT, single-molecule real-time sequencing
- STIM, stop imatinib
- TKD, tyrosine kinase domain
- TKI, tyrosine kinase inhibitor
- WHO, World Health Organisation
- ZMW, zero-mode wave-guided
- allo-SCT, Allogeneic Stem Cell Transplantation
- cDNA, coding or complimentary DNA
- dMIQE, Minimum Information for Publication of Quantitative Digital PCR Experiments
- dPCR
- dPCR, digital polymerase chain reaction
- emPCR, emulsion PCR
- gDNA, genomic deoxyribonucleic acid
- m-bcr, minor-breakpoint cluster region
- mRNA, messenger RNA
- nM, manomolar
- μ-bcr, micro-breakpoint cluster region
- μg, microgram
- μl, microliter
Collapse
|
14
|
The satiating hormone amylin enhances neurogenesis in the area postrema of adult rats. Mol Metab 2016; 5:834-843. [PMID: 27688997 PMCID: PMC5034493 DOI: 10.1016/j.molmet.2016.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE Adult neurogenesis in the subgranular zone and subventricular zone is generally accepted, but its existence in other brain areas is still controversial. Circumventricular organs, such as the area postrema (AP) have recently been described as potential neurogenic niches in the adult brain. The AP is the major site of action of the satiating hormone amylin. Amylin has been shown to promote the formation of neuronal projections originating from the AP in neonatal rodents but the role of amylin in adult neurogenesis remains unknown. METHODS To test this, we first performed an RNA-sequencing of the AP of adult rats acutely injected with either amylin (20 μg/kg), amylin plus the amylin receptor antagonist AC187 (500 μg/kg) or vehicle. Second, animals were subcutaneously equipped with minipumps releasing either amylin (50 μg/kg/day) or vehicle for 3 weeks to assess cell proliferation and differentiation with the 5'-bromo-2-deoxyuridine (BrdU) technique. RESULTS Acute amylin injections affected genes involved in pathways and processes that control adult neurogenesis. Amylin consistently upregulated NeuroD1 transcript and protein in the adult AP, and this effect was blocked by the co-administration of AC187. Further, chronic amylin treatment increased the number of newly proliferated AP-cells and significantly promoted their differentiation into neurons rather than astrocytes. CONCLUSION Our findings revealed a novel role of the satiating hormone amylin in promoting neurogenesis in the AP of adult rats.
Collapse
Key Words
- AP, area postrema
- Adult neurogenesis
- Amylin
- Area postrema
- BrdU
- BrdU, 5′-bromo-2-deoxyuridine
- CR, calretinin
- CTR, calcitonin receptor
- CVO, circumventricular organs
- Circumventricular organs
- ERK1/2, extracellular signal-regulated kinase 1 and 2
- EphRs, ephrin receptors
- FDR, false discovery rate
- GO, gene ontology
- ME, median eminence
- NGS, next generation sequencing
- NSC, neural stem cells
- NeuroD, neuronal differentiation
- NeuroD1, neuronal differentiation-1
- RAMP, receptor activity-modifying protein
- Wnt, Wingless-Type MMTV Integration Site Family
- bHLH, basic helix-loop-helix
Collapse
|
15
|
Recent advances in genetic testing and counseling for inherited arrhythmias. J Arrhythm 2016; 32:389-397. [PMID: 27761163 PMCID: PMC5063262 DOI: 10.1016/j.joa.2015.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/01/2015] [Accepted: 12/17/2015] [Indexed: 12/19/2022] Open
Abstract
Inherited arrhythmias, such as cardiomyopathies and cardiac ion channelopathies, along with coronary heart disease (CHD) are three most common disorders that predispose adults to sudden cardiac death. In the last three decades, causal genes in inherited arrhythmias have been successfully identified. At the same time, it has become evident that the genetic architectures are more complex than previously known. Recent advancements in DNA sequencing technology (next generation sequencing) have enabled us to study such complex genetic traits. This article discusses indications for genetic testing of patients with inherited arrhythmias. Further, it describes the benefits and challenges that we face in the era of next generation sequencing. Finally, it briefly discusses genetic counseling, in which a multidisciplinary approach is required due to the increased complexity of the genetic information related to inherited arrhythmias.
Collapse
Key Words
- ARVD/C, arrhythmogenic right ventricular dysplasia/cardiomyopathy
- BrS, Brugada syndrome
- CHD, coronary heart disease
- CPVT, catecholaminergic polymorphic ventricular tachycardia
- Cardiac ion channelopathies
- Cardiomyopathies
- DCM, dilated cardiomyopathy
- GWAS, genome wide association study
- Genetic counseling
- Genetic testing
- HCM, hypertrophic cardiomyopathy
- HF, heart failure
- ICD, implantable cardioverter defibrillator
- Inherited arrhythmias
- LQTS, long QT syndrome
- NGS, next generation sequencing
- SCD, sudden cardiac death
- VA, ventricular arrhythmia
- VF, ventricular fibrillation
- WES, whole exome sequencing
Collapse
|
16
|
Abstract
Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from rRNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods.
Collapse
Key Words
- DEGs, differentially expressed genes
- NGS, next generation sequencing
- RNA abundance
- RNA expression
- RNAome
- eRNA, enhancer RNA
- isomiRs, microRNA isoforms.
- lncRNAs, long non-coding RNA
- mRNASeq, mRNA sequencing
- non-coding RNA
- poly(A), poly-adenylation
- rRNA, ribosomal RNA
- smallRNASeq, small non-coding RNA sequencing
- snoRNAs, small nucleolar RNAs
- strand-specific RNA-sequencing
- whole transcriptome
Collapse
|
17
|
A systematic review and meta-analysis of randomized trials on the role of targeted therapy in the management of advanced gastric cancer: Evidence does not translate? Cancer Biol Ther 2015; 16:1148-59. [PMID: 26061272 PMCID: PMC4623405 DOI: 10.1080/15384047.2015.1056415] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/12/2015] [Accepted: 05/24/2015] [Indexed: 12/15/2022] Open
Abstract
It is still uncertain if targeted therapy-based regimens in advanced gastric cancer actually produce survival benefit. To shed light on this important question, we performed a systematic review and meta-analyses on each relevant targeted-pathway. By searching literature databases and proceedings of major cancer meetings in the time-frame 2005-2014, 22 randomized clinical trials exploring targeted therapy for a total of 7022 advanced gastric cancer patients were selected and included in the final analysis. Benefit was demonstrated for antiangiogenic agents in terms of overall survival (HR 0.759; 95%CI 0.655-0.880; p < 0.001). Conversely no benefit was found for EGFR pathway (HR 1.077; 95%CI 0.847-1.370; p = 0.543). Meta-analysis of HER-2 pathway confirmed improvement in terms of survival outcome, already known for this class of drugs (HR 0.823; 95%CI 0.722-0.939; p = 0.004). Pooled analysis demonstrated a significant survival benefit (OS: HR 0.823; PFS: HR 0.762) with acceptable tolerability profile for targeted-based therapies as compared to conventional treatments. This finding conflicts with the outcome of most individual studies, probably due to poor trial design or patients selection. In conclusion, our findings demonstrate a significant survival benefit for targeted therapy in its whole, which can be ascribed to anti-angiogenic and anti-HER2 agents.
Collapse
Key Words
- ADME, absorption, distribution, metabolism, and excretion
- Ab, monoclonal antibody
- BSC, best supportive care
- CHT, chemotherapy
- EGFR, epidermal growth factor receptor
- GC, gastric cancer
- HER2, human epidermal growth factor receptor 2
- HER3, human epidermal growth factor receptor 3
- MET, mesenchymal epithelial transition factor
- NGS, next generation sequencing
- NSCLC, non-small cell lung cancer
- OR, odds-ratio
- OS, overall survival
- PARP, poly ADP ribose polymerase
- PFS, progression free survival
- PI3K, phosphatidylinositide 3-kinases
- PRISMA, preferred reporting items for systematic reviews and meta-analyses
- RAF, rapidly accelerated fibrosarcoma
- RAS, rat sarcoma viral oncogene homolog
- RCTs, randomized clinical trials
- RR, response rate
- TKI, tyrosine kinase inhibitor
- VEGF, vascular endothelial growth factor
- VEGFR: VEGF receptor
- aGC, advanced gastric cancer
- angiogenesis
- gastric cancer
- mTOR, mammalian target of rapamycin
- mTORC, mTOR complex
- meta-analysis
- randomized clinical trials
- systemic chemotherapy
- targeted pathways
- targeted therapy
Collapse
|
18
|
8p deletion is strongly linked to poor prognosis in breast cancer. Cancer Biol Ther 2015; 16:1080-7. [PMID: 25961141 PMCID: PMC4623106 DOI: 10.1080/15384047.2015.1046025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/16/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022] Open
Abstract
Deletions of chromosome 8p occur frequently in breast cancers, but analyses of its clinical relevance have been limited to small patient cohorts and provided controversial results. A tissue microarray with 2,197 breast cancers was thus analyzed by fluorescence in-situ hybridization using an 8p21 probe in combination with a centromere 8 reference probe. 8p deletions were found in 50% of carcinomas with no special type, 67% of papillary, 28% of tubular, 37% of lobular cancers and 56% of cancers with medullary features. Deletions were always heterozygous. 8p deletion was significantly linked to advanced tumor stage (P < 0.0001), high-grade (P < 0.0001), high tumor cell proliferation (Ki67 Labeling Index; P < 0.0001), and shortened overall survival (P < 0.0001). For example, 8p deletion was seen in 32% of 290 grade 1, 43% of 438 grade 2, and 65% of 427 grade 3 cancers. In addition, 8p deletions were strongly linked to amplification of MYC (P < 0.0001), HER2 (P < 0.0001), and CCND1 (p = 0.001), but inversely associated with ER receptor expression (p = 0.0001). Remarkably, 46.5% of 8p-deleted cancers harbored amplification of at least one of the analyzed genes as compared to 27.5% amplifications in 8p-non-deleted cancers (P < 0.0001). In conclusion, 8p deletion characterizes a subset of particularly aggressive breast cancers. As 8p deletions are easy to analyze, this feature appears to be highly suited for future DNA based prognostic breast cancer panels. The strong link of 8p deletion with various gene amplifications raises the possibility of a role for regulating genomic stability.
Collapse
Key Words
- 8p
- ER, estrogen receptor
- FISH
- FISH, fluorescence in situ hybridization
- HER2, human epidermal growth factor receptor 2
- Ki67LI, Ki67 Labeling index
- LOH, loss of heterozygosity
- NGS, next generation sequencing
- NST, no special type
- PR, progesterone receptor
- TMA, tissue microarray
- breast cancer
- deletion
- pN, nodal stage
- pT, pathological tumor stage
- prognosis
Collapse
|
19
|
Abstract
Clostridium difficile is mainly a nosocomial pathogen and is a significant cause of antibiotic-associated diarrhea. It is also implicated in the majority of cases of pseudomembranous colitis. Recently, advancements in next generation sequencing technology (NGS) have highlighted the extent of damage to the gut microbiota caused by broad-spectrum antibiotics, often resulting in C. difficile infection (CDI). Currently the treatment of choice for CDI involves the use of metronidazole and vancomycin. However, recurrence and relapse of CDI, even after rounds of metronidazole/vancomycin administration is a problem that must be addressed. The efficacy of alternative antibiotics such as fidaxomicin, rifaximin, nitazoxanide, ramoplanin and tigecycline, as well as faecal microbiota transplantation has been assessed and some have yielded positive outcomes against C. difficile. Some bacteriocins have also shown promising effects against C. difficile in recent years. In light of this, the potential for emerging treatment options and efficacy of anti-C. difficile vaccines are discussed in this review.
Collapse
Key Words
- ATCC, American Type Culture Collection
- CDI, Clostridium difficile infection
- CdtLoc, binary toxin locus
- Clostridium difficile
- DNA, deoxyribonucleic acid
- DPC, Dairy Products Collection
- ESCMID, European Society of Clinical Microbiology and Infectious Diseases
- ETEC, enterotoxigenic E. coli
- FDA, Food and Drug Administration
- FMT, faecal microbiota transplantation
- GIT, gastrointestinal tract
- HIV, human immunodeficiency virus
- IDSA, Infectious Diseases Society of America
- IgG, immunoglobulin G
- LTA, lipoteichoic acid
- M21V, methionine to valine substitution at residue 21
- MIC, minimum inhibitory concentration
- NGS, next generation sequencing
- NVB, Novacta Biosystems Ltd
- PMC, pseudomembranous colitis
- PaLoc, pathogenicity locus
- R027, ribotype 027
- RBD
- RBS, ribosome binding site
- RNA, ribonucleic acid
- SHEA, Society for Healthcare Epidemiology of America
- V15F, valine to phenylalanine substitution at residue 15
- antibiotics
- faecal microbiota transplantation
- receptor binding domain
- toxins
- vaccines
Collapse
|
20
|
Plant exomics: concepts, applications and methodologies in crop improvement. PLANT SIGNALING & BEHAVIOR 2015; 10:e976152. [PMID: 25482786 PMCID: PMC4622497 DOI: 10.4161/15592324.2014.976152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 08/17/2014] [Accepted: 08/18/2014] [Indexed: 05/17/2023]
Abstract
Molecular breeding has a crucial role in improvement of crops. Conventional breeding techniques have failed to ameliorate food production. Next generation sequencing has established new concepts of molecular breeding. Exome sequencing has proven to be a significant tool for assessing natural evolution in plants, studying host pathogen interactions and betterment of crop production as exons assist in interpretation of allelic variation with respect to their phenotype. This review covers the platforms for exome sequencing, next generation sequencing technologies that have revolutionized exome sequencing and led toward development of third generation sequencing. Also discussed in this review are the uses of these sequencing technologies to improve wheat, rice and cotton yield and how these technologies are used in exploring the biodiversity of crops, providing better understanding of plant-host pathogen interaction and assessing the process of natural evolution in crops and it also covers how exome sequencing identifies the gene pool involved in symbiotic and other co-existential systems. Furthermore, we conclude how integration of other methodologies including whole genome sequencing, proteomics, transcriptomics and metabolomics with plant exomics covers the areas which are left untouched with exomics alone and in the end how these integration will transform the future of crops.
Collapse
Key Words
- BAC, bacterial artificial chromosome
- BGR, bacterial grain rot
- CBOL, consortium for 860 the barcode of life
- ETI, effector-triggered immunity
- HPRT, hypoxanthineguanine phosphoribosyl transferase
- MMs, molecular markers
- NGS, next generation sequencing
- NITSR, nuclear internal transcribed spacer region
- OPC, open promoter complex
- QTL, quantitative trait locus
- SMRT, single molecule real time
- SNPs, single nucleotide poly-morphisms
- SOLiD, sequencing by oligonucleotide ligation and detection
- WES, whole exome sequencing
- WGS, whole genome sequencing
- WGS, whole genome shotgun
- biodiversity
- crop improvement
- dNMPs, deoxyribosenucleoside monophosphates
- exome sequencing
- plant biotechnology
- plant-host pathogen interactions
Collapse
|
21
|
Intratumoral heterogeneity: Clonal cooperation in epithelial-to-mesenchymal transition and metastasis. Cell Adh Migr 2014; 9:265-76. [PMID: 25482627 DOI: 10.4161/19336918.2014.972761] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Although phenotypic intratumoral heterogeneity was first described many decades ago, the advent of next-generation sequencing has provided conclusive evidence that in addition to phenotypic diversity, significant genotypic diversity exists within tumors. Tumor heterogeneity likely arises both from clonal expansions, as well as from differentiation hierarchies existent in the tumor, such as that established by cancer stem cells (CSCs) and non-CSCs. These differentiation hierarchies may arise due to genetic mutations, epigenetic alterations, or microenvironmental influences. An additional differentiation hierarchy within epithelial tumors may arise when only a few tumor cells trans-differentiate into mesenchymal-like cells, a process known as epithelial-to-mesenchymal transition (EMT). Again, this process can be influenced by both genetic and non-genetic factors. In this review we discuss the evidence for clonal interaction and cooperation for tumor maintenance and progression, particularly with respect to EMT, and further address the far-reaching effects that tumor heterogeneity may have on cancer therapy.
Collapse
Key Words
- CLL, chronic lymphoblastic leukemia
- CSC, cancer stem cell
- EMP, epithelial-mesenchymal plasticity
- EMT, epithelial-to-mesenchymal transition
- GFP, green fluorescent protein.
- MET, mesenchymal-to-epithelial transition
- MMTV, mouse mammary tumor virus
- NGS, next generation sequencing
- OxR, oxaliplatin resistant
- SCLC, small cell lung cancer
- TGF-β, transforming growth factor-β
- cancer stem cells/CSCs
- clonal evolution
- epithelial-mesenchymal transition (EMT)
- hPDGF human platelet-derived growth factor
- intratumoral heterogeneity
- metastasis
- miRNA, microRNA
- non-cell autonomous
- tumor microenvironment
Collapse
|
22
|
Draft Genome Sequences of Yersinia pestis Strains from the 1994 Plague Epidemic of Surat and 2002 Shimla Outbreak in India. Indian J Microbiol 2014; 54:480-2. [PMID: 25320451 DOI: 10.1007/s12088-014-0475-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022] Open
Abstract
We report the first draft genome sequences of the strains of plague-causing bacteria, Yersinia pestis, from India. These include two strains from the Surat epidemic (1994), one strain from the Shimla outbreak (2002) and one strain from the plague surveillance activity in the Deccan plateau region (1998). Genome size for all four strains is ~4.49 million bp with 139-147 contigs. Average sequencing depth for all four genomes was 21x.
Collapse
|
23
|
Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP). Indian J Microbiol 2014; 54:255-61. [PMID: 24891731 DOI: 10.1007/s12088-014-0461-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/22/2014] [Indexed: 11/30/2022] Open
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) is a rapid, robust, inexpensive and simple tool for microbial community profiling. Methods used for DNA extraction, PCR amplification and digestion of amplified products have a considerable impact on the results of T-RFLP. Pitfalls of the method skew the similarity analysis and compromise its high throughput ability. Despite a high throughput method of data generation, data analysis is still in its infancy and needs more attention. Current article highlights the limitations of the methods used for data generation and analysis. It also provides an overview of the recent methodological developments in T-RFLP which will assist the readers in obtaining real and authentic profiles of the microbial communities under consideration while eluding the inherent biases and technical difficulties.
Collapse
|