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Novel Co-Occurrence of Germline EGFR p.V843I and Somatic EGFR Exon 19 Deletion in NSCLC: Insights into Reduced Sensitivity to EGFR-TKIs.

Germline EGFR pathogenic variants (PVs) are rare and define a distinct hereditary subset of NSCLC with unique clinical characteristics. Germline EGFR p.T790M is the most frequent and best characterized, with reported sensitivity to first- and second-generation EGFR-TKIs. Yet, the response of germline EGFR variants, especially the rarer ones such as p.V843I, to osimertinib remains poorly characterized. Given the very low frequency of germline non-p.T790M variants, their clinical relevance can only be investigated via case reports. Herein, we report what is, to the best of our knowledge, the first case of advanced lung adenocarcinoma harboring a germline EGFR p.V843I variant coexisting in cis with the unusual somatic EGFR exon 19 C-helix deletion, p.S752_I759del. Additionally, a somatic TP53 variant was detected. Treatment with afatinib induced a partial response lasting only six months, as rapid disease progression occurred without identifiable acquired resistance mechanisms. Subsequently, no objective response to osimertinib or afatinib rechallenge was observed. Acquired EGFR and MET amplification were detected in corresponding rebiopsies. Overall survival was 29 months. Our findings suggest that, despite the presence of the previously reported EGFR-TKI-sensitive, EGFR p.S752_I759del, the co-occurrence of germline p.V843I may have contributed to reduced sensitivity to afatinib and osimertinib. This case expands the molecular spectrum of hereditary EGFR-mutated NSCLC and, together with our narrative review of the literature, supports an emerging model in which germline EGFR PVs may act both as tumor-predisposing events and as potential mechanisms of early resistance to EGFR-TKIs.

Humans↗

Isolation and characterization of rat testis H1t. An H1 histone variant associated with spermatogenesis.

Rat testis contains a unique H1 histone variant (H1t) not detected in a variety of other rat organs. H1t is extracted from chromatin by salt as expected for an H1 component (released by 0.6 M NaCl but not by 0.3 M); however, in contrast to other mammalian H1 species, H1t is not extracted in significant amounts by 5% (w/v) trichloroacetic acid. H1t is undetectable in testes from 3-or 15-day-old rats, but is evident in extracts from 21-day-old animals. Its initial appearance in the developing testis thus correlates with the progression of germinal cells to the meiotic stage of differentiation. H1t was isolated in homogeneous form by extraction of whole tissue with 0.75 M perchloric acid, fractional precipitation with trichloroacetic acid, and two cycles of chromatography over a cation exchange resin (Bio Rex 70). The amino acid composition of H1t differs significantly from that of somatic type H1 variants (for example, higher arginine and methionine content). Its identification as an H1 species is supported by analysis of the two fragments resulting from treatment of the protein with N-bromosuccinimide. H1t, as well as the six recognized somatic type H1 components of rat testis may be resolved by two-dimensional polyacrylamide gel electrophoresis run in the absence of denaturants at pH 4.5 in the first dimension and in the presence of sodium dodecyl sulfate in the second dimension.

Aging↗

Body image disturbance in body dysmorphic disorder and eating disorders. Obsessions or delusions?

At this time, the question posed by this article's title--body image disturbance in body dysmorphic disorder and eating disorders: obsessions or delusions?--is probably best answered "both." Both disorders appear to be characterized by obsessional and delusional thinking. In addition, it is likely that their nondelusional and delusional variants constitute a single disorder encompassing a spectrum of insight, with the entire spectrum characterized by obsessional thinking. This view represents a considerable departure from DSM-III-R, in which the psychotic disorders were encapsulated in a separate section of the manual and considered different disorders from their nonpsychotic variants. The one exception was the mood disorders, which were acknowledged to have psychotic variants that were classified in the manual's "nonpsychotic" section. In DSM-IV, on the basis of emerging empirical evidence about the dimensional nature of the psychotic/nonpsychotic boundary, the dichotomy between delusional and nondelusional disorders is less clear. The double coding allowed for BDD acknowledges that BDD and its delusional disorder variant may constitute a single disorder; that allowed for OCD acknowledges that OCD may be delusional. With regard to eating disorders, however, DSM-IV is surprisingly silent, perhaps because delusional preoccupations are less common than in BDD. These issues also may apply to other disorders. Like BDD, hypochondriasis is classified as a somatoform disorder, with its delusional variant a type of delusional disorder, somatic type. Do the delusional and nondelusional variants of hypochondriasis constitute the same disorder? Do other types of somatic delusional disorder, such as parasitosis and olfactory reference syndrome (the belief that one emits a foul body odor) have nondelusional variants? It is likely that a number of disorders span a spectrum from delusional to nondelusional thinking, with unlimited shades of gray in between. Future research may indicate that obsessional disorders such as BDD, anorexia, OCD, and hypochondriasis, as well as other disorders such as major depression, should have qualifiers or subtypes--for example, "with good insight," "with poor insight," and "with delusional (or psychotic) thinking"--with an implied continuum of insight embraced by a single disorder. Such an approach, which scatters psychosis throughout the nomenclature, ultimately may be shown to be a more valid and clinically useful classification approach. Answers to these questions will not only improve our classification system but also may have important treatment implications. For example, the preliminary finding that delusional BDD responds preferentially to SRIs but not to neuroleptic agents contradicts conventional wisdom about the treatment of psychosis.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗

Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.

The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of approximately 30,000 nonredundant human mRNA sequences with identified coding regions representing 17,000 distinct loci. These high-quality mRNA sequences allow for the identification of transcribed regions in the human genome sequence, and many researchers accept them as the correct representation of each defined gene sequence. Computational comparison of these mRNA sequences and the recently published essentially finished human genome sequence reveals several thousand undocumented nonsynonymous substitution and frame shift discrepancies between the two resources. Additional analysis is undertaken to verify that the euchromatic human genome is sufficiently complete--containing nearly the whole mRNA collection, thus allowing for a comprehensive analysis to be undertaken. Many of the discrepancies will prove to be genuine polymorphisms in the human population, somatic cell genomic variants, or examples of RNA editing. It is observed that the genome sequence variant has significant additional support from other mRNAs and ESTs, almost four times more often than does the mRNA variant, suggesting that the genome sequence is more accurate. In approximately 15% of these cases, there is substantial support for both variants, suggestive of an undocumented polymorphism. An initial screening against a 24-individual genomic DNA diversity panel verified 60% of a small set of potential single nucleotide polymorphisms from which successful results could be obtained. We also find statistical evidence that a few of these discrepancies are due to RNA editing. Overall, these results suggest that the mRNA collections may contain a substantial number of errors. For current and future mRNA collections, it may be prudent to fully reconcile each genome sequence discrepancy, classifying each as a polymorphism, site of RNA editing or somatic cell variation, or genome sequence error.

Computational Biology↗

[Psychogenic and somatic interactions in diabetes mellitus].

As a result of 10-year follow-up study of 250 patients with diabetes mellitus, type I (58) and type II (192) 4 predictable psychological crises have been singled out: the first one was related to reaction to the diagnosis; the second--to the assignment of insulin therapy; the third--to the development of diabetes complications and the fourth--to hospitalization and a subsequent communication with other, more "experienced", patients. In the progress of the disease, an interaction of psychogenic, somatic and personality factors caused development of psycho-somatic cycles (psycho-somatic balancing according to H. Baruk), which is realized in 3 variants: predominantly psychogenic, predominantly somatic and psycho-somatic.

Adult↗

Genetic analysis of dexamethasone resistance in L cells by somatic cell hybridization.

Stable dexamethasone resistant and receptor-containing (R+) variants of L cells have been characterized by somatic cell hybridization. Neither of the variants had a clearly dominant phenotype in hybrids with dexamethasone-sensitive fibroblast lines, i.e. the resistance of the variants was not due to transdominant factors. Somatic cell hybrids formed between one of the R+-resistant clones and an independent resistant fibroblast cell line showed complementation--the hybrid clones were as sensitive to the steroid as the sensitive parental lines. Complementation, however, disappeared after continued culture of the clones. The return of the dexamethasone-sensitive phenotype was not always linked with similar changes in the responsiveness to another steroid, e.g. progesterone. Our clones can be considered to be resistant variants, designated death-less (d-), where the cells are defective in a non-receptor component involved in the hormone response. The fact that complementation can occur indicates the existence of at least two such steps in the pathway.

Animals↗

Change of karyoskeleton during mammalian spermatogenesis: expression pattern of nuclear lamin C2 and its regulation.

Nuclear lamins are a multigene family of major karyoskeletal proteins. The expression pattern of members of the lamin family has been shown to be developmentally regulated. Of particular interest have been the findings that mammalian spermatogenic cells express two small lamin isoforms (B3 and C2) which are shorter splicing variants of their somatic counterparts (the lamins B2 and C, respectively). Although lamins B3 and C2 appear to be specific for the germ line, the expression pattern and localization of these proteins is not known. In the present study, we present evidence that during rat spermatogenesis lamin C2 is selectively expressed in spermatocytes, i.e., the cells undergoing meiosis. As in the case of other members of the family, lamin C2 was detected at the nuclear periphery. Northern blotting and in situ hybridization indicate that meiotic expression of lamin C2 is regulated at the transcriptional level. This is in contrast to the situation during amphibian oogenesis, where lamin expression is largely posttrascriptionally regulated. Interestingly, the expression pattern of lamin C2 temporally coincides with that of structural protein components of another meiosis-specific karyoskeletal structure, the synaptonemal complex (SC). Taken together, we conclude that pairing and recombination of homologous chromosomes during meiotic prophase is accompanied by significant changes in the organization of the karyoskeleton which are accomplished by the expression of stage-specific proteins.

Amino Acid Sequence↗

The mouse histone H1 genes: gene organization and differential regulation.

There are six mouse histone H1 genes present in the histone gene cluster on mouse chromosome 13. These genes encode five histone H1 variants expressed in somatic cells, H1a to H1e, and the testis-specific H1t histone. Two of the genes that have not been assigned previously to the five somatic H1 subtypes have been identified as encoding the H1b and H1d subtypes. Three of the H1 genes, H1a, H1c and H1t, are present on an 80 kb segment of DNA that contains nine core histone genes. Two others, H1d and H1e, are present in a second patch, while the H1b gene is at least 500 kb away in a patch containing 14 core histone genes. The histone H1 genes are differentially expressed. All five genes for the somatic histone H1 proteins are expressed in exponentially growing cells. However, the levels of H1a, H1b and H1d mRNAs are greatly reduced in cells that are terminally differentiated or arrested in G0, while the H1c and H1e mRNAs continue to be expressed. In addition to the major RNA that ends at the stem-loop, the H1c gene expresses a longer, polyadenylated mRNA in differentiated cells, although in varying amounts. None of the other histone H1 genes encodes detectable amounts of polyadenylated mRNAs.

Aging↗

Nuclear proteins in spermatogenesis.

Mammalian somatic type histone variants are replaced or supplemented in early primary spermatocytes and possibly spermatogonia by testis specific and testis enriched histone variants. The testis complement of histones is replaced entirely by transition basic proteins in mid-spermatids. This transition is accompanied by a dramatic reduction of thermal stability of mid-spermatid chromatin which may be due in part to hyperacetylation of histone H4. The transition basic proteins are replaced by protamines which are arginine-rich and contain cysteine.

Animals↗

Human natural chimerism: an acquired character or a vestige of evolution?

Analysis on five common classes of human natural chimeras (cytomictical, whole body, fetal-maternal, germ cell, and tumor chimeras) reveals that (1) they initiate only during pregnancy, (2) the most common class are chimeras which contain maternal cells, and (3) the primary mechanisms that are involved in their formation and establishment are still elusive. These classes of natural chimerism, are involved only with maladaptive phenomena such as malignancy and autoimmune diseases and without any documented benefit. A recent review has challenged the accepted dogma that the evolution of immunity is pathogen-directed and asserted that preserving individuality from littering the soma and the germline by conspecific alien cells might have been the original function of the innate immunity. Following this tenet, I propose here that human natural chimerism is a by-product of the new role evolved from primitive components of immunity to "educate" the developing embryo with the armamentarium of effector mechanisms, dedicated to purge the individual from pervasive somatic and germline variants, and is not a vestige of evolution.

Animals↗

AID-GFP chimeric protein increases hypermutation of Ig genes with no evidence of nuclear localization.

Somatic hypermutation generates variants of antibody genes and underpins the affinity maturation of antibodies. It is restricted to the V-gene segments, and although it decays exponentially toward the 3'end, it includes recognizable hot spots. Although the detailed mechanism of hypermutation remains elusive, the process may take place in two separate stages, preferentially targeting G/Cs in the first and A/Ts in the second stage. It seems that MSH2 is involved in the second stage, and that activation induced deaminase (AID) is implicated in the control of hypermutation. The constitutively hypermutating cell line Ramos expresses AID, and we have prepared transfectants that express a chimeric AID-green fluorescent protein. The fluorescence is strongly detected in the cytoplasm but not in the nucleus. Yet, the chimeric protein increases the hypermutation rate either directly or, more likely, indirectly, by favoring the transport of AID into the nucleus. Thus, in Ramos, AID seems to be rate limiting. Unexpectedly, the proportion of deletions also is increased. The increase in mutation rate detected by a fast cytofluorimetric method based on the accumulation of sIgM-loss mutants correlates with the increase measured by mutations defined by sequence analysis. The higher mutation rate is largely explained by the higher proportion of mutated clones, indicating that AID controls the number of cells that undergo hypermutation but not the number of mutations that are incorporated in each mutation round.

Base Sequence↗

Immunological alteration of leukemic cells in vivo after treatment with an antitumor drug.

L1210 leukemia was transplanted serially in CDF(1) mice treated with 5-(3,3-dimethyl-1-triazeno)imidazole-4-carboxamide (DIC, NSC 45388). After four different lines (C lines) had been treated for several generations, a marked increase in survival time of untreated mice was observed. In contrast, mice treated with DIC or immunosuppressed with cyclophosphamide succumbed earlier with generalized leukemia. Furthermore, a C line showed unusually high sensitivity to chemotherapeutic treatment with 1,3 bis(2-chloroethyl)-1-nitrosourea. The data suggest that C lines acquired strong antigenicity for CDF(1) and DBA/2 hosts. DIC treatment may have selected highly antigenic variants or induced somatic mutations resulting in the appearance of strong new transplantation antigen(s).

Animals↗

A putative DNA binding surface in the globular domain of a linker histone is not essential for specific binding to the nucleosome.

A fundamental step in the assembly of native chromatin is the specific recognition and binding of linker histones to the nucleoprotein subunit known as the nucleosome. A first step in defining this important interaction is the determination of residues within linker histones that are important for the structure-specific recognition of the nucleosome core. By combining in vitro assays for the native binding activity of linker histones and site-directed mutagenesis, we have examined a cluster of basic residues within the globular domain of H1(0), a somatic linker histone variant from Xenopus laevis. We show that these residues, which comprise a putative DNA binding surface within the globular domain, do not play an essential role in the structure-specific binding of a linker histone to the nucleosome.

Animals↗

Regulation of macrophage growth and antiviral activity by interferon-gamma.

Interferons, in addition to their antiviral activity, induce a multiplicity of effects on different cell types. Interferon (IFN)-gamma exerts a unique regulatory effect on cells of the mononuclear phagocyte lineage. To investigate whether the antiviral and antiproliferative effects of IFN-gamma in macrophages can be genetically dissociated, and whether IFN-alpha and IFN-gamma use the same cellular signals and/or effector mechanisms to achieve their biologic effects, we have derived a series of somatic cell genetic variants resistant to the antiproliferative and/or antiviral activities of IFN-gamma. Two different classes of variants were found: those resistant to the antiproliferative and antiviral effects of IFN-gamma against vesicular stomatitis virus (VSV) and those resistant to the antiproliferative effect, but protected against VSV and encephalomyocarditis virus (EMCV) lysis by IFN-gamma. In addition, a third class of mutants was obtained that was susceptible to the growth inhibitory activity, but resistant to the antiviral activity of IFN-gamma. Analysis of these mutants has provided several insights regarding the regulatory mechanisms of IFN-gamma and IFN-alpha on the murine macrophage cell lines. The antiproliferative activity of IFN-gamma on these cells, in contrast to that of IFN-alpha, is mediated by a cAMP-independent pathway. The antiproliferative and antiviral activities of IFN-gamma were genetically dissociated. Variants were obtained that are growth resistant but antivirally protected, or are growth inhibited but not antivirally protected against VSV or EMCV. The genetic analysis indicated that IFN-alpha and IFN-gamma regulate the induction of the dsRNA-dependent P1/eIF-2 alpha protein kinase and 2',5'-oligoadenylate synthetase enzymatic activities via different pathways. Finally, a unique macrophage mutant was obtained that was protected by IFN-gamma against infection by VSV, but not EMCV, suggesting that antiviral mechanisms involved in protection against these different types of RNA viruses must be distinct at some level.

2',5'-Oligoadenylate Synthetase↗

Large-scale simulation of coverage and error rate tradeoffs for cancer detection in cell-free DNA whole-genome sequencing.

MOTIVATION: Cell-free DNA (cfDNA) whole-genome sequencing (WGS) is a promising approach for detecting cancer recurrence. It enables cancer detection by identifying all tumor-derived cfDNA (ctDNA) molecules carrying somatic single nucleotide variants (sSNVs). While ideally, a sequencing platform should be highly accurate for reliable ctDNA detection, in reality, all sequencing platforms introduce sequencing errors that generate false positives indistinguishable from true SNVs. Understanding how sequencing parameters influence ctDNA detection sensitivity at low tumor fractions (TFs) in cfDNA samples is essential for guiding sequencing strategies in clinical contexts. To model cfDNA sequencing for tumor detection, which contains asymmetric noise and multiple interacting parameters, analytical modeling is intractable, motivating large-scale parallelized simulation. RESULTS: We developed a simulation framework to generate in silico cfDNA data across 10 cancer types. In total, 480 million cfDNA samples were simulated from tumor WGS profiles. Overall, the lowest detectable TF differs substantially between cancer types under identical sequencing conditions due to variations in mutational load. For cancers with high mutational load, 3× coverage with low-error techniques reliably detects TFs below 0.1%. In contrast, cancers with low mutational load require at least six-fold higher coverage to achieve comparable detection thresholds. Increasing sequencing quality scores from Q30 to Q55 at 30× coverage further enhances sensitivity, enabling detection of TFs as low as 1 × 10-5. This study provides a comprehensive framework for optimizing sequencing parameters, offering valuable guidance for tailoring future technology development for specific cancer types and clinical applications. AVAILABILITY AND IMPLEMENTATION: The code is publicly available at https://github.com/UMCUGenetics/cfdetect/tree/main.

Whole Genome Sequencing↗

Recurrent patterns of widespread neuronal genomic damage shared by major neurodegenerative disorders.

Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease (AD) are common neurodegenerative disorders for which the mechanisms driving neuronal death remain unclear. Single-cell whole-genome sequencing of 429 neurons from three C9ORF72 ALS, six C9ORF72 FTD, seven AD, and twenty-three neurotypical control brains revealed significantly increased burdens in somatic single nucleotide variant (sSNV) and insertion/deletion (sIndel) in all three disease conditions. Mutational signature analysis identified a disease-associated sSNV signature suggestive of oxidative damage and an sIndel process, affecting 28% of ALS, 79% of FTD, and 65% of AD neurons but only 5% of control neurons (diseased vs. control: OR=31.20, p = 2.35×10-10). Disease-associated sIndels were primarily two-basepair deletions resembling signature ID4, which was previously linked to topoisomerase 1 (TOP1)-mediated mutagenesis. Duplex sequencing confirmed the presence of sIndels and identified similar single-strand events as potential precursor lesions. TOP1-associated sIndel mutagenesis and resulting genome instability may thus represent a common mechanism of neurodegeneration.

Journal Article↗

Sleep-disordered breathing in Möbius syndrome.

Möbius syndrome is a complex neurologic disorder characterized by congenital bilateral facial paralysis associated with lateral gaze paralysis. The syndrome has variable manifestations and several variants, some with somatic stigmata. In 1990, Möbius syndrome is conceptualized as a spectrum of clinical caudal brain-stem signs. Some deficits are manifested by laryngeal paralysis and aspiration. Sleep-disordered breathing syndromes have not been previously reported in association with Möbius syndrome. We report two children with Möbius syndrome and sleep-disordered breathing. Based on known pathologic findings and clinical manifestations, we believe that sleep-disordered breathing may be a common complication of Möbius syndrome and should be sought, since potential outcomes of such complications include serious morbidity.

Child↗

Apoptosis and the B cell response to antigen.

The primary B cell response to T cell dependent antigens comprises two pathways of differentiation; one resulting in formation of foci of antibody forming cells in the extrafollicular regions of secondary lymphoid organs and the other giving rise to germinal centers within the follicles. Foci of antibody forming cells are detectable for only a limited time, before involuting due to apoptosis of the plasma cells. Similarly in the germinal center, regulation of cell number, selection of high affinity variants generated by somatic hypermutation, and the resolution of the germinal center itself all involve the death of unwanted B cells. In this review we describe recent experiments which have allowed determination of the role of certain forms of apoptosis in the B cell response to antigen.

Animals↗