The dual journey: The development of twins' relationships throughout childhood.

Twin bonds, likely the most enduring of human relationships, provide both solace and rivalry for twins. Using an evolutionary psychology perspective, this chapter scrutinizes twins' bonds from prenatal stages to childhood to better understand their unique relationships. Twins' interactions, which begin in the womb, establish patterns of cooperation and competition. The initial years pose parenting challenges that shape the twins' experiences of dependency and rivalry. As twins grow, five dimensions-closeness, dependence, conflict, rivalry, and dominance-emerge, evolving distinctly between monozygotic twins (MZ: sharing close to 100% of their genes) and dizygotic twins (DZ: sharing on average 50% of their genetic variance). The chapter notes the closer relationship MZ twins share compared to DZ twins. While the closeness and dependence among DZ twins decline throughout childhood, these elements remain stable in MZ twins. The effect of zygosity on conflict and rivalry is less clear. For both MZ and DZ twins, conflict stays steady, while rivalry intensifies with school entry, probably driven by external comparisons, but lessens as twins develop into late childhood. Unlike singletons, where birth order dictates dominance dynamics, in twins, this dynamic is more variable and becomes more defined by around 6.5 years of age. Several factors are presented as impacting the nature of the twins' relationships: the evolvement of 'twin language', the parenting style and the differential parenting they receive. This exploration into the development of twins' relationships underlines the importance of tailored caregiving and invites further research into the genetic and environmental factors that shape close bonds.

Commentary: Assortative parenting and assortative cross-parenting: New views of parental preference for selected children.

The commentary delves into the implications of "assortative parenting" and "assortative cross-parenting," as introduced by N. L. Segal, and situates these concepts within the framework of current research. It addresses the joys and complexities of raising twins, highlighting how their concurrent development stages can amplify parental favoritism and heighten the challenge of addressing each twin's unique needs. This interplay provides a rich context to investigate assortative parenting practices. Additionally, this paper contemplates the broader picture of twin studies, particularly how the care of monozygotic twins (who share 100 % of their genes) and dizygotic twins (who share 50 % of their genes, on average) may reveal the intertwined nature of genetics and environment in parenting strategies. It also proposes that twins' interactions with other family members, their spouses, and peers can offer profound insights into the phenomena of phenotypic assortative affiliation, enriching our understanding of close relational bonds.

Amplitude-integrated electroencephalography showed no differences in cerebral activity between preterm singletons and twins in the first 4 weeks of life.

AIM: Genetic influences on cerebral activity have been described previously, but data are scarce in preterms. We aimed to investigate whether a genetic influence causes amplitude-integrated electroencephalography (aEEG) signals to differ between singletons and twin preterm newborns. METHODS: This was a retrospective single-centre study conducted at Innsbruck Medical University Hospital, Austria. Preterm infants born before 32 weeks of gestation between 6 November 2010 and 6 December 2022 were eligible for the study. The aEEG was analysed for the total maturation score, its component scores and the number of sleep-wake cycles per hour. RESULTS: We enrolled 240 preterm twin infants (57.5% male) with a mean gestational age of 30 (range: 24-32) weeks and a mean birth weight of 1324 (range: 600-2116) grams. We compared 240 singleton matched preterms. No differences were found between preterm singletons and twin preterm infants regarding the total maturation and component scores, or the number of sleep-wake cycles. aEEG showed no difference between monozygotic and dizygotic twins. CONCLUSION: Compared to singletons, twin infants born preterm showed no differences in aEEG signals in the first 4 weeks of life. Future studies should include more complex non-invasive functional neuroimaging methods to gain more insight into this important topic.

New insights into the (epi)genetics of twinning.

Spontaneous dizygotic (DZ) twins, i.e. twins conceived without the use of ARTs, run in families and their prevalence varies widely around the globe. In contrast, monozygotic (MZ) twins occur at a constant rate across time and geographical regions and, with some rare exceptions, do not cluster in families. The leading hypothesis for MZ twins, which arise when a zygote splits during preimplantation stages of development, is random occurrence. We have found the first series of genes underlying the liability of being the mother of DZ twins and have shown that being an MZ twin is strongly associated with a stable DNA methylation signature in child and adult somatic tissues. Because identical twins keep this molecular signature across the lifespan, this discovery opens up completely new possibilities for the retrospective diagnosis of whether a person is an MZ twin whose co-twin may have vanished in the early stages of pregnancy. Here, we summarize the gene finding results for mothers of DZ twins based on genetic association studies followed by meta-analysis, and further present the striking epigenetic results for MZ twins.

A novel pyrosequencing strategy for RHD zygosity for predicting risk of hemolytic disease of the fetus and newborn.

OBJECTIVE: The aim of this study was the development of an accurate and quantitative pyrosequence (PSQ) method for paternal RHD zygosity detection to help risk management of hemolytic disease of the fetus and newborn (HDFN). METHODS: Blood samples from 96 individuals were genotyped for RHD zygosity using pyrosequencing assay. To validate the accuracy of pyrosequencing results, all the samples were then detected by the mismatch polymerase chain reaction with sequence-specific primers (PCR-SSP) method and Sanger DNA sequencing. Serological tests were performed to assess RhD phenotypes. RESULTS: Serological results revealed that 36 cases were RhD-positive and 60 cases were RhD-negative. The concordance rate between pyrosequencing assay and mismatch PCR-SSP assay was 94.8% (91/96). There were 5 discordant results between pyrosequencing and the mismatch PCR-SSP assay. Sanger sequencing confirmed that the pyrosequencing assay correctly assigned zygosity for the 5 samples. CONCLUSION: This DNA pyrosequencing method accurately detect RHD zygosity and will help risk management of pregnancies that are at risk of HDFN.

Schrödinger's yeast: the challenge of using transformation to compare fitness among Saccharomyces cerevisiae that differ in ploidy or zygosity.

How the number of genome copies modifies the effect of random mutations remains poorly known. In yeast, researchers have investigated these effects for knock-out or other large-effect mutations, but have not accounted for differences at the mating-type locus. We set out to compare fitness differences among strains that differ in ploidy and/or zygosity using a panel of spontaneously arising mutations acquired in haploid yeast from a previous study. To ensure no genetic differences, even at the mating-type locus, we embarked on a series of transformations, which first sterilized and then temporarily introduced plasmid-borne mating types. Despite these attempts to equalize the haplotypes, fitness variation introduced during transformation swamped the differences among the original mutation-accumulation lines. While colony size looked normal, we observed a bi-modality in the maximum growth rate of our transformed yeast and determined that many of the slow growing lines were respiratory deficient ("petite"). Not previously reported, we found that yeast that were TID1/RDH54 knockouts were less likely to become petite. Even for lines with the same petite status, however, we found no correlation in fitness between the two replicate transformations performed. These results pose a challenge for any study using transformation to measure the fitness effect of genetic differences among strains. By attempting to hold haplotypes constant, we introduced more mutations that overwhelmed our ability to measure fitness differences between the genetic states. In this study, we transformed over one hundred different lines of yeast, using two independent transformations, and found that this common laboratory procedure can cause large changes to the microbe studied. Our study provides a cautionary tale of the need to use multiple transformants in fitness assays.

An accurate, reliable, and universal qPCR method to identify homozygous single insert T-DNA with the example of transgenic rice.

Early determination of transgenic plants that are homozygous for a single locus T-DNA insert is highly desirable in most fundamental and applied transgenic research. This study aimed to build on an accurate, rapid, and reliable quantitative real-time PCR (qPCR) method to fast-track the development of multiple homozygous transgenic rice lines in the T1 generation, with low copy number to single T-DNA insert for further analyses. Here, a well-established qPCR protocol, based on the OsSBE4 reference gene and the nos terminator, was optimized in the transgenic Japonica rice cultivar Nipponbare, to distinguish homozygous single-insert plants with 100% accuracy. This method was successfully adapted to transgenic Indica rice plants carrying three different T-DNAs, without any modifications to quickly develop homozygous rice plants in the T1 generation. The accuracy of this qPCR method when applied to transgenic Indica rice approached 100% in 12 putative transgenic lines. Moreover, this protocol also successfully detected homozygous single-locus T-DNA transgenic rice plants with two-transgene T-DNAs, a feature likely to become more popular in future transgenic research. The assay was developed utilizing universal primers targeting common sequence elements of gene cassettes (the nos terminator). This assay could therefore be applied to other transgenic plants carrying the nos terminator. All procedures described here use standardized qPCR reaction conditions and relatively inexpensive dyes, such as SYBR Green, thus the qPCR method could be cost-effective and suitable for lower budget laboratories that are involved in rice transgenic research.

Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes.

Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.

Frameshift coding sequence variants in the LPL gene: identification of two novel events and exploration of the genotype-phenotype relationship for variants reported to date.

BACKGROUND: Lipoprotein lipase (LPL) is the rate-limiting enzyme for triglyceride hydrolysis. Homozygous or compound heterozygous LPL variants cause autosomal recessive familial chylomicronemia syndrome (FCS), whereas simple heterozygous LPL variants are associated with hypertriglyceridemia (HTG) and HTG-related disorders. LPL frameshift coding sequence variants usually cause complete functional loss of the affected allele, thereby allowing exploration of the impact of different levels of LPL function in human disease. METHODS: All exons and flanking intronic regions of LPL were Sanger sequenced in patients with HTG-related acute pancreatitis (HTG-AP) or HTG-AP in pregnancy. Previously reported LPL frameshift coding sequence variants were collated from the Human Gene Mutation Database and through PubMed keyword searching. Original reports were manually evaluated for the following information: zygosity status of the variant, plasma LPL activity of the variant carrier, disease referred for genetic analysis, patient's age at genetic analysis, and patient's disease history. SpliceAI was employed to predict the potential impact of collated variants on splicing. RESULTS: Two novel rare variants were identified, and 53 known LPL frameshift coding sequence variants were collated. Of the 51 variants informative for zygosity, 30 were simple heterozygotes, 12 were homozygotes, and 9 were compound heterozygotes. Careful evaluation of the 55 variants with respect to their clinical and genetic data generated several interesting findings. First, we conclude that 6-7% residual LPL function could significantly delay the age of onset of FCS and reduce the prevalence of FCS-associated syndromes. Second, whereas a large majority of LPL frameshift coding sequence variants completely disrupt gene function through their "frameshift" nature, a small fraction of these variants may act wholly or partly as "in-frame" variants, leading to the generation of protein products with some residual LPL function. Third, we identified two candidate LPL frameshift coding sequence variants that may retain residual function based on genotype-phenotype correlation or SpliceAI-predicted data. CONCLUSIONS: This study reported two novel LPL variants and yielded new insights into the genotype-phenotype relationship as it pertains to LPL frameshift coding sequence variants.

Villitis of unknown etiology, chronic deciduitis, chronic chorioamnionitis and chronic histiocytic intervillositis in monozygotic and dizygotic twin pregnancies. A retrospective analysis of 16 cases.

INTRODUCTION: Villitis of unknown etiology (VUE), chronic chorioamnionitis (CC), chronic deciduitis (CD) and chronic histiocytic intervillositis (CHI) are most likely the result of a pathologic immune reaction caused by maternal anti-fetal rejection. We analyzed placentas of twin pregnancies with manifestation of these lesions in monozygotic and dizygotic instances. METHODS: Twin pregnancies from our archive with at least one chronic inflammatory lesion were selected for further analysis and assessed concerning zygosity (gender, chorionicity, short tandem repeat (STR)-analysis). RESULTS: The cohort comprised sixteen twin placentas, monozygotic in five cases and dizygotic in 11 cases, respectively. VUE (n = 4), CC (n = 1) and CHI (n = 3) manifested concordantly in both placentas of the monozygotic pregnancies and affected discordantly one of the twin placentas in the dizygotic instances. CD (n = 10) manifested concordantly in two and discordantly in one of the monozygotic placentas, and concordantly in three and discordantly in four of the dizygotic instances. Intrauterine fetal demise (n = 3), preterm birth (n = 9) and low birth weight (n = 2) were recognized. Discordant fetal growth in live born children was recognized in two dizygotic cases with discordant manifestation of VUE and CHI. DISCUSSION: The concordant manifestation of VUE, CC and CHI in monozygotic and the discordant pattern of inflammation in dizygotic pregnancies points to pathologic immune mechanisms against genetically determined fetal antigens being essential for the development of these entities. The heterogenous manifestation of CD could be a hint for diverse fetal or maternal etiologic factors that may contribute to this lesion.

Iranian school-aged twin registry: preliminary reports and project progress.

BACKGROUND: National Persian school-aged twin registry was established to provide a platform for twin studies. In this report, we describe defining registry characteristics, database design, and preliminary results regarding gathered data in the first phase of the registry program. METHOD: Through focus group discussions, the required data elements to design the database and data collection process were defined. First, a list of twins in school-aged groups was retrieved from the electronic database of the Ministry of Education. Tehran schools were selected for the first phase of our registry. Standard "Pea-in-Pods" questionnaire and twins' similarity questionnaires were filled out by the parents themselves in addition to demographic information. Data were analyzed using SPSS v.22. RESULTS: The first national school-aged twin registry was established in 2018. Firstly, the required data sets and data collection process were defined using focus group discussions. At the country level, the initial information on 189,738 students was retrieved from the national database of the Ministry of Education. They were born between 2003 and 2017, of which 94,997 are boys (50.1%) and 94,741 are girls (49.9%). Of them, a total of 5,642 pairs of school-aged twins participated in the first phase of our program. Our sample size comprised 9772 twins, 906 triples, and 92 quadruplets. The analysis of the zygosity questionnaire showed that 14% of twin pairs were identified as monozygotic twins. CONCLUSION: Recruiting school-aged twins through school health assistants leads to high enrollment and decreasing costs for the twin registry. The study showed a high rate of dizygotic twins that need to be verified by twin bio-sample in the next phase of studies.

Sex-specific differences in immunogenomic features of response to immune checkpoint blockade.

Introduction: The magnitude of response to immune checkpoint inhibitor (ICI) therapy may be sex-dependent, as females have lower response rates and decreased survival after ICI monotherapy. The mechanisms underlying this sex dimorphism in ICI response are unknown, and may be related to sex-driven differences in the immunogenomic landscape of tumors that shape anti-tumor immune responses in the context of therapy. Methods: To investigate the association of immunogenic mutations with HLA haplotypes, we leveraged whole exome sequence data and HLA genotypes from 482 non-small cell lung cancer (NSCLC) tumors from The Cancer Genome Atlas (TCGA). To explore sex-specific genomic features linked with ICI response, we analyzed whole exome sequence data from patients with NSCLC treated with ICI. Tumor mutational burden (TMB), HLA class I and II restricted immunogenic missense mutation (IMM) load, and mutational smoking signature were defined for each tumor. IMM load was combined with HLA class I and II haplotypes and correlated with therapeutic response and survival following ICI treatment. We examined rates of durable clinical benefit (DCB) for at least six months from ICI treatment initiation. Findings were validated utilizing whole exome sequence data from an independent cohort of ICI treated NSCLC. Results: Analysis of whole exome sequence data from NSCLC tumors of females and males revealed that germline HLA class II diversity (≥9 unique HLA alleles) was associated with higher tumor class II IMM load in females (p=0.01) and not in males (p=0.64). Similarly, in tumors of female patients, somatic HLA class II loss of heterozygosity was associated with increased IMM load (p=0.01) while this association was not observed in tumors in males (p=0.20). In females, TMB (p=0.005), class I IMM load (p=0.005), class II IMM load (p=0.004), and mutational smoking signature (p<0.001) were significantly higher in tumors responding to ICI as compared to non-responding tumors. In contrast, among males, there was no significant association between DCB and any of these features. When IMM was considered in the context of HLA zygosity, high MHC-II restricted IMM load and high HLA class II diversity was significantly associated with overall survival in males (p=0.017). Conclusions: Inherent sex-driven differences in immune surveillance affect the immunogenomic determinants of response to ICI and likely mediate the dimorphic outcomes with ICI therapy. Deeper understanding of the selective pressures and mechanisms of immune escape in tumors in males and females can inform patient selection strategies and can be utilized to further hone immunotherapy approaches in cancer.

RHD 1227 A and hybrid Rhesus box analysis in Thai RhD+ and RhD- blood donors: Prevalence, RHD zygosity, and molecular screening.

BACKGROUND AND OBJECTIVES: DEL (D-elute) red blood cells (RBCs) are typed as D- by routine serological methods, as they carry a very weak form of D variant. Asia type DEL (c.1227 G>A) is the most prevalent DEL allele in East Asian populations that can lead to alloimmunization in D negative transfusion recipients. This study aimed to screen D+ and D- Thai blood donors for the Asia type DEL and its zygosity. MATERIALS AND METHODS: Blood samples of 723 D+ , and 191 D- Thai blood donors were collected. D antigen was typed by the routine serological method and adsorption-elution test to screen DEL phenotype. The hybrid Rhesus box, RHD 1227 G, RHD 1227 A and RHD exon 4 were analyzed with polymerase chain reaction using sequence specific primers, PCR-SSP. RESULTS: Among 191 D- blood donors, 52 (27.2%) RHD 1227 A allele carriers were detected, and 39 out of these 52 (75.0%) were positive for the hybrid Rhesus box (i.e. hemizygous RHD 1227 A). The remaining carriers were RHD 1227 A homozygous. RHD zygosity analysis in Thai D+ blood donors showed that only 4% (29/723) had a Dd genotype (hemizygous RHD 1227 G). Five (0.69%) blood donors were detected with RHD 1227 A alleles among 723 D+ blood donors. They were all G/A heterozygous at the RHD 1227 site. CONCLUSION: This study indicates that the high prevalence of RHD 1227 A allele among serologically apparent D- blood donors in Thais. Furthermore, the screening of hybrid Rhesus box, RHD 1227 A combined with RHD exon 4 is useful for analyses of Asia type DEL and its zygosity.

Twinning rates in Chennai, India - A cross-sectional study.

Context: The city of Chennai is one of the largest metropolitan cities in India where apart from a large traditional population, there has been a continuous migration from rural areas and growing sophistication in lifestyle. Twinning rates trend in the present world would be interesting to study. Aims: The aim of the present study was to analyse the twinning rate in the city of Chennai, the distribution amongst various city zones and the present trends in the co-relation between the maternal age of the twins with the zygosity. Settings and Design: A population-based study was conducted on twin births in various corporation Zones in the Chennai Metropolitan, between 2010 and 2012. As per the Chennai corporation and Health Department register, there were a total of 2,32,884 births registered in the city of which 4,500 were twin births over the 3 years. Only 1371 pairs were found residing in Chennai at the time of study, and hence, a study was conducted on this population only. Satistical Analysis Used: The data were analysed with Epiinfo software. Results: A twining rate of 19.3 per 1000 births was observed as per Corporation records. In the present study, the sample of 150 pairs, 34 pairs (22.6%) comprised of monozygotic (MZ) twins and 116 pairs (77.3%) comprised of dizygotic twins giving a ratio of 1:3. The maternal age groups 25-30 and 30-35 years comprised of the maximum twinning rates. Most twin births were of the first order. An analysis of Weinberg's Differential Rule method to determine zygosity showed a significant difference compared to the Questionnaire method. Conclusions: The twinning rate observed in Chennai in the present study is interestingly very high, compared to the overall twinning rate reported in the past in the state of Tamilnadu. The Wienberg's Differential method for zygosity determination is again found to be questionable. The zygosity proportion, maternal age and parity relations are not very different from previously available data.

Development of a facile genetic transformation system for the Spanish elite rice paella genotype Bomba.

We report the development of an efficient and reproducible genetic transformation system for the recalcitrant Spanish elite rice paella genotype, Bomba. Preconditioned embryos derived from dry seeds were bombarded with gold particles carrying a plasmid containing a screenable and a selectable marker. We confirmed integration and expression of hpt and gusA in the rice genome. Transformation frequency was ca: 10% in several independent experiments. We show Mendelian inheritance of the input transgenes and zygosity determination of the transgenic lines in the T1 generation. A unique and critical step for the regeneration of plants from transformed tissue was shading during the early stages of regeneration, combined with a specific cytokinin:auxin ration at the onset of shifting callus to regeneration media.

Estimating heritability of height without zygosity information for twins under five years in low- and middle-income countries: An application of normal finite mixture distribution models.

Twin studies are widely used to estimate heritability of traits and typically rely on knowing the zygosity of twin pairs in order to determine variation attributable to genetics. Most twin studies are conducted in high resource settings. Large scale household survey data, such as the Demographic and Health Surveys, collect various biomarkers for children under five years old in low- and middle-income countries. These data include twins but no information on zygosity. We applied mixture models to obtain heritability estimates without knowing zygosity of twins, using 249 Demographic and Health Surveys from 79 low- and middle-income countries (14,524 twin pairs). We focused on height of children, adjusted for age and sex, but also provided estimates for other biomarkers available in the data. We estimated that the heritability of height in our sample was 46%.

Concordance and comorbidities among monozygotic twins with tic disorders.

Gilles de la Tourette Syndrome (GTS) is a multifactorial neurodevelopmental disorder characterized by tics and multiple comorbidities. The pathophysiology is not yet fully understood, but both environmental and genetic risk factors seem to be involved. Twin studies provide important knowledge on genetic factors. We assessed the concordance of GTS and chronic tic disorders (CTD) in monozygotic (MZ) twins, and examined tic severity, symptoms of obsessive-compulsive disorder (OCD), attention deficit/hyperactivity disorder and autism spectrum disorder. Twin pairs, where at least one twin was diagnosed with any tic disorder, were identified through Danish Twin Registry, Psychiatric Central Registry, Danish National Patient Registry and National Tourette Clinic, Copenhagen University Hospital, Herlev. Zygosity was tested with single-nucleotide polymorphism (SNP) genotyping and clinical assessment was done with validated tools. 14 MZ twin pairs were included: five were discordant. Seven twin pairs were concordant for GTS, and for two pairs one twin had GTS and the other CTD. Among the twins with CTD or GTS, 50% had at least one comorbidity, which is higher than in background populations. The GTS + OCD-phenotype was significantly more frequent among GTS-concordant than among discordant twins. No statistically significant differences were found between the GTS-concordant and discordant twin pairs regarding tic severity or comorbidities. Thorough clinical assessment and SNP-based genotyping are important when conducting clinical twin studies. We found high concordance of GTS and CTD, which supports the notion that both disorders have common genetic risk factors. Further studies with larger cohorts including dizygotic twins are warranted for more conclusive results.

Individual Oligogenic Background in p.D91A-SOD1 Amyotrophic Lateral Sclerosis Patients.

The p.D91A is one of the most common ALS-causing SOD1 mutations and is known to be either recessive or dominant. The homozygous phenotype is characterized by prolonged survival and slow progression of disease, whereas the affected heterozygous phenotypes can vary. To date, no genetic protective factors located close to SOD1 have been associated with the mild progressive homozygous phenotype. Using Next Generation Sequencing (NGS), we characterized a small cohort of sporadic and familial p.D91A-SOD1 heterozygous (n = 2) or homozygous (n = 5) ALS patients, to reveal any additional contributing variant in 39 ALS-related genes. We detected unique sets of non-synonymous variants, four of which were of uncertain significance and several in untranslated regions of ALS-related genes. Our results supported an individual oligogenic background underlying both sporadic and familial p.D91A cases irrespective of their p.D91A mutant alleles. We suggest that a comprehensive genomic view of p.D91A-SOD1 ALS patients may be useful in identifying emerging variants and improving disease diagnosis as well as guiding precision medicine.

High-Throughput and Accurate Determination of Transgene Copy Number and Zygosity in Transgenic Maize: From DNA Extraction to Data Analysis.

It is vital to develop high-throughput methods to determine transgene copy numbers initially and zygosity during subsequent breeding. In this study, the target sequence of the previously reported endogenous reference gene hmg was analyzed using 633 maize inbred lines, and two SNPs were observed. These SNPs significantly increased the PCR efficiency, while the newly developed hmg gene assay (hmg-taq-F2/R2) excluding these SNPs reduced the efficiency into normal ranges. The TaqMan amplification efficiency of bar and hmg with newly developed primers was calculated as 0.993 and 1.000, respectively. The inter-assay coefficient of variation (CV) values for the bar and hmg genes varied from 1.18 to 2.94%. The copy numbers of the transgene bar using new TaqMan assays were identical to those using dPCR. Significantly, the precision of one repetition reached 96.7% of that of three repetitions of single-copy plants analyzed by simple random sampling, and the actual accuracy reached 95.8%, confirmed by T1 and T2 progeny. With the high-throughput DNA extraction and automated data analysis procedures developed in this study, nearly 2700 samples could be analyzed within eight hours by two persons. The combined results suggested that the new hmg gene assay developed here could be a universal maize reference gene system, and the new assay has high throughput and high accuracy for large-scale screening of maize varieties around the world.

Wild-Type KRAS Allele Effects on Druggable Targets in KRAS Mutant Lung Adenocarcinomas.

KRAS mutations are one of the most common oncogenic drivers in non-small cell lung cancer (NSCLC) and in lung adenocarcinomas in particular. Development of therapeutics targeting KRAS has been incredibly challenging, prompting indirect inhibition of downstream targets such as MEK and ERK. Such inhibitors, unfortunately, come with limited clinical efficacy, and therefore the demand for developing novel therapeutic strategies remains an urgent need for these patients. Exploring the influence of wild-type (WT) KRAS on druggable targets can uncover new vulnerabilities for the treatment of KRAS mutant lung adenocarcinomas. Using commercially available KRAS mutant lung adenocarcinoma cell lines, we explored the influence of WT KRAS on signaling networks and druggable targets. Expression and/or activation of 183 signaling proteins, most of which are targets of FDA-approved drugs, were captured by reverse-phase protein microarray (RPPA). Selected findings were validated on a cohort of 23 surgical biospecimens using the RPPA. Kinase-driven signatures associated with the presence of the KRAS WT allele were detected along the MAPK and AKT/mTOR signaling pathway and alterations of cell cycle regulators. FoxM1 emerged as a potential vulnerability of tumors retaining the KRAS WT allele both in cell lines and in the clinical samples. Our findings suggest that loss of WT KRAS impacts on signaling events and druggable targets in KRAS mutant lung adenocarcinomas.