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OBJECTIVES: The Nobel Prize in Physiology or Medicine for 2023 awarded to Dr. Katalin Karikó and Dr. Drew Weissman recognized their seminal discoveries in nucleoside modifications of messenger RNA that were pivotal to developing the first mRNA vaccines for clinical use in humans. These novel vaccines were key for prophylactic control of a pandemic caused by the new coronavirus SARS-CoV-2 that emerged abruptly in late 2019/early 2020. This breakthrough capped years of previous research in coronaviruses that included SARS- CoV and MERS-CoV associated with earlier human outbreaks, developments of more efficient formulations to deliver nucleic acids in vivo, and applications of a novel mRNA technology to generate a new generation of better vaccines cost-effectively. Such successful outcomes herald a wide range of advances with this highly adaptable mRNA technology. These include vaccines against existing infectious agents of medical significance but also emerging pathogens, cancer immunotherapies, and protein-replacement therapies, while at the same time, other uses are also under active investigation.
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OBJECTIVES: The latest study with whole genome sequencing (WGS) in pediatric B-ALL validated its use as a standalone test to detect underlying clinically significant genetic abnormalities (Rezayee et al., 2023). This was a retrospective molecular survey in bone marrows previously collected and stored from 88 patients who were enrolled in NOPHO trials. The testing was done through 150 bp paired-end WGS applied to a paired analysis of leukemia-germline samples (L-N) (n=64), and to the analysis of leukemia-only samples (L) (n=88). The results demonstrated a full concordance between both WGS approaches and between the results from WGS and previous standard of care tests (SOCTs). All the mandatory aberrations that require testing in the current ALLTogether trial protocol were identified in 38 patients. In addition, WGS accurately identified the majority of aberrations characteristic of B-other ALL (35/36 cases), copy number abnormalities (CNAs) in eight critical genes or regions, CNAs that characterize the IKZF1plus profile, and the abnormalities in patients with Down syndrome. An adapted methodology was necessary for the detection of DUX4::IGH rearrangements in four patients. A comparison between sequencing coverages of 90X and 30X demonstrated that a lower 30X coverage was sufficient to detect all the relevant abnormalities. This successful testing was accomplished through filtering of WGS data focusing on just genes and genomic regions that are routinely implicated in pediatric B-ALL. As a result, it simplified the extraction of data and facilitated the interpretation of results. Overall, the precise identification of abnormalities that was accomplished by WGS allowed the assignment of patients to distinct genetic subtypes. The conclusion of this study was that WGS is quite reliable and can replace the use of SOCTs to profile pediatric B-ALL.
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OBJECTIVES: A new study demonstrated the power of WGS to comprehensively and accurately profile the genetic abnormalities in cases of childhood B-ALL that were previously studied with standard cytogenetics, FISH and MLPA (Ryan et al., 2023). Two cohorts with a total of 210 patients were studied. One cohort carried cytogenetic abnormalities of known significance (n=38). The other cohort (n=172) lacked cytogenetic abnormalities detectable by standard methods (B-other ALL group), and was treated within the UKALL2003 clinical trial. The WGS approaches used were a tumor-normal (T-N) pipeline and a tumor-only (T-only) pipeline. Most patients (202/210) carried a distinct abnormality already known or a new one that defined a genetic subtype. WGS identified almost all the abnormalities in the cohort with typical cytogenetic abnormalities previously detected (37/38 in the T-only pipeline, 34/38 in the T-N pipeline). The B-other ALL cohort showed two types of abnormalities by WGS. Some were cytogenetic abnormalities emblematic of B-ALL that were missed by previous standard methods (19/172 cases) due to poor samples or incomplete testing at the time of diagnosis. The remaining abnormalities were cryptic (145/153 cases) and defined genetic subtypes. Some new molecular variants emerged with WGS, the profile of PAX5 rearrangements and the ETV6::RUNX1-like subtype was characterized in more detail, and the detection of DUX4 rearrangements was markedly improved by a novel bioinformatic pipeline. Whole transcriptome sequencing (WTS) conducted in a subset of 85 patients was consistent with the results of WGS and standard cytogenomic techniques. This study validated the diagnostic use of WGS to uncover and characterize in detail the genetic aberrations in pediatric B-ALL. As a result, Ryan et al. endorsed the routine use of WGS to discover more abnormalities of clinical significance that define new genetic subtypes, as well as to improve diagnosis, risk stratification, and therapy.
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OBJECTIVES: A recent landmark study reported the value of next-generation sequencing (NGS) to uncover pathogenic abnormalities of clinical significance in patients with pediatric B-ALL enrolled in the UKALL2003 clinical trial (Schwab et al., 2023). NGS, as whole genome sequencing (WGS) or targeted NGS (t-NGS), was combined with previous data (cytogenetics, FISH and MLPA) from 351 pediatric patients with precursor B-ALL who lacked a defining genetic abnormality (B-other ALL). This integration of tests classified patients into 15 distinct subtypes, each one characterized by a specific abnormality. The most frequent subtypes were defined by abnormalities of PAX5, DUX4, ZNF384, an ABL class, and an ETV6::RUNX1-like with a gene expression profile similar to the typical ETV6::RUNX1 but without the specific abnormality. Quite conspicuously, WGS detected some classical abnormalities that remained undetected by standard cytogenomic methods. This application of NGS integrated into standard cytogenomic assays is a decisive advance in classifying patients with B-other ALL into distinct subtypes characterized by unique genomic changes. The addition of NGS improved the identification of pathogenic abnormalities and refined the classification as well as the risk stratification to determine clinical prognosis.
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OBJECTIVES: The Nobel Assembly at the Karolinska Institute awarded the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany). This award acknowledged his discoveries about the genomes of extinct hominins (Neandertal man and the Denisovans), the molecular genetic insights of human origin and evolutionary history, and the understanding of phylogenetic relationships between archaic hominins and modern humans. The scientific advances included detection of Neandertal and Denisovan DNA carried by modern humans due to past admixture events, which in turn stimulated active research about the functional and phenotypic significance of such archaic ancestry on non-disease and disease phenotypic features in modern populations. In addition, comparative genomic studies started to delineate the genes and genetic regulation mechanisms that distinguish modern-day humans from the archaic hominins and our immediate ancestors, the anatomically modern humans. These breakthroughs allowed a more thorough understanding of ancestral and modern human population genetics, and propelled the take-off of human paleogenomics as a new scientific discipline in its own right.
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OBJECTIVES: A recent report described a novel use of CMA for the first time in dogs that uncovered three cases of constitutional aneuploidy among 2,053 purebred and mixed-breed dogs. This advance is very significant because cytogenetic analysis by traditional methods in domestic dogs is technically difficult and may not conclusively identify all the abnormalities. This success with CMA testing anticipates the potential to discover more cases of canine aneuploidies as this technology becomes part of routine clinical genetic testing. As a whole, extended use of CMA is likely to uncover a wider range of chromosomal abnormalities that cause canine diseases, characterize in more detail the canine karyotype (normal and abnormal), and provide thorough cytogenomic data of an animal model useful to study human diseases. Since the platform developed for CMA that was used also allows mutation analysis for canine gene diseases, this additional technical feature permits a cost-effective and comprehensive genetic testing for diagnosis in only one step.
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OBJECTIVES: A recent NGS study in patients with MDS demonstrated that molecular as well as cytogenetic abnormalities in cfDNA from peripheral blood mirror the profile in bone marrow. Such results give further support to a promising option of testing cfDNA to characterize and monitor MDS instead of using invasive bone marrow biopsies. This breakthrough expands the potential of cfDNA studies in hematologic disorders. It also suggests that the routine testing could incorporate cfDNA in the future once validation and standardization procedures are established and large clinical trials are completed.
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OBJECTIVES: Optical Genome Mapping (OGM) has emerged as a very powerful technology to diagnose in a single step a large variety of chromosomal abnormalities with high accuracy, at an unprecedented resolution, and in a time- and cost-effective way. A few recent studies provided a proof-of-principle that OGM can replace traditional cytogenomic assays (karyotyping, FISH, and SNP-arrays) in constitutional studies and the evaluation of hematologic disorders. OGM not only identified abnormalities previously diagnosed by standard methods, it highlighted the structural complexity of some rearrangements and uncovered novel findings with potential diagnostic, prognostic and therapeutic significance. While OGM still seems to have some technical and diagnostic limitations that require fine-tuning and improvement, it has so far shown so many promising advantages that future routine use heralds a revolutionary era in next-generation cytogenomic analysis. Keywords: Optical Genome Mapping, cytogenetic diagnosis, chromosome abnormalities detection, cancer cytogenetics, constitutional chromosome aberrations, cytogenomic variation, structural variants (SVs), copy number variants (CNVs)
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OBJECTIVES: Recent NGS studies in multiple myeloma identified in one step and with comparable high accuracy to the concurrent cytogenomic tests the characteristic IGH translocations and copy number abnormalities. In addition, NGS allowed detection of gene mutations. This unprecedented success of a comprehensive genomic analysis suggests the possibility of replacing the separate tests in current use (cytogenetics, FISH, SNPs microarray and mutation analysis) with a single more efficient NGS assay. Down the road, NGS appears to have the potential to improve routine patient care with the clinical application of a detailed genomic profile.
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Two recent studies demonstrated that array CGH and NGS allow identification of chromosomal abnormalities in fetal trophoblasts circulating in maternal blood. This remarkable breakthrough paves the way for an improved assay that supersedes the performance of non-invasive prenatal testing (NIPT) in cell-free fetal DNA. Furthermore, it is foreseeable to expand the use of this new genomic analysis in trophoblasts to uncover single gene mutations of clinical significance prenatally.
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We report on a patient with a rec(20)dup(20q) chromosome abnormality derived from a paternal chromosome 20 inversion [inv(20)(p13q13.1)]. The rearrangement results in a duplication of 20q13.1 to 20qter and a deletion of 20p13 to 20pter. The patient is a girl with craniofacial features and multiple congenital malformations that overlap with the abnormalities previously described in trisomy 20q syndrome. To our knowledge this is the first report of a patient with rec(20)dup 20q.
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Anomalías Múltiples/genética , Inversión Cromosómica , Cromosomas Humanos Par 20/genética , Trisomía , Anomalías Múltiples/patología , Bandeo Cromosómico , Padre , Femenino , Humanos , Hibridación Fluorescente in Situ , Lactante , Cariotipificación , FenotipoRESUMEN
We describe a newborn male with a constitutional deletion of proximal chromosome 20p involving band p11.2. The phenotype included panhypopituitarism, craniofacial dysmorphism, a small phallus with a semi bifid scrotum, and bilateral widely separated first and second toes. The deletion was inherited from his mother, a mosaic carrier of the same deletion in peripheral lymphocytes. The only other similar case with a deletion of 20p11.22-p11.23 exhibited a phenotype that also included abnormal neural development (autism, craniofacial dysmorphism, and Hirschsprung disease). Our patient expands the spectrum of neurodevelopmental abnormalities associated with haploinsufficiency of band 20p11.2, and is the second deletion of 20p inherited from a normal mosaic carrier mother.
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Anomalías Múltiples/genética , Deleción Cromosómica , Cromosomas Humanos Par 20/genética , Anomalías Craneofaciales , Hipopituitarismo/patología , Anomalías Múltiples/patología , Adulto , Bandeo Cromosómico , Femenino , Heterocigoto , Humanos , Recién Nacido , Cariotipificación , Masculino , Mosaicismo , MadresRESUMEN
A rec(4) dup 4p inherited from a maternal inv(4)(p15q35) was detected in a four-year-old girl with malformations, developmental delay, and behavioral problems that resemble those for trisomy 4p. A review of eight other liveborns with rec(4) dup 4p shows that about 40% of them also have manifestations in common with trisomy 4p, but the rest have a variable spectrum of malformations. Overall, the rec(4) dup 4p phenotype is not specific, and a diagnosis would not have been feasible without cytogenetic studies. This lack of a clinically recognizable phenotype could reflect the effects of the variable sizes of deletions of 4q, molecular differences in the break points, or the known variable expression of trisomy 4p. The fact that 79% of the recombinants in the offspring of inv(4)(p13-p15q35) carriers are rec(4) dup 4p suggests that meiotic recombination favors its generation or that rec(4) dup 4q are more lethal in utero.
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Aberraciones Cromosómicas , Inversión Cromosómica , Cromosomas Humanos Par 4/genética , Anomalías Múltiples/genética , Anomalías Múltiples/patología , Trastornos de la Conducta Infantil/patología , Preescolar , Deleción Cromosómica , Anomalías Craneofaciales/patología , Discapacidades del Desarrollo/patología , Salud de la Familia , Femenino , Duplicación de Gen , Trastornos del Crecimiento/patología , Humanos , Discapacidad Intelectual/patología , Cariotipificación , TrisomíaRESUMEN
A mathematical model is developed to describe the dynamic behavior of mesophilic (35 +/- 5 degrees C) and thermophilic digestion (55 +/- 5 degrees C). Special emphasis is given to acetotrophic methanogenesis and propionate degradation, as the steps that determine the stability of anaerobic digestion, as well as to hydrolysis rate, which determines the degradation efficiency of particulate degradable organic carbon. Within the range of 6-20 (mesophilic) and 2-8 d (thermophilic) hydraulic retention time (HRT), the observed maximum growth rates for acetotrophic methanogens are 0.33 and 1.3 d(-1), respectively, with a 15% decay rate. Temperature and pH dependence as well as ammonia inhibition of acetate and propionate conversion are determined and included in the model, which allows us to simulate the effect of protein- and nitrogen-rich waste addition and the consequences of temporarily increased free ammonia at high pH. No inhibition of hydrogen conversion was observed in the same free ammonia range. The pH optimum is between 6.6 and 7.3. Acetotrophic methanogenesis is strongly inhibited below pH 6.2, whereas above pH 7.4 it can be inhibited by free ammonia. For digesters fed with ordinary municipal sewage sludge, free ammonia inhibition of acetate conversion leads to an increase in acetate at about 35 and 140 mg of N/L for mesophilic (HRT = 20 d) and thermophilic (HRT = 6 d) conditions, respectively. The hydrolysis rate constant is 0.25 and 0.4 d(-1) respectively for these two conditions. The model is validated with load variation experiments in laboratory and full-scale digesters for step and shock loads.
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Bacterias Anaerobias/fisiología , Modelos Teóricos , Aguas del Alcantarillado/microbiología , Eliminación de Residuos Líquidos/métodos , Euryarchaeota/fisiología , Concentración de Iones de Hidrógeno , Hidrólisis , TemperaturaRESUMEN
Se estudiaron las aberraciones cromosómicas de intercambio inducidas "in vitro" por rayos X (150 rads) en linfocitos de pacientes con retinoblastoma y de individuos normales. El retinoblastoma unilateral esporádico (no hereditario) mostró una radiosensibilidad cromosómica normal. Algunos casos de retinoblastoma bilateral esporádico (hereditario) tuvieron una exagerada respuesta a los rayos X, mientras que otros casos se comportaron en forma similar a los controles. Todos los casos de retinoblastoma unilateral hereditario demostraron ser hipersensibles a las radiaciones. La hipersensibilidad a los rayos X presente en algunos individuos con retinoblastoma hereditario, probablemente está relacionada con su labilidad para desarrollar carcinomas secundarios por acción de la radioterapia
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Humanos , Masculino , Femenino , Neoplasias del Ojo/etiología , Técnicas In Vitro , Tolerancia a Radiación , Retinoblastoma/etiología , Rayos XRESUMEN
Se estudiaron las aberraciones cromosómicas de intercambio inducidas "in vitro" por rayos X (150 rads) en linfocitos de pacientes con retinoblastoma y de individuos normales. El retinoblastoma unilateral esporádico (no hereditario) mostró una radiosensibilidad cromosómica normal. Algunos casos de retinoblastoma bilateral esporádico (hereditario) tuvieron una exagerada respuesta a los rayos X, mientras que otros casos se comportaron en forma similar a los controles. Todos los casos de retinoblastoma unilateral hereditario demostraron ser hipersensibles a las radiaciones. La hipersensibilidad a los rayos X presente en algunos individuos con retinoblastoma hereditario, probablemente está relacionada con su labilidad para desarrollar carcinomas secundarios por acción de la radioterapia (AU)
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Humanos , Masculino , Femenino , Técnicas In Vitro , Estudio Comparativo , Neoplasias del Ojo/etiología , Rayos X , Retinoblastoma/etiología , Tolerancia a RadiaciónRESUMEN
El acetato de medroxiprogesterona (Depo-Provera) es un progestageno de uso terapeutico en el ser humano y del que poco se conoce acerca de su mutagenicidad. El test de intercambio de cromatides hermanas (ICH) es el mas sensible indicador para medir dano cromosomico inducido por carcinogenos-mutagenos. Por este motivo se estudio la accion mutagenica in vivo del acetato de medroxiprogesterona utilizando el test de ICH en cultivos de linfocitos de conejos tratados con este compuesto. A 5 conejos machos New Zealand se les extrajo sangre para determinar la tasa espontanea de ICH. Posteriormente fueron inyectados con 75 mg de Depo-Provera via intramuscular.Veinticuatro horas mas tarde se les extrajo nuevamente sangre estudiandose la frecuencia de ICH inducida por la droga. Los valores medios de ICH luego del tratamiento con DepoProvera (0.171 +/- 0.036) fueron significativamente mayores que los correspondientes a la tasa control (0.137 +/- 0.021) (p < 0.05).Los datos obtenidos demuestran que la droga posee accion mutagenica en el conejo y concuerdan con los referentes a otros progestagenos. Sin embargo, se considera oportuno realizar el test de ICH en celulas humanas in vivo o in vitro para evaluar el riesgo que implica el uso terapeutico de esta droga en el ser humano
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Medroxiprogesterona , Intercambio de Cromátides Hermanas , Linfocitos , Mutágenos , ConejosRESUMEN
El acetato de medroxiprogesterona (Depo-Provera) es un progestageno de uso terapeutico en el ser humano y del que poco se conoce acerca de su mutagenicidad. El test de intercambio de cromatides hermanas (ICH) es el mas sensible indicador para medir dano cromosomico inducido por carcinogenos-mutagenos. Por este motivo se estudio la accion mutagenica in vivo del acetato de medroxiprogesterona utilizando el test de ICH en cultivos de linfocitos de conejos tratados con este compuesto. A 5 conejos machos New Zealand se les extrajo sangre para determinar la tasa espontanea de ICH. Posteriormente fueron inyectados con 75 mg de Depo-Provera via intramuscular.Veinticuatro horas mas tarde se les extrajo nuevamente sangre estudiandose la frecuencia de ICH inducida por la droga. Los valores medios de ICH luego del tratamiento con DepoProvera (0.171 +/- 0.036) fueron significativamente mayores que los correspondientes a la tasa control (0.137 +/- 0.021) (p < 0.05).Los datos obtenidos demuestran que la droga posee accion mutagenica en el conejo y concuerdan con los referentes a otros progestagenos. Sin embargo, se considera oportuno realizar el test de ICH en celulas humanas in vivo o in vitro para evaluar el riesgo que implica el uso terapeutico de esta droga en el ser humano