BACKGROUND: The triple combination of elexacaftor/tezacaftor/ivacaftor (ETI) has dramatically improved the outcome of people with Cystic Fibrosis (pwCF) with at least one F508del mutation. However, carriers of rare cystic fibrosis transmembrane conductance regulator (CFTR) variants are not candidates for this innovative treatment.
METHODS: In this observational study, we report the results of the compassionate use of ETI in 10 pwCF carriers of rare mutations after 2 months of treatment. Rectal organoids and short-term cultures of nasal epithelium obtained from rectal suction biopsies and nasal brushing were obtained from four subjects.
RESULTS: After 2 months of ETI, all patients (4 males, mean age 30.1 ± 13.3 years) showed a significant increase of FEV1% predicted values [+8.0 (3.5-12.7) %, p < 0.010], body mass index [+0.85 (0-1.22) kg/m2, p < 0.020] and cystic fibrosis questionnaire-revised [+19.5 (6.3-29.2) points, p < 0.009]. A significant decrease of sweat chloride concentration [-11.2 (-1.7 to -34.0) mmol/L, p < 0.020] and exacerbations [-1.5 (-2 to -1), p < 0.008] was also recorded. Overall, 7 out of 10 participants were considered full responders. All patients reported cough disappearance (n = 3) or reduction (n = 7). Long-term oxygen was discontinued in two out of three patients and one also stopped noninvasive ventilation and was removed from the lung transplantation waiting list.
CONCLUSIONS: Despite the limited number of cases, our results support the use of CFTR modulators in patients with rare CFTR variants that are not currently approved for ETI in Europe.

We proposed a single-color fluorogenic DNA decoding sequencing method designed to improve sequencing accuracy, increase read length and throughput, as well as decrease scanning time. This method involves the incorporation of a mixture of four types of 3\'-O-modified nucleotide reversible terminators into each reaction. Among them, two nucleotides are labeled with the same fluorophore, while the remaining two are unlabeled. Only one nucleotide can be extended in each reaction, and an encoding that partially defines base composition can be obtained. Through cyclic interrogation of a template twice with different nucleotide combinations, two sets of encodings are sequentially obtained, enabling the determination of the sequence. We demonstrate the feasibility of this method using established sequencing chemistry, achieving a cycle efficiency of approximately 99.5 %. Notably, this strategy exhibits remarkable efficacy in the detection and correction of sequencing errors, achieving a theoretical error rate of 0.00016 % at a sequencing depth of ×2, which is lower than Sanger sequencing. This method is theoretically compatible with the existing sequencing-by-synthesis (SBS) platforms, and the instrument is simpler, which may facilitate further reductions in sequencing costs, thereby broadening its applications in biology and medicine. Moreover, we demonstrate the capability to detect known mutation sites using information from only a single sequencing run. We validate this approach by accurately identifying a mutation site in the human mitochondrial DNA.

Lung cancer is still the leading cause of cancer-related mortality. Over the past two decades, the management of non-small cell lung cancer (NSCLC) has undergone a significant revolution. Since the first identification of activating mutations in the epidermal growth factor receptor (EGFR) gene in 2004, several genetic aberrations, such as anaplastic lymphoma kinase rearrangements (ALK), neurotrophic tropomyosin receptor kinase (NTRK) and hepatocyte growth factor receptor (MET), have been found. With the development of gene sequencing technology, the development of targeted drugs for rare mutations, such as multikinase inhibitors, has provided new strategies for treating lung cancer patients with rare mutations. Patients who harbor this type of oncologic driver might acquire a greater survival benefit from the use of targeted therapy than from the use of chemotherapy and immunotherapy. To date, more new agents and regimens can achieve satisfactory results in patients with NSCLC. In this review, we focus on recent advances and highlight the new approval of molecular targeted therapy for NSCLC patients with rare oncologic drivers.

Given their good antitumor effects, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are standard first-line therapy for EGFR-sensitive mutations, including exon 19 deletions and exon 21 L858R mutations. EGFR fusion mutations and EGFR amplification are very rare in non-small cell lung cancer (NSCLC). We describe 2 patients with NSCLC harboring EGFR fusion mutations (EGFR-MACF1 and EGFR-GNAT3) combined with EGFR amplification. Both patients received EGFR-TKI treatment, and 1 of them showed an antitumor response.

Sequencing of DNA is normally the final procedure carried out to determine the actual pathogenic variants when the techniques used for genotyping are unable to provide complete identification of both AAT alleles. Gene sequencing of complete SERPINA1 gene by using the Sanger method or next-generation sequencing (NGS) is crucial to enable correct diagnosis in patients with alpha1-antitrypsin deficiency caused by uncommon AAT variants.This protocol explains how to correctly sequence SERPINA1 gene both with Sanger method and NGS.

With the rapid development of lung cancer molecular detection and precision therapy, targeted therapy has covered the entire process of diagnosis and treatment of nonsmall cell lung cancer patients. Overall mortality from lung cancer has decreased significantly over the past 20 years, especially since the introduction of targeted drugs in 2013. In 2022, targeted therapy for lung cancer has developed rapidly. The optimization of treatment modes and the exploration of new target drugs such as antibody-drug conjugates will broaden the selection range of nonsmall cell lung cancer patients with positive driver genes. This article reviews the latest advances in targeted therapy for driver gene-positive lung cancer in 2022.

In evidence-based medicine, N-of-1 trials are increasingly attractive for rare and heterogeneous conditions. A recent French study illustrates this convincingly in the field of cystic fibrosis. A highly effective triple therapy (ETI) is currently available in Europe, which will eventually help the 85 % of Belgian patients carrying at least one copy of the F508del mutation. Most other 2.000 or so putative mutations of this gene are poorly characterised and very rare or private. To predict the efficacy of ETI at the individual level in currently ineligible patients, sophisticated tools are advocated, but they are expensive, not widely available, often partially standardised and there still remains a «grey area» concerning their reliability in this context. With-out using them, the French study suggests that more than half of these patients show clinically meaningful responses to a 4-6 weeks trial of ETI. What makes this pragmatic, cost-effective, non-invasive and simplified approach possible (type 2 N-of-1 trials) is the dramatic and rapid efficacy of a life-saving treatment without alternative and the fact that it can be assessed using simple and robust clinical and paraclinical outcomes. Here, we describe one such trial and discuss the value and limitations of this approach.
Dans la médecine basée sur les preuves, les essais de taille 1 suscitent un intérêt croissant dans les affections rares et hétérogènes. Une récente étude française l’illustre de manière convaincante dans la mucoviscidose. Une trithérapie extrêmement efficace (ETI) est actuellement disponible en Europe, concernant à terme en Belgique les 85 % de patients porteurs d’au moins une copie de la mutation F508del. La majorité des quelque 2.000 autres mutations putatives de ce gène sont mal caractérisées et rarissimes. Des techniques sophistiquées sont évoquées pour prédire, à l’échelle individuelle, l’efficacité d’ETI chez les patients actuellement non éligibles, mais elles sont peu disponibles, coûteuses, souvent imparfaitement standardisées et leur interprétabilité conserve une «zone grise». Sans y recourir, l’étude française montre que plus de la moitié de ces patients répondent d’une manière évidente à un essai d’ETI pendant quelques semaines seulement. Ce qui permet cette approche pragmatique, économique, non invasive et simplifiée (essai de taille 1, de type 2), c’est l’efficacité spectaculaire et rapide d’un traitement salvateur sans alternative et le fait qu’elle puisse être appréhendée à partir de critères cliniques et paracliniques simples et robustes. Nous rapportons ici un essai de ce type et discutons l’intérêt et les limites de cette approche.

Schizophrenia and affective disorder are two major complex mental disorders with high heritability. Evidence shows that rare variants with significant clinical impacts contribute to the genetic liability of these two disorders. Also, rare variants associated with schizophrenia and affective disorders are highly personalized; each patient may carry different variants. We used whole genome sequencing analysis to study the genetic basis of two families with schizophrenia and major depressive disorder. We did not detect de novo, autosomal dominant, or recessive pathogenic or likely pathogenic variants associated with psychiatric disorders in these two families. Nevertheless, we identified multiple rare inherited variants with unknown significance in the probands. In family 1, with singleton schizophrenia, we detected four rare variants in genes implicated in schizophrenia, including p.Arg1627Trp of LAMA2, p.Pro1338Ser of CSMD1, p.Arg691Gly of TLR4, and Arg182X of AGTR2. The p.Arg691Gly of TLR4 was inherited from the father, while the other three were inherited from the mother. In family 2, with two affected sisters diagnosed with major depressive disorder, we detected three rare variants shared by the two sisters in three genes implicated in affective disorders, including p.Ala4551Gly of FAT1, p.Val231Leu of HOMER3, and p.Ile185Met of GPM6B. These three rare variants were assumed to be inherited from their parents. Prompted by these findings, we suggest that these rare inherited variants may interact with each other and lead to psychiatric conditions in these two families. Our observations support the conclusion that inherited rare variants may contribute to the heritability of psychiatric disorders.

Despite the promising results of new CFTR targeting drugs designed for the recovery of F508del- and class III variants activity, none of them have been approved for individuals with selected rare mutations, because uncharacterized CFTR variants lack information associated with the ability of these compounds in recovering their molecular defects. Here we used both rectal organoids (colonoids) and primary nasal brushed cells (hNEC) derived from a CF patient homozygous for A559T (c.1675G>A) variant to evaluate the responsiveness of this pathogenic variant to available CFTR targeted drugs that include VX-770, VX-809, VX-661 and VX-661 combined with VX-445. A559T is a rare mutation, found in African-Americans people with CF (PwCF) with only 85 patients registered in the CFTR2 database. At present, there is no treatment approved by FDA (U.S. Food and Drug Administration) for this genotype. Short-circuit current (Isc) measurements indicate that A559T-CFTR presents a minimal function. The acute addition of VX-770 following CFTR activation by forskolin had no significant increment of baseline level of anion transport in both colonoids and nasal cells. However, the combined treatment, VX-661-VX-445, significantly increases the chloride secretion in A559T-colonoids monolayers and hNEC, reaching approximately 10% of WT-CFTR function. These results were confirmed by forskolin-induced swelling assay and by western blotting in rectal organoids. Overall, our data show a relevant response to VX-661-VX-445 in rectal organoids and hNEC with CFTR genotype A559T/A559T. This could provide a strong rationale for treating patients carrying this variant with VX-661-VX-445-VX-770 combination.

Afatinib, the world\'s first irreversible ErbB family (containing four different cancer cell epidermal growth factor receptors, including EGFR, HER2, ErbB3, and ErbB4) inhibitor, is a second-generation oral epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI). It can be used as a first-line treatment for locally advanced or metastatic non-small-cell lung cancer (NSCLC) with an EGFR-sensitive mutation or for patients with locally advanced or metastatic squamous lung cancer whose disease progresses during or after platinum-containing chemotherapy. Currently, with the use of third-generation EGFR-TKIs, afatinib is no longer clinically indicated as the first choice for patients with NSCLC who have EGFR-sensitive mutations. However, afatinib showed a considerable inhibitory effect in NSCLC patients with uncommon EGFR mutations (G719X, S768I, and L861Q) according to a combined post hoc analysis of the LUX-Lung2/3/6 trials. With the development of genetic testing technology, the detection rate of uncommon EGFR mutations is increasing. The aim of this paper is to describe in detail the sensitivity of rare EGFR mutations to afatinib and to provide information and a reference for those suffering from advanced NSCLC who have uncommon EGFR mutations.