Unidad de Genómica, Proteómica y Metabolómica, Cinvestav-Zacatenco

16/05/2026

¡Para todos los interesados!

🌱🔬 La ciencia y la innovación se unen en el
III Congreso Nacional de Biociencias y Química Aplicada y el Simposio Internacional Ambiente y Bioenergía 2026.
📍Durango, Dgo., México
📅 23 al 25 de septiembre de 2026

15/05/2026

The most common ocular neoplasia among children is retinoblastoma. Currently, the diagnosis of this disease is essentially clinical, taking a biopsy is contraindicated owing to the high risk of causing metastasis. Therefore, it is imperative the development of a method to diagnose this disease through a non-invasive fashion. We choose tears as they fulfill the former precept. Through proteomic analysis we observed 52 up regulated and 48 down regulated proteins among retinoblastoma cases as compared to healthy children. Among these proteins, we identified several previously associated with retinoblastoma such as apolipoprotein A-1 (APOA1). We confirmed up regulation of APOA1 and S100 binding calcium A9 (S100A9) which revealed faithful concordance to the predicted values from mass spectrometry.

https://www.journalofliquidbiopsy.com/article/S2950-1954(26)00017-2/fulltext

14/05/2026

Breast cancer, the leading cause of death in women worldwide, shows significant heterogeneity that makes this disease extremely difficult to treat. Many reports point to metabolic shifts, mainly those carried out into mitochondria, as key processes governing the behavior and heterogeneity of several types of breast cancer. In this study, we performed label-free proteomics analysis on mitochondria-enriched fractions from T47D and MDA-MB-231 breast cancer cell lines, which have distinct molecular classifications, using bioinformatics analyses to identify differentially expressed proteins compared to MCF-12F healthy breast cells. Cancer cells exhibited down-regulated protein levels of subunits from the respiratory chain's Complex I. However, both showed differentially abundant proteins involved in ligase and oxidoreductase activities, including enzymes of glycolysis, pyruvate metabolism, the Krebs cycle, and gluconeogenesis. Many of these enzymes also participate in other metabolic processes, such as mitochondrial localization, mitochondrial gene expression, and the metabolism of amino acids, fatty acids, purines, and pyrimidines. Gene Set Enrichment Analysis revealed that OXPHOS subunits are integrated as signatures of neurodegenerative disease pathways. A protein set with little or no evidence in breast cancer was identified, which could lead to future research in breast cancer mitochondrial metabolism. Data are available via ProteomeXchange with identifier PXD069883. Significance: This manuscript determined the protein expression profiles of mitochondria-enriched fractions from T47D (Luminal A, stage IV) and MDA-MB-231 (triple negative, Stage IV) breast cancer cell lines compared to the MCF-12F healthy breast cell line. We found that breast cancer cell lines exhibited low expression levels of Complex I subunits from the respiratory chain. However, both breast cancer cell lines presented high expression levels of some proteins related to ligase and oxidoreductase activities, the latter on CH-OH groups in cellular respiration processes, such as some enzymes from glycolysis, pyruvate metabolism, Krebs cycle and gluconeogenesis. Moreover, many of these enzymes also participate in other metabolic processes, such as localization to the mitochondrion, mitochondrial gene expression, amino acid, fatty acid, purine, and pyrimidine metabolism. We also observed through Gene Set Enrichment Analysis that OXPHOS enzymes have a key role in many neurodegenerative disease pathways as well. Finally, we found a protein set with little or no evidence in breast cancer that could lead to future pivotal research in the mitochondrial metabolism of breast cancer

https://www.sciencedirect.com/science/article/pii/S1874391926000643

12/05/2026

Estimada comunidad,

En nuestros análisis metabolómicos multivariados podemos integrar el uso del software AcquireX™ Intelligent Data Acquisition Workflow; el cual es una estrategia de adquisición inteligente para LC-MS/MS ya que optimiza experimentos DDA mediante corridas iterativas de un pool representativo de todas las muestras. El software primero analiza un blanco de extracción para generar una lista de exclusión con señales de fondo, contaminantes y iones irrelevantes; posteriormente compara el pool contra el blanco para construir una lista de inclusión con features reales candidatas a fragmentación. Durante cada corrida DDA del pool, AcquireX selecciona automáticamente precursores prioritarios para MS/MS y agrega los iones ya fragmentados a una lista dinámica de exclusión, evitando adquirir espectros redundantes y permitiendo explorar progresivamente especies de menor abundancia. Finalmente, las muestras individuales se adquieren típicamente en Full MS utilizando la información generada previamente, logrando una mayor cobertura química y biológica, más espectros MS/MS únicos y una caracterización más profunda y reproducible del metaboloma.

Cualquier duda, favor de preguntar.

08/05/2026

En este estudio piloto, investigadores de la UASLP, CINVESTAV Zacatenco, Hospital Metodista de Houston y del Hospital Central "Ignacio Morones Prieto" de San Luis; usaron los servicios de espectrometría de masas de la UGPM y proponen el uso de lágrimas como fuente biológica no invasiva para la identificación de biomarcadores mediante proteómica shotgun basada en espectrometría de masas. Se analizaron muestras de lágrimas de niños con retinoblastoma y de controles sanos, utilizando el método de Schirmer para la recolección, seguido de extracción proteica y análisis cuantitativo mediante LC-MS/MS en modo DIA. Se identificaron en total 1035 proteínas, de las cuales 188 resultaron diferencialmente expresadas: 52 sobreexpresadas, 48 subexpresadas y 77 exclusivas de los pacientes con retinoblastoma. Entre las proteínas alteradas se encontraron varias previamente asociadas con el cáncer, destacando la sobreexpresión de APOA1 y S100A9, cuyos resultados fueron validados mediante Western blot, lo que mostró una concordancia significativa con los datos proteómicos. El análisis funcional reveló una predominancia de proteínas asociadas a funciones de unión, actividad catalítica y remodelación del citoesqueleto, así como a rutas vinculadas a la proliferación tumoral, la invasión y la metástasis. En conjunto, los resultados demuestran que las lágrimas son una fuente viable y prometedora para la identificación de biomarcadores moleculares del retinoblastoma, lo que abre la posibilidad de desarrollar métodos diagnósticos tempranos, no invasivos y complementarios a la práctica clínica actual.

Autor: Andrés Rodríguez-Rodríguez y col.

The most common ocular neoplasia among children is retinoblastoma. Currently, the diagnosis of this disease is essentially clinical, taking a biopsy is contraindicated owing to the high risk of causing metastasis. Therefore, it is imperative the development of a method to diagnose this disease through a non-invasive fashion. We choose tears as they fulfill the former precept. Through proteomic analysis we observed 52 up regulated and 48 down regulated proteins among retinoblastoma cases as compared to healthy children. Among these proteins, we identified several previously associated with retinoblastoma such as apolipoprotein A-1 (APOA1). We confirmed up regulation of APOA1 and S100 binding calcium A9 (S100A9) which revealed faithful concordance to the predicted values from mass spectrometry

https://www.sciencedirect.com/science/article/pii/S2950195426000172

07/05/2026

Para todos nuestros usuarios o colaboradores, es una buena oportunidad para presentar sus trabajos en un foro especializado.

La Sociedad Mexicana de Proteómica se complace en invitarlos a su 10.º simposio “MultiOmics and Integrative Biology: Advances and Applications”, que se celebrará en la ESIQIE del IPN, en la Ciudad de México, del 9 al 13 de noviembre de 2026. Contaremos con la participación de excelentes ponentes nacionales e internacionales, así como con cursos y talleres. Pueden consultar más detalles en: https://www.smp.org.mx/xsymposium/

The Mexican Proteomics Society is pleased to invite you to its 10th Symposium, “MultiOmics and Integrative Biology: Advances and Applications,” which will be held at ESIQIE-IPN in Mexico City from November 9 to 13, 2026. The event will feature excellent national and international speakers, as well as courses and workshops. Further details are available at: https://www.smp.org.mx/xsymposium/

30/04/2026

En este estudio colaborativo, los autores analizan la reprogramación metabólica mitocondrial en cáncer de mama mediante un enfoque proteómico comparativo (equipo Synapt G2-Si) entre las líneas celulares T47D (Luminal A) y MDA‑MB‑231 (triple negativo), usando la línea mamaria no tumorigénica MCF‑12F como control. A partir de fracciones enriquecidas en mitocondria, se realizó un análisis proteómico cuantitativo sin marcaje que permitió identificar 2,446 proteínas, de las cuales 530 presentaron localización mitocondrial confirmada.
Ambas líneas cancerígenas mostraron una disminución consistente de subunidades del Complejo I de la cadena respiratoria, junto con alteraciones en enzimas del metabolismo energético central. MDA‑MB‑231 exhibió un perfil claramente glucolítico, compatible con el efecto Warburg, mientras que T47D conservó un fenotipo mitocondrial más cercano al estado basal. Ensayos funcionales revelaron un aumento en la masa mitocondrial, pero una reducción en la actividad dependiente del potencial de membrana, particularmente en la línea triple negativa.
En conjunto, los resultados demuestran que la mitocondria es un nodo central de la plasticidad metabólica en cáncer de mama y señalan proteínas mitocondriales poco estudiadas como posibles blancos para investigación futura.

Autor: Hersson David Vázquez Narváez, et al.

Abstract: Breast cancer, the leading cause of death in women worldwide, shows significant heterogeneity that makes this disease extremely difficult to treat. Many reports point to metabolic shifts, mainly those carried out into mitochondria, as key processes governing the behavior and heterogeneity of several types of breast cancer. In this study, we performed label-free proteomics analysis on mitochondria-enriched fractions from T47D and MDA-MB-231 breast cancer cell lines, which have distinct molecular classifications, using bioinformatics analyses to identify differentially expressed proteins compared to MCF-12F healthy breast cells. Cancer cells exhibited down-regulated protein levels of subunits from the respiratory chain's Complex I. However, both showed differentially abundant proteins involved in ligase and oxidoreductase activities, including enzymes of glycolysis, pyruvate metabolism, the Krebs cycle, and gluconeogenesis. Many of these enzymes also participate in other metabolic processes, such as mitochondrial localization, mitochondrial gene expression, and the metabolism of amino acids, fatty acids, purines, and pyrimidines. Gene Set Enrichment Analysis revealed that OXPHOS subunits are integrated as signatures of neurodegenerative disease pathways. A protein set with little or no evidence in breast cancer was identified, which could lead to future research in breast cancer mitochondrial metabolism. Data are available via ProteomeXchange with identifier PXD069883. Significance: This manuscript determined the protein expression profiles of mitochondria-enriched fractions from T47D (Luminal A, stage IV) and MDA-MB-231 (triple negative, Stage IV) breast cancer cell lines compared to the MCF-12F healthy breast cell line. We found that breast cancer cell lines exhibited low expression levels of Complex I subunits from the respiratory chain. However, both breast cancer cell lines presented high expression levels of some proteins related to ligase and oxidoreductase activities, the latter on CH-OH groups in cellular respiration processes, such as some enzymes from glycolysis, pyruvate metabolism, Krebs cycle and gluconeogenesis. Moreover, many of these enzymes also participate in other metabolic processes, such as localization to the mitochondrion, mitochondrial gene expression, amino acid, fatty acid, purine, and pyrimidine metabolism. We also observed through Gene Set Enrichment Analysis that OXPHOS enzymes have a key role in many neurodegenerative disease pathways as well. Finally, we found a protein set with little or no evidence in breast cancer that could lead to future pivotal research in the mitochondrial metabolism of breast cancer.

https://www.sciencedirect.com/science/article/pii/S1874391926000643

10/04/2026

¡Realizamos servicios de metabolómica de plantas en nuestro equipo Orbitrap Exploris 120!

08/04/2026

Datos obtenidos en la UGPM

Human activities such as industrialization, recreation, domestic water use, agriculture, and energy production have significantly increased pollution in water bodies, especially within urban regions. This pollution affects ecological biodiversity, exerting broad impacts on various environmental and public health factors. In response, this study utilized proteomic analysis to characterize the macro- and microbiota community compositions of natural water bodies located across diverse urban and semi-urban regions. Our strategy involved collecting samples from Mexico City as well as the Mexican states of Mexico, Morelos and Guanajuato. Samples were analyzed using liquid chromatography, coupled with High Resolution Mass Spectrometry (LC-HDMS), to detect organisms. Using this approach, we identified protein peptide sequences belonging to diverse taxa, including Plantae, Animalia, Protozoa and Bacteria, encompassing both pathogenic and non-pathogenic organisms. Some identified pathogens are known contributors to disease outbreaks in Mexico. Additionally, other detected organisms provided insights into the ecological structure and biodiversity of the regions surrounding each sampled water body. Further analyses included assessments of species richness, relative abundance, and overall biological diversity. Results provide a fundamental proteomic basis for studying biodiversity in Mexican water bodies, which may serve as a reference for future longitudinal research. Moreover, this approach offers a powerful method for detecting and modeling water contamination caused by human activity.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0342705

17/03/2026

El presente estudio demuestra que suplementar con cisteína a Ustilago maydis en condiciones respiratorias aumenta fuertemente la producción endógena de sulfuro de hidrógeno (H₂S), lo cual desencadena una remodelación celular global: se incrementa la biogénesis mitocondrial, se induce un cambio respiratorio hacia la vía alternativa dependiente de AOX, se altera el balance redox con mayor generación de H₂O₂ y un aumento de modificaciones redox como la S-sulfenilación y S-persulfidación, además de observarse redistribución y disminución de lípidos. Estos cambios se acompañan de una profunda reprogramación proteómica, destacando la sobreexpresión de proteínas mitocondriales, metabólicas y proteasomales, así como de algunas proteínas asociadas a la virulencia. Aunque la eficiencia de infección en maíz no cambia, las plantas infectadas con células que producen más H₂S desarrollan tumores más grandes y síntomas más severos, lo que indica que el H₂S modula la patogenicidad al conectar el metabolismo del azufre con la respiración mitocondrial, el estado redox y la interacción hongo-hospedero.

Título: Endogenous hydrogen sulfide reprograms mitochondrial respiration and modulates pathogenicity in Ustilago maydis

ABSTRACT
Sulfur metabolism is a central determinant of microbial physiology and adaptation to environmental conditions. Hydrogen sulfide (H2S), a reactive sulfur species during cysteine metabolism, has recently emerged as a key regulator of mitochondrial function and redox signaling. However, its role in phytopathogenic fungi and its potential impact on fungal pathogenic behavior remain poorly understood. Here, we show that metabolic conditions that enhance endogenous H2S production in the maize phytopathogen Ustilago maydis trigger coordinated cellular remodeling. Elevated intracellular H2S levels were associated with mitochondrial biogenesis, a shift from cytochrome-dependent respiration toward alternative oxidase (AOX)-dependent respiration, and widespread proteomic reprogramming affecting mitochondrial, metabolic, and proteasomal pathways. These changes were accompanied by increased global protein S-sulfenylation and S-persulfidation, altered lipid distribution, and elevated hydrogen peroxide levels, indicating substantial remodeling of cellular redox homeostasis. Functional consequences of this metabolic state were evaluated in maize infection assays. Although infection rates were not significantly altered, plants infected with cells exhibiting elevated endogenous H2S levels displayed increased tumor formation and modified symptom progression. Together, our findings indicate that increased H2S production acts as a metabolism with mitochondrial respiration, redox regulation, and fungal pathogenic behavior in Ustilago maydis. This work highlights endogenous H2S as an important regulatory node connecting microbial metabolism with host-pathogen interactions.

https://papers.ssrn.com/sol3/papers.cfm?abstract_id=6402747

11/03/2026

En este trabajo en colaboración con investigadores del departamento de Fisiología y de Toxicología del Cinvestav Zacatenco, se evaluó cómo la restricción alimentaria crónica —aplicada desde antes del apareamiento y mantenida hasta los 90 días de edad— altera la distribución sistémica de metales esenciales en ratas Wistar. La metalómica reveló una pérdida marcada de cobre en el riñón (−51%) y de hierro en el bazo (−61%), órganos clave de almacenamiento fisiológico. De forma complementaria, hubo acumulación de hierro, cobre, zinc y manganeso en hígado y páncreas, órganos con vías de excreción de metales, lo que sugiere una redistribución interna compensatoria. A pesar de estos cambios severos, las concentraciones séricas de los metales permanecieron sin alteraciones, lo que indica que los mecanismos homeostáticos para mantener los niveles circulantes se mantuvieron incluso bajo desnutrición prolongada.

El análisis proteómico sérico, realizado con una metodología label-free en un equipo Synapt G2-Si, mostró la ausencia de cambios en ceruloplasmina, lo cual coincide con la estabilidad del cobre sérico, pero reveló marcadores compatibles con hemólisis intravascular, como el aumento de las subunidades de hemoglobina (Hba1, Hbb, Hba-a2) y la disminución de haptoglobina y hemopexina. Asimismo, se identificó la sobreexpresión de BPIFA2 y BPIFA1, proteínas con posibles funciones en la tensión superficial, la inmunomodulación o incluso la participación indirecta en procesos hemolíticos. Estos hallazgos sugieren que, ante una disponibilidad energética críticamente baja, podrían activarse respuestas proteómicas asociadas al manejo de eritrocitos y a la movilización alternativa de recursos, lo que acompaña la profunda reorganización metalómica observada.

Autor: Alma Isabel Santos Dáz, et al.

The effects on metal accumulation in various organs of the Wistar rat were analyzed after applying a protocol of dietary restriction to half the quantity of food consumed by the mother prior to mating, during gestation, lactation, and applied also to the offspring, postweaning. The present paper reports a follow-up study that tested whether changes of metal ion distribution in the main organs of 60-day-old rats of both sexes exposed to this treatment were reproduced when the dietary restriction was extended another month, resulting in 90-day-old rats. Here, additional analyses of serum metal ions and serum proteomics were included. Results confirmed that copper normally stored in the kidney of animals fed ad libitum accumulates instead in the liver and pancreas of animals from the dietary restriction group, without any change in serum. Consistently, proteomic analysis revealed no changes in ceruloplasmin and instead showed hallmarks of intravascular hemolysis in the dietary restricted group of rats. Iron was low in spleen and high in liver and pancreas. Thus, dietary restriction led to physiological redistribution of iron and copper between different organs. We discuss these changes in the framework of systemic metal homeostasis.

https://academic.oup.com/metallomics/article/18/1/mfag005/8482763