DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data.

MOTIVATION: Many diseases, such as cancer, are characterized by an alteration of cellular metabolism allowing cells to adapt to changes in the microenvironment. Stable isotope-resolved metabolomics (SIRM) and downstream data analyses are widely used techniques for unraveling cells' metabolic activity to understand the altered functioning of metabolic pathways in the diseased state. While a number of bioinformatic solutions exist for the differential analysis of SIRM data, there is currently no available resource providing a comprehensive toolbox. RESULTS: In this work, we present DIMet, a one-stop comprehensive tool for differential analysis of targeted tracer data. DIMet accepts metabolite total abundances, isotopologue contributions, and isotopic mean enrichment, and supports differential comparison (pairwise and multi-group), time-series analyses, and labeling profile comparison. Moreover, it integrates transcriptomics and targeted metabolomics data through network-based metabolograms. We illustrate the use of DIMet in real SIRM datasets obtained from Glioblastoma P3 cell-line samples. DIMet is open-source, and is readily available for routine downstream analysis of isotope-labeled targeted metabolomics data, as it can be used both in the command line interface or as a complete toolkit in the public Galaxy Europe and Workfow4Metabolomics web platforms. AVAILABILITY AND IMPLEMENTATION: DIMet is freely available at https://github.com/cbib/DIMet, and through https://usegalaxy.eu and https://workflow4metabolomics.usegalaxy.fr. All the datasets are available at Zenodo https://zenodo.org/records/10925786.

Single-Cell Transcriptomic Analysis of Mononuclear Cell Populations in Skeletal Muscle.

Skeletal muscle possesses a remarkable regenerative capacity, mainly relying on a population of undifferentiated and unipotent muscle progenitors, called muscle stem cells (MuSCs) or satellite cells, and their interplay with various cell types within the niche. Investigating the cellular composition of skeletal muscle tissues and the heterogeneity among various cell populations is crucial to the unbiased understanding of how cellular networks work in harmony at the population level in the context of skeletal muscle homeostasis, regeneration, aging, and diseases. As opposed to probing the average profile in a cell population, single-cell RNA-seq has unlocked access to the transcriptomic landscape characterization of individual cells in a highly parallel manner. This chapter describes the workflow for single-cell transcriptomic analysis of mononuclear cells in skeletal muscle by taking advantage of the droplet-based single-cell RNA-seq platform, Chromium Single Cell 3' solution from 10x Genomics®. Using this protocol, we can reveal insights into muscle-resident cell-type identities, which can be exploited to study the muscle stem cell niche further.

Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis.

Lactate is a central metabolite in brain physiology but also contributes to tumor development. Glioblastoma (GB) is the most common and malignant primary brain tumor in adults, recognized by angiogenic and invasive growth, in addition to its altered metabolism. We show herein that lactate fuels GB anaplerosis by replenishing the tricarboxylic acid (TCA) cycle in absence of glucose. Lactate dehydrogenases (LDHA and LDHB), which we found spatially expressed in GB tissues, catalyze the interconversion of pyruvate and lactate. However, ablation of both LDH isoforms, but not only one, led to a reduction in tumor growth and an increase in mouse survival. Comparative transcriptomics and metabolomics revealed metabolic rewiring involving high oxidative phosphorylation (OXPHOS) in the LDHA/B KO group which sensitized tumors to cranial irradiation, thus improving mouse survival. When mice were treated with the antiepileptic drug stiripentol, which targets LDH activity, tumor growth decreased. Our findings unveil the complex metabolic network in which both LDHA and LDHB are integrated and show that the combined inhibition of LDHA and LDHB strongly sensitizes GB to therapy.

Male patient 46,XX SRY-negative and unambiguous genitalia: A case report / Paciente masculino con cariotipo 46 XX negativo para el gen SRY y sin ambigüedad genital: reporte de un caso

In most cases, male sexual differentiation occurs with SRY gene mediation. However, exceptional genotypes have been identified, as shown in this paper. This was a male adult patient seen at the Servicio de Paternidades, Instituto de Genética, Universidad Nacional de Colombia. The following procedures were carried out: Amelogenin gene and short tandem repeat analyses using human identification commercial kits, conventional karyotype, SRY fluorescent in situ hybridization, PCR analysis for Y chromosome microdeletions, clinical evaluation, and genetic counseling. We present an adult male with unambiguous genitalia, karyotype 46,XX, and an SRY negative and ZFY positive molecular profile. The diagnosis of nonsyndromic 46,XX testicular disorder of sex development (DSD) -a rare genetic condition- was established. Only 20 % of similarly diagnosed patients are SRY negative and exhibit diverse molecular profiles. Until now, available evidence seems to indicate that, even in the absence of SRY, the ZFY factor is involved in male sexual differentiation.

En la mayoría de los casos, la diferenciación sexual masculina ocurre con la participación del gen SRY. Sin embargo, se pueden presentar otros genotipos excepcionales, como en el caso que se presenta en este reporte. Se trata de un paciente adulto de sexo masculino atendido en el Servicio de Paternidades del Instituto de Genética de la Universidad Nacional de Colombia. Se le hicieron los análisis del gen de la amelogenina y de repeticiones cortas en tándem (Short Tandem Repeat, STR) específicas para el gen SRY con estuches comerciales de identificación humana, así como los de cariotipo convencional e hibridación in situ fluorescente del SRY, y el estudio de microdeleciones del cromosoma Y mediante reacción en cadena de la polimerasa (PCR). Se le hizo la evaluación clínica y se le brindó asesoramiento genético. El paciente no presentaba ambigüedad genital, su cariotipo era 46 XX, y el perfil molecular era negativo para el gen SRY y positivo para el ZFY. Se le diagnosticó un trastorno de diferenciación sexual 46 XX testicular no sindrómico, una rara condición genética. Solo el 20 % de los pacientes con este diagnóstico son negativos para SRY y exhiben perfiles moleculares diversos. La información disponible parece indicar que el ZFY está relacionado con la diferenciación sexual masculina, aún en ausencia del gen SRY.

Paciente masculino con cariotipo 46 XX negativo para el gen SRY y sin ambigüedad genital: reporte de un caso / Male patient 46, XX SRY -negative and unambiguous genitalia: A case report

En la mayoría de los casos, la diferenciación sexual masculina ocurre con la participación del gen SRY. Sin embargo, se pueden presentar otros genotipos excepcionales, como en el caso que se presenta en este reporte. Se trata de un paciente adulto de sexo masculino atendido en el Servicio de Paternidades del Instituto de Genética de la Universidad Nacional de Colombia. Se le hicieron los análisis del gen de la amelogenina y de repeticiones cortas en tándem (Short Tandem Repeat, STR) específicas para el gen SRY con estuches comerciales de identificación humana, así como los de cariotipo convencional e hibridación in situ fluorescente del SRY, y el estudio de microdeleciones del cromosoma Y mediante reacción en cadena de la polimerasa (PCR). Se le hizo la evaluación clínica y se le brindó asesoramiento genético. El paciente no presentaba ambigüedad genital, su cariotipo era 46 XX, y el perfil molecular era negativo para el gen SRY y positivo para el ZFY. Se le diagnosticó un trastorno de diferenciación sexual 46 XX testicular no sindrómico, una rara condición genética. Solo el 20 % de los pacientes con este diagnóstico son negativos para SRY y exhiben perfiles moleculares diversos. La información disponible parece indicar que el ZFY está relacionado con la diferenciación sexual masculina, aún en ausencia del gen SRY.

In most cases, male sexual differentiation occurs with SRY gene mediation. However, exceptional genotypes have been identified, as shown in this paper. This was a male adult patient seen at the Servicio de Paternidades, Instituto de Genética, Universidad Nacional de Colombia. The following procedures were carried out: Amelogenin gene and short tandem repeat analyses using human identification commercial kits, conventional karyotype, SRY fluorescent in situ hybridization, PCR analysis for Y chromosome microdeletions, clinical evaluation, and genetic counseling. We present an adult male with unambiguous genitalia, karyotype 46,XX, and an SRY negative and ZFY positive molecular profile. The diagnosis of nonsyndromic 46,XX testicular disorder of sex development (DSD) -a rare genetic condition- was established. Only 20 % of similarly diagnosed patients are SRY negative and exhibit diverse molecular profiles. Until now, available evidence seems to indicate that, even in the absence of SRY, the ZFY factor is involved in male sexual differentiation.

A pathogenic homozygous variant of the BBS10 gene in a patient with Bardet Biedl syndrome

The Bardet-Biedl syndrome is an autosomal recessive hereditary disorder with vast locus heterogeneity that belongs to the so-called ciliopathies, whose proteins are localized in the primary cilia and present functional deficiency. The multisystemic features of the disease include ocular, renal, cognitive, skeletal, as well as gonadal involvement and obesity, among others, with high inter- and intrafamilial variability. We describe the clinical case of an adolescent male patient with Bardet-Biedl syndrome, including the approach, the results from a 22-gene sequencing panel, and the analysis of updated scientific literature. We collected the clinical data of the patient and, after obtaining the informed consent, we conducted a multigenic sequencing panel oriented to known implicated genes. The patient was born to consanguineous parents and was the first affected member of the family. He presented with postaxial polydactyly, obesity, micropenis, retinitis pigmentosa, and learning disability. The multigenic panel allowed the identification of the homozygous pathogenic variant c.39_46del in the BBS10 gene and in other BBS genes variants associated with obesity. As the Bardet-Biedl syndrome is a rare disease, it is challenging to interpret its pleiotropism and gene/allelic heterogeneity. Its confirmation by molecular tests allows an adequate approach, follow-up, and genetic counseling of the patient and the family.

Genética clínica comunitaria: exploración de patología genética en Boyacá, Colombia / Clinical community genetics: exploring genetic disorders in Boyacá, Colombia

RESUMEN Objetivo Explorar la presencia de patología genética sindrómica en el Departamento de Boyacá, mediante un acercamiento de medicina genética comunitaria. Materiales y Métodos Un grupo conformado por genetistas, neurólogo pediátrico y genetista bioquímico, llevó a cabo jornadas clínicas en las cuales se evaluaron pacientes con sospecha de enfermedad genética. Se obtuvieron datos demográficos, epidemiológicos y clínicos y se realizó el cálculo de frecuencias de los mismos. En los centros de referencia visitados se realizaron actividades de capacitación al personal médico. Resultados Se encontraron dos agrupamientos genéticos: MPSIII y Síndrome de Ellis Van Creveld, con incidencias mayores a lo reportado en la literatura, además una alta frecuencia de patologías de herencia autosómica recesiva, así como sospecha de síndromes de microdeleción-microduplicación. Conclusiones Se deben establecer mecanismos no convencionales de atención médica para facilitar el acceso a las comunidades a un diagnóstico y tratamiento adecuados en genética. Se espera que el apoyo brindado a los pacientes, familias y personal asistencial de los hospitales a través de las jornadas clínicas y la capacitación, permitan alcanzar este objetivo y a la vez sea un punto de inicio de procesos de prevención primaria y secundaria.(AU)

ABSTRACT Objectives To explore the incidence of syndromic genetic pathologies in Boyacá, Colombia, through a community genetics approach. Materials and Methods A group made up by different medical specialists (geneticists, a pediatric neurologist, and a biochemical geneticist) developed clinical campaigns, in which patients with clinical suspicion of genetic diseases were involved. Demographic, epidemiological and clinical data were collected, and frequency calculations were made based on the collected data. Several training workshops for health personnel were done in each center visited. Results Two genetic clusters were found: mucopolysaccharidosis type III, and Ellis-Van Creveld Syndrome, both of them with higher incidences than those found in the literature. Also, a high frequency of autosomal recessive diseases was found, as well as microdeletion/microduplication syndromes. Conclusions Conventional mechanisms of medical attention must be established, in order to facilitate the access to an appropriate diagnosis and treatment. This work intended to provide support to patients, families and health care services personnel through the workshops and clinical campaigns, and to become a starting point to develop primary and secondary prevention processes.(AU)

[Clinical community genetics: exploring genetic disorders in Boyacá, Colombia]. / Genética clínica comunitaria: exploración de patología genética en Boyacá, Colombia.

OBJECTIVES: To explore the incidence of syndromic genetic pathologies in Boyacá, Colombia, through a community genetics approach. MATERIALS AND METHODS: A group made up by different medical specialists (geneticists, a pediatric neurologist, and a biochemical geneticist) developed clinical campaigns, in which patients with clinical suspicion of genetic diseases were involved. Demographic, epidemiological and clinical data were collected, and frequency calculations were made based on the collected data. Several training workshops for health personnel were done in each center visited. RESULTS: Two genetic clusters were found: mucopolysaccharidosis type III, and Ellis-Van Creveld Syndrome, both of them with higher incidences than those found in the literature. Also, a high frequency of autosomal recessive diseases was found, as well as microdeletion/microduplication syndromes. CONCLUSIONS: Conventional mechanisms of medical attention must be established, in order to facilitate the access to an appropriate diagnosis and treatment. This work intended to provide support to patients, families and health care services personnel through the workshops and clinical campaigns, and to become a starting point to develop primary and secondary prevention processes.

OBJETIVO: Explorar la presencia de patología genética sindrómica en el Departamento de Boyacá, mediante un acercamiento de medicina genética comunitaria. MATERIALES Y MÉTODOS: Un grupo conformado por genetistas, neurólogo pediátrico y genetista bioquímico, llevó a cabo jornadas clínicas en las cuales se evaluaron pacientes con sospecha de enfermedad genética. Se obtuvieron datos demográficos, epidemiológicos y clínicos y se realizó el cálculo de frecuencias de los mismos. En los centros de referencia visitados se realizaron actividades de capacitación al personal médico. RESULTADOS: Se encontraron dos agrupamientos genéticos: MPSIII y Síndrome de Ellis Van Creveld, con incidencias mayores a lo reportado en la literatura, además una alta frecuencia de patologías de herencia autosómica recesiva, así como sospecha de síndromes de microdeleción-microduplicación. CONCLUSIONES: Se deben establecer mecanismos no convencionales de atención médica para facilitar el acceso a las comunidades a un diagnóstico y tratamiento adecuados en genética. Se espera que el apoyo brindado a los pacientes, familias y personal asistencial de los hospitales a través de las jornadas clínicas y la capacitación, permitan alcanzar este objetivo y a la vez sea un punto de inicio de procesos de prevención primaria y secundaria.

Deep Genotyping of the IDS Gene in Colombian Patients with Hunter Syndrome.

BACKGROUND: Mucopolysaccharidosis type II (MPSII), also known as Hunter syndrome, is an X-linked disorder caused by mutations in the iduronate 2 sulfatase (IDS) gene. This enzyme catalyzes the initial step in the catabolism of heparan sulfate and dermatan sulfate; thus, its deficiency leads to the accumulation of these glycosaminoglycans. MPS II has significant allelic heterogeneity, making the establishment of genotype-phenotype correlations difficult. This study assessed clinical features in combination with deep genotyping of a group of Colombian patients with MPS II and attempted to establish a degree of genotype-phenotype correlation by employing bioinformatic tools. METHODS: Eighteen patients were included in this study, 11% of whom were non-neuronopathic, and the other 89% were neuronopathic. Samples were all analyzed using three molecular methodologies: MLPA, direct exon sequencing, and RFLP analysis. RESULTS: A total of 13 mutations were identified, 6 of which were novel (c.548_564dup16, c.477insT, c.595_607del12, c. 549_562del13, c.182delC, and a complete deletion of exon 7). The frequency of common mutations (R468Q, Q465X, K347Q, K236N, S71N, R88H, and a conversion phenomenon) was 53.85%. The S71N mutation was frequent among the attenuated phenotype, while private frameshift mutations and rearrangements were seen in patients with severe phenotypes. Molecular docking was performed on the wild-type and mutant IDS proteins, which revealed changes in the enzyme-substrate interaction for the mutant IDS. CONCLUSION: The frequency of novel mutations (46.15%) is similar to what has been reported elsewhere. The use of bioinformatic tools showed differences in enzyme-substrate interactions. Studies with larger groups of patients are needed.