Minimally invasive biomarkers in human and non-human primate evolutionary biology: Tools for understanding variation and adaptation.

BACKGROUND: The use of minimally invasive biomarkers (MIBs - physiological biomarkers obtained from minimally invasive sample types) has expanded rapidly in science and medicine over the past several decades. The MIB approach is a methodological strength in the field of human and non-human primate evolutionary biology (HEB). Among humans and our closest relatives, MIBs provide unique opportunities to document phenotypic variation and to operationalize evolutionary hypotheses. AIMS: This paper overviews the use of MIBs in HEB. Our objectives are to (1) highlight key research topics which successfully implement MIBs, (2) identify promising yet under-investigated areas of MIB application, and (3) discuss current challenges in MIB research, with suggestions for advancing the field. DISCUSSION AND CONCLUSIONS: A range of MIBs are used to investigate focal topics in HEB, including energetics and life history variation/evolution, developmental plasticity, and social status and dominance relationships. Nonetheless, we identify gaps in existing MIB research on traits such as physical growth and gut function that are central to the field. Several challenges remain for HEB research using MIBs, including the need for additional biomarkers and methods of assessment, robust validations, and approaches that are standardized across labs and research groups. Importantly, researchers must provide better support for adaptation and fitness effects in hypothesis testing (e.g., by obtaining complementary measures of energy expenditure, demonstrating redundancy of function, and performing lifetime/longitudinal analyses). We point to continued progress in the use of MIBs in HEB to better understand the past, present, and future of humans and our closest primate relatives.

Single nucleotide polymorphisms and Zn transport by ZIP11 shape functional phenotypes of HeLa cells.

Zinc (Zn) is a vital micronutrient with essential roles in biological processes like enzyme function, gene expression, and cell signaling. Disruptions in the cellular regulation of Zn2+ ions often lead to pathological states. Mammalian Zn transporters, such as ZIP11, play a key role in homeostasis of this ion. ZIP11 resides predominately in the nucleus and Golgi apparatus. Our laboratory reported a function of ZIP11 in maintaining nuclear Zn levels in HeLa cervical cancer cells. Analyses of cervical and ovarian cancer patients' datasets identified four coding, single nucleotide polymorphisms (SNPs) in SLC39A11, the gene that encodes ZIP11, correlating with disease severity. We hypothesized that these SNPs might translate to functional changes in the ZIP11 protein by modifying access to substrate availability. We also proposed that a metal-binding site (MBS) in ZIP11 is crucial for transmembrane Zn2+ transport and required for maintenance of various pathogenic phenotypes observed in HeLa cells. Here, we investigated these claims by re-introducing single the SLC39A11 gene encoding for mutant residues associated with the SNPs, as well as MBS mutations into HeLa cells knocked down for the transporter. Some SNPs-encoding ZIP11 variants rescued Zn levels, proliferation, migration, and invasiveness of knockdown (KD) cells. Conversely, single MBS mutations mimicked the traits of KD cells, confirming the transporter's role in establishing and maintaining proliferative, migratory, and invasive traits. Overall, the intricate role of Zn in cellular dynamics and cancer progression underscores the significance of Zn transporters like ZIP11 in potential therapeutic interventions.

Structural basis for the intracellular regulation of ferritin degradation.

The interaction between nuclear receptor coactivator 4 (NCOA4) and the iron storage protein ferritin is a crucial component of cellular iron homeostasis. The binding of NCOA4 to the FTH1 subunits of ferritin initiates ferritinophagy-a ferritin-specific autophagic pathway leading to the release of the iron stored inside ferritin. The dysregulation of NCOA4 is associated with several diseases, including neurodegenerative disorders and cancer, highlighting the NCOA4-ferritin interface as a prime target for drug development. Here, we present the cryo-EM structure of the NCOA4-FTH1 interface, resolving 16 amino acids of NCOA4 that are crucial for the interaction. The characterization of mutants, designed to modulate the NCOA4-FTH1 interaction, is used to validate the significance of the different features of the binding site. Our results explain the role of the large solvent-exposed hydrophobic patch found on the surface of FTH1 and pave the way for the rational development of ferritinophagy modulators.

Determinants of multidrug-resistant tuberculosis clusters, California, USA, 2004-2007.

Laboratory and epidemiologic evidence suggests that pathogen-specific factors may affect multidrug-resistant (MDR) tuberculosis (TB) transmission and pathogenesis. To identify demographic and clinical characteristics of MDR TB case clustering and to estimate the effect of specific isoniazid resistance-conferring mutations and strain lineage on genotypic clustering, we conducted a population-based cohort study of all MDR TB cases reported in California from January 1, 2004, through December 31, 2007. Of 8,899 incident culture-positive cases for which drug susceptibility information was available, 141 (2%) were MDR. Of 123 (87%) strains with genotype data, 25 (20%) were aggregated in 8 clusters; 113 (92%) of all MDR TB cases and 21 (84%) of clustered MDR TB cases occurred among foreign-born patients. In multivariate analysis, the katG S315T mutation (odds ratio 11.2, 95% confidence interval 2.2-Yen; p = 0.004), but not strain lineage, was independently associated with case clustering.

Novel hot spot of IS6110 insertion in Mycobacterium tuberculosis.

We describe a hot spot for the insertion of IS6110 in Mycobacterium tuberculosis located in the area of region of difference 724 (RD724). Because RD724 defines sublineage 724 of M. tuberculosis, caution must be exercised when screening for RD724, as different polymorphisms can be observed in this region.

Comparison of restriction fragment length polymorphism with the polymorphic guanine-cytosine-rich sequence and spoligotyping for differentiation of Mycobacterium tuberculosis isolates with five or fewer copies of IS6110.

The use of IS6110 as a marker for molecular epidemiological studies is limited when a Mycobacterium tuberculosis isolate has five or fewer copies of IS6110. Restriction fragment length polymorphism analysis with a highly polymorphic GC-rich repetitive sequence located in the plasmid pTBN12 (PGRS RFLP) and spoligotyping (based on the polymorphism of the DR region) are two frequently used secondary typing methods. The aim of this study was to compare the performance of these two methods in a population-based study in San Francisco. We included all patients with culture-positive tuberculosis from 1999 to 2007 with IS6110 RFLP results presenting five or fewer bands. PGRS RFLP and spoligotyping were performed using standardized methods. We determined the concordance between the two methods regarding cluster status and the risk factors for an isolate to be in a cluster with each of the methods. Our data indicate that both methods had similar discriminatory power and that the risk factors associated with clustering by either method were the same. Although the cluster/unique status was concordant in 84% of the isolates, patients were clustered differently depending on the method. Therefore, the methods are not interchangeable, and the same method should be used for longitudinal studies.

Mycoplasma pneumoniae-Induced Rash and Mucositis in a Previously Healthy Man: A Case Report and Brief Review of the Literature.

We describe a case of a 33-year-old-male with Mycoplasma pneumoniae-induced rash and mucositis and review the literature on this newly described syndrome.

Use of multiplex allele-specific polymerase chain reaction (MAS-PCR) to detect multidrug-resistant tuberculosis in Panama.

The frequency of individual genetic mutations conferring drug resistance (DR) to Mycobacterium tuberculosis has not been studied previously in Central America, the place of origin of many immigrants to the United States. The current gold standard for detecting multidrug-resistant tuberculosis (MDR-TB) is phenotypic drug susceptibility testing (DST), which is resource-intensive and slow, leading to increased MDR-TB transmission in the community. We evaluated multiplex allele-specific polymerase chain reaction (MAS-PCR) as a rapid molecular tool to detect MDR-TB in Panama. Based on DST, 67 MDR-TB and 31 drug-sensitive clinical isolates were identified and cultured from an archived collection. Primers were designed to target five mutation hotspots that confer resistance to the first-line drugs isoniazid and rifampin, and MAS-PCR was performed. Whole-genome sequencing confirmed DR mutations identified by MAS-PCR, and provided frequencies of genetic mutations. DNA sequencing revealed 70.1% of MDR strains to have point mutations at codon 315 of the katG gene, 19.4% within mabA-inhA promoter, and 98.5% at three hotspots within rpoB. MAS-PCR detected each of these mutations, yielding 82.8% sensitivity and 100% specificity for isoniazid resistance, and 98.4% sensitivity and 100% specificity for rifampin resistance relative to DST. The frequency of individual DR mutations among MDR strains in Panama parallels that of other TB-endemic countries. The performance of MAS-PCR suggests that it may be a relatively inexpensive and technically feasible method for rapid detection of MDR-TB in developing countries.

Influence of M. tuberculosis lineage variability within a clinical trial for pulmonary tuberculosis.

Recent studies suggest that M. tuberculosis lineage and host genetics interact to impact how active tuberculosis presents clinically. We determined the phylogenetic lineages of M. tuberculosis isolates from participants enrolled in the Tuberculosis Trials Consortium Study 28, conducted in Brazil, Canada, South Africa, Spain, Uganda and the United States, and secondarily explored the relationship between lineage, clinical presentation and response to treatment. Large sequence polymorphisms and single nucleotide polymorphisms were analyzed to determine lineage and sublineage of isolates. Of 306 isolates genotyped, 246 (80.4%) belonged to the Euro-American lineage, with sublineage 724 predominating at African sites (99/192, 51.5%), and the Euro-American strains other than 724 predominating at non-African sites (89/114, 78.1%). Uneven distribution of lineages across regions limited our ability to discern significant associations, nonetheless, in univariate analyses, Euro-American sublineage 724 was associated with more severe disease at baseline, and along with the East Asian lineage was associated with lower bacteriologic conversion after 8 weeks of treatment. Disease presentation and response to drug treatment varied by lineage, but these associations were no longer statistically significant after adjustment for other variables associated with week-8 culture status.