Enrique Hernández-Lemus

Instituto Nacional de Medicina Genómica · Computational Genomics

Introduction Mexico ranks second in the global prevalence of obesity in the adult population, which increases the probability of developing dyslipidemia. Dyslipidemia is closely related to cardiovascular diseases, which are the leading cause of death in the country. Therefore, developing tools that facilitate the prediction of dyslipidemias is esse...

Neuroblastoma represents a neoplastic expansion of neural crest cells in the developing sympathetic nervous system and is childhood’s most common extracranial solid tumor. The hetero- geneity of gene expression in different types of cancer is well-documented, and genetic features of neuroblastoma have been described by classification, development s...

Introduction: The COVID-19 pandemic brought with it a large number of adverse consequences for public health with serious socioeconomic repercussions. In this study we characterize the social, demographic, morbidity and mortality conditions of individuals treated for COVID-19 in one of the SARS-CoV-2 reference hospitals in Mexico City. Method: A...

Renal carcinomas are a group of malignant tumors often originating in the cells lining the small tubes in the kidney responsible for filtering waste from the blood and urine production. Kidney tumors arise from the uncontrolled growth of cells in the kidneys and are responsible for a large share of global cancer-related morbidity and mortality. Und...

During the previous years, particularly at the beginning of the COVID- 19 pandemic, the potential role of metabo-nutritional comorbidities in the severity and lethality of SARS-CoV2 infection has been widely dis- cussed, often describing ambiguous outcomes. Here we investigate the prevalence of metabo-nutritional comorbidities among COVID-19 patien...

Breast cancer is a complex disease that is influenced by the concurrent influence of multiple genetic and environmental factors. Recent advances in genomics and other high throughput biomolecular techniques (-omics) have provided numerous insights into the molecular mechanisms underlying breast cancer development and progression. A number of these...

Background The COVID-19 pandemic led to global social confinement that had a significant impact on people's lives. This includes changes such as increased loneliness and isolation, changes in sleep patterns and social habits, increased substance use and domestic violence, and decreased physical activities. In some cases, it has increased mental hea...

Breast cancer is characterized as being a heterogeneous pathology with a broad phenotype variability. Breast cancer subtypes have been developed in order to capture some of this heterogeneity. Each of these breast cancer subtypes, in turns retains varied characteristic features impacting diagnostic, prognostic and therapeutics. Basal breast tumors,...

Inequalities in oral health are influenced by the social strata of the population. Few studies have focused on the multitude of factors related to social development as indicators of living conditions and periodontal health status. The aim of this study is to evaluate the association between self-reported periodontal conditions and the Social Devel...

Gene co-expression networks are a useful tool in the study of interactions that have allowed the visualization and quantification of diverse phenomena, including the loss of co-expression over long distances in cancerous samples. This characteristic, which could be considered fundamental to cancer, has been widely reported in various types of tumor...

Cancer cells display common traits and enabling-characteristics previously described as the Hallmarks of Cancer. These occur alongside alterations in the regulatory mechanisms controlling gene transcription. Gene co-expression networks (GCNs) identify correlated sets of genes that might share these mechanisms. We have previously reported loss of lo...

Multi-omic approaches are expected to deliver a broader molecular view of cancer. However, the promised mechanistic explanations have not quite settled yet. Here, we propose a theoretical and computational analysis framework to semi-automatically produce network models of the regulatory constraints influencing a biological function. This way, we id...

Background From the existing knowledge of viruses, those infecting plants and bacteria and affecting animals are particularly interesting. This is because such viruses have an ability to vertically transmit to other species, including humans, and therefore could represent a public health issue of significant proportions. Objective This study aims...

Background: The Brugada syndrome (BrS) is a heart rhythm condition that is commonly associated with a strong predisposition for sudden cardiac death. Malignant ventricular arrhythmias could occur secondary to the dysfunction of the cardiac sodium voltage-gated Na(v)1.5 channel (SCN5A). Objective: This study aimed to perform a multiparametric com...

Background: We compared the probability of hospitalization and death caused by COVID-19 in patients with comorbidities during three periods defined for this study: first-wave (FW), interwave period (IP), and second-wave (SW) observed in Mexico City. Methods: In this registry-based study, we included individuals over 20 years of age. During the F...

Follicle-stimulating hormone exists as different major glycoforms defined by distinct glycosylation patterns. It has been documented that variations in glycosylation confer differential biological effects to FSH when multiple in vitro biochemical changes are considered. In fact, transcriptomic data from cultured granulosa cells support those observ...

Cancer cells display common traits and enabling-characteristics previously described as the Hallmarks of Cancer. These occur alongside alterations in the regulatory mechanisms controlling gene transcription. Gene co-expression networks (GCNs) identify correlated sets of genes that might share these mechanisms. We have previously reported loss of lo...

Background: Zika virus, which is widely spread and infects humans through the bites of Aedes albopictus and Aedes aegypti female mosquitoes, represents a serious global health issue. Objective: The objective of the present study is to computationally characterize Zika virus polyproteins (UniProt Name: PRO_0000443018 [residues 1-3423], PRO_000044...

Clear cell renal carcinoma (ccRC) comprises a set of heterogeneous, fast-progressing pathologies with poor prognosis. Analyzing ccRC progression in terms of modifications at the molecular level may provide us with a broader understanding of the disease, paving the way for improved diagnostics and therapeutics. The role of micro-RNAs (miRs) in cance...

Breast cancer is a complex phenotype (or better yet, several complex phenotypes) characterized by the interplay of a large number of cellular and biomolecular entities. Biological networks have been successfully used to capture some of the heterogeneity of intricate pathophenotypes, including cancer. Gene coexpression networks, in particular, have...

The fast, exponential increase of COVID-19 infections and their catastrophic effects on patients' health have required the development of tools that support health systems in the quick and efficient diagnosis and prognosis of this disease. In this context, the present study aims to identify the potential factors associated with COVID-19 infections,...

[This corrects the article DOI: 10.1371/journal.pone.0249773.].

Retinoblastoma (Rb) is a rare intraocular tumour in early childhood, with an approximate incidence of 1 in 18 000 live births. Experimental studies for Rb are complex due to the challenges associated with obtaining a normal retina to contrast with diseased tissue. In this work, we reanalyse a dataset that contains normal retina samples. We identifi...

Background During the COVID-19 pandemic, the slope of the epidemic curve in Mexico City has been quite unstable. Changes in human activity led to changes in epidemic activity, hampering attempts at economic and general reactivation of the city. Methods We have predicted that where a fraction of the population above a certain threshold returns to t...

Gene co-expression networks have become a usual approach to integrate the vast amounts of information coming from gene expression studies in cancer cohorts. The reprogramming of the gene regulatory control and the molecular pathways depending on such control are central to the characterization of the disease, aiming to unveil the consequences for c...

Health equity is a rather complex issue. Social context and economical disparities, are known to be determining factors. Cultural and educational constrains however, are also important contributors to the establishment and development of health inequities. As an important starting point for a comprehensive discussion, a detailed analysis of the lit...

A main goal of Precision Medicine is that of incorporating and integrating the vast corpora on different databases about the molecular and environmental origins of disease, into analytic frameworks, allowing the development of individualized, context-dependent diagnostics, and therapeutic approaches. In this regard, artificial intelligence and mach...

The function of a protein is strongly dependent on its structure. During evolution, proteins acquire new functions through mutations in the amino-acid sequence. Given the advance in deep mutational scanning, recent findings have found functional change to be position dependent, notwithstanding the chemical properties of mutant and mutated amino aci...

Cardiovascular diseases are the leading cause of morbidity and mortality worldwide. High blood pressure in particular, continues to increase throughout the global population at an increasingly fast pace. The relationship between arterial hypertension and periodontitis has been recently discussed in the context of its origins and implications. Parti...

Background: The COVID-19 pandemic has caused an exponential increase in the demand for medical care worldwide. In Mexico, the COVID Medical Units (CMUs) conversion strategy was implemented. Objective: To evaluate the CMU coverage strategy in the Mexico City Metropolitan Area (MCMA) by territory. Materials: The CMU directory was used, as were C...

High-throughput genomic technologies have revolutionized the study of cancer. Current research in oncology is now limited more for the capacity of analyzing and interpreting data, rather than the availability of data itself. Integrative approaches to obtain functional information from data are at the core of the disciplines gathered under the syste...

Background Worldwide, it has been observed that there is a strong association between the severity of COVID-19 and with being over 40 years of age, having diabetes mellitus (DM), hypertension and/or obesity. Objective To compare the probability of death caused by COVID-19 in patients with comorbidities during three periods defined for this study a...

Gene regulatory and signaling phenomena are known to be relevant players underlying the establishment of cellular phenotypes. It is also known that such regulatory programs are disrupted in cancer, leading to the onset and development of malignant phenotypes. Gene co-expression matrices have allowed us to compare and analyze complex phenotypes such...

The COVID-19 pandemic has caused an exponential increase in the demand for medical care worldwide. In Mexico, the COVID Medical Units (CMU) conversion strategy was implemented. Objective. To evaluate the CMU coverage strategy in the Mexico City Metropolitan Area (MCMA) by territory. Materials. The CMU directory was used, as were COVID-19 infection...

Periodontitis is a common inflammatory disease of infectious origins that often evolves into a chronic condition. Aside from its importance as a stomatologic ailment, chronic periodontitis has gained relevance since it has been shown that it can develop into a systemic condition characterized by unresolved hyper-inflammation, disruption of the inna...

Network modeling, from the ecological to the molecular scale has become an essential tool for studying the structure, dynamics and complex behavior of living systems. Graph representations of the relationships between biological components open up a wide variety of methods for discovering the mechanistic and functional properties of biological syst...

Gene co-expression networks (GCNs) have been developed as relevant analytical tools for the study of the gene expression patterns behind complex phenotypes. Determining the association between structure and function in GCNs is a current challenge in biomedical research. Several structural differences between GCNs of breast cancer and healthy phenot...

Breast cancer is a complex, heterogeneous disease at the phenotypic and molecular level. In particular, the transcriptional regulatory programs are known to be significantly affected and such transcriptional alterations are able to capture some of the heterogeneity of the disease, leading to the emergence of breast cancer molecular subtypes. Recent...

Luminal A is the most common breast cancer molecular subtype in women worldwide. These tumors have characteristic yet heterogeneous alterations at the genomic and transcriptomic level. Gene co-expression networks (GCNs) have contributed to better characterize the cancerous phenotype. We have previously shown an imbalance in the proportion of intra-...

A random field is the representation of the joint probability distribution for a set of random variables. Markov fields, in particular, have a long standing tradition as the theoretical foundation of many applications in statistical physics and probability. For strictly positive probability densities, a Markov random field is also a Gibbs field, i....

There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history. Here we report high coverage whole genome sequencing of 76 unrelated individuals, from 27 indigenous groups across Mexico, with more than 97% average N...

Lung cancer is one of the deadliest, most aggressive cancers. Abrupt changes in gene expression represent an important challenge to understand and fight the disease. Gene co-expression networks (GCNs) have been widely used to study the genomic regulatory landscape of human cancer. Here, based on 1,143 RNA-Seq experiments from the TCGA collaboration...

Breast cancer is a complex, highly heterogeneous disease at multiple levels ranging from its genetic origins and molecular processes to clinical manifestations. This heterogeneity has given rise to the so-called intrinsic or molecular breast cancer subtypes. Aside from classification, these subtypes have set a basis for differential prognosis and t...

Cardiovascular diseases (CVD) are the leading causes of morbidity and mortality worldwide. The complex etiology of CVD is known to be significantly affected by environmental and social factors. There is, however, a lag in our understanding of how population level components may be related to the onset and severity of CVD, and how some indicators of...

It is known that cancer onset and development arise from complex, multi-factorial phenomena spanning from the molecular, functional, micro-environmental, and cellular up to the tissular and organismal levels. Important advances have been made in the systematic analysis of the molecular (mostly genomic and transcriptomic) within large studies of hig...

Understanding the spatial and temporal patterns of mortality rates in a highly heterogeneous metropolis, is a matter of public policy interest. In this context, there is no, to the best of our knowledge, previous studies that correlate both spatio-temporal and age-specific mortality rates in Mexico City. Spatio-temporal Kriging modeling was used ov...

Cancer is a set of complex pathologies that has been recognized as a major public health problem worldwide for decades. A myriad of therapeutic strategies is indeed available. However, the wide variability in tumor physiology, response to therapy, added to multi-drug resistance poses enormous challenges in clinical oncology. The last years have wit...

Assessment of the air quality in metropolitan areas is a major challenge in environmental sciences. Issues related include the distribution of monitoring stations, their spatial range, or missing information. In Mexico City, stations have been located spanning the entire Metropolitan zone for pollutants, such as CO, NO2, O3, SO2, PM2.5, PM10, NO, N...

Metabolism is loosely defined as the set of physical and chemical interactions associated with the processes responsible for sustaining life. Two evident features arise whenever one looks at metabolism: first, metabolism is conformed as a very complex and intertwined construct of the many associated biomolecular processes. Second, metabolism is cha...

Clear cell renal carcinoma (ccRC) is a highly heterogeneous and progressively malignant disease. Analyzing ccRC progression in terms of modifications at the molecular and genetic level may help us to develop a broader understanding of its patho-physiology and may give us a glimpse toward improved therapeutics. In this work, by using TCGA data, we s...

Objectives: There is no consensus on how to evaluate inflammatory activity in Takayasu's arteritis (TAK). Here we compare biochemical tests and three clinical scores, which evaluate inflammatory activity (IA) in TAK, versus quantitative 18F-FDG PET/CT as the gold standard. Methods: This prospective study included patients with TA diagnosed accor...

The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π − π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π − π stack...

Introducción. Como una iniciativa para mejorar la calidad de la atención sanitaria se ha incrementado la tendencia en investigación biomédica centrada en las disparidades en salud y el sexo. Objetivo. Realizar una caracterización de la evidencia científica sobre la disparidad en salud definida como la brecha existente entre la distribución de la sa...

During the COVID-19 pandemic, the slope of the epidemic curve in Mexico City has been quite unstable. We have predicted that in the case that a fraction of the population above a certain threshold returns to the public space, the negative tendency of the epidemic curve will revert. Such predictions were based on modeling the reactivation of economi...

Abstract The study of co-expression programs in the context of cancer can help to elucidate the genetic mechanisms that are altered and lead to the disease. The identification of gene co-expression patterns, unique to healthy profiles (and absent in cancer) is an important step in this direction. Networks are a good tool for achieving this as they...

PurposeExpression microarrays are powerful technology that allows large-scale analysis of RNA profiles in a tissue; these platforms include underexploited detection scores outputs. We developed an algorithm using the detection score, to generate a detection profile of shared elements in retinoblastoma as well as to determine its transcriptomic size...

Background: Cardiovascular diseases are the leading causes of mortality worldwide. One reason behind this lethality lies in the fact that often cardiovascular illnesses develop into systemic failure due to the multiple connections to organismal metabolism. This in turn is associated with co-morbidities and multimorbidity. The prevalence of coexisti...

At the end of December of 2019, a new type of coronavirus, now called COVID-19 started spreading in Wuhan, China and later throughout the world. Due to the global emergency state the World Health Organization declared and the need to know more about the danger Mexico is in, we worked on analyzing the risk of the COVID-19 importation to Mexico throu...