Resistance Mutations Research Articles

A multicenter, open-label, first-in-human study of TYRA-200 in advanced intrahepatic cholangiocarcinoma and other solid tumors with activating FGFR2 gene alterations (SURF201).

TPS646 Background: Approved Fibroblast Growth Factor Receptor (FGFR) inhibitors have demonstrated clinical benefit in locally advanced or metastatic cholangiocarcinoma harboring oncogenic FGFR2 fusions or other rearrangements. However, the emergence of acquired resistance mutations limits the clinical activity and duration of responses to currently available inhibitors. TYRA-200 is an orally bioavailable FGFR1/2/3 inhibitor designed to specifically address these clinically observed acquired resistance alterations in FGFR2. Methods: SURF201 is a single arm, multicenter, open-label, first-in-human, dose escalation and expansion study designed to investigate TYRA-200 in patients (pts) with advanced intrahepatic cholangiocarcinoma and other solid tumors with primary activating FGFR2 gene alterations and on-target acquired known FGFR2 resistance mutations. The study is being conducted in two parts. Part A dose escalation uses an i3+3 design and is evaluating the safety, tolerability, and the pharmacokinetic profile of TYRA-200. Part B dose expansion will further characterize the safety profile and evaluate the preliminary anti-tumor activity of TYRA-200 by RECIST v1.1 in pts with unresectable locally advanced/metastatic intrahepatic cholangiocarcinoma who have previously received an FGFR inhibitor(s) and have developed acquired FGFR2 kinase domain resistance mutations. The study is currently planned for approximately four centers in the US and is actively enrolling (NCT06160752). Clinical trial information: NCT06160752 .

Tinengotinib in patients with advanced, metastatic cholangiocarcinoma: Overall survival results and biomarker correlative analysis from a phase 2 clinical trial.

608 Background: Tinengotinib, a spectrum-selective multi-kinase inhibitor with unique binding properties to FGFR , potently inhibited FGFR2 fusion/rearrangement and acquired resistant/gatekeeper mutations in pre-clinical models and exhibited antitumor activity in cholangiocarcinoma (CCA) patients (pts) in phase 1/2 trials. Here we present the overall survival (OS) data and biomarker correlative analysis from a phase 2 clinical trial of tinengotinib in CCA. Methods: Eligible pts with advanced/metastatic CCA who had received ≥ 1 prior systemic chemotherapy with ECOG PS 0-1 were treated with tinengotinib 10 mg QD across four Cohorts: A1: FGFR2 fusion(s) with primary progression on previous FGFR inhibitor ( FGFR i); A2: FGFR2 fusion(s) with progression after prior response to FGFR i; B: FGFR alteration(s) without FGFR2 fusion(s); C: FGFR wild-type. Efficacy was evaluated per RECIST v1.1 and safety was assessed by CTCAE v5.0. Genomic alterations in circulating tumor DNA (ctDNA) were assessed by Foundation Medicine NGS panel at baseline, C3D1 and EOT. Planned correlative analyses of response (PR+SD>6 months) and PFS in pt subgroups based on ctDNA mutational status were performed. Results: 55 eligible pts were enrolled (18 in A1, 11 in A2, 13 in B, 13 in C) with median age 61.0 [range 24-81] years, ECOG PS 0 in 50.9% pts, 56.4% female, and 60.0% with ≥ 3 lines of prior therapy. Among 42 pts with FGFR alterations, 78.4% had ≥ 1 prior FGFR i, and 97.6% had prior chemotherapy. Median follow up time was 8.6 months (0.4-30.5). The median OS (months) was 17.1 (95%CI 7.5-19.5) in A1; not reached (95%CI 9.6, -) in A2; 18.0 (95%CI 9.6, -) in A1+A2; not reached (95%CI 8.0, -) in B; 6.5 (95%CI 4.8-16.4) in C. The OS rate in A, B and C was 100%, 91.7% and 75% at month 3; 83.7%, 83.3% and 66.7% at month 6, and 65.8%, 55.6% and 23.8% at month 12. Partial response was observed in 26% (10/39) of evaluable FGFR-altered pts (A1+A2+B). The safety profile was consistent with previous reports. The most common any-grade treatment-related AEs were hypertension (63.6%) and diarrhea (47.3%). Baseline ctDNA results were available in 46 pts, 35 in cohorts A+B and 11 in C. A positive correlation was shown in MED12 mutation vs response (P=0.03476). BCOR and ARID1A mutation were found to be negatively associated with PFS (P=0.01366 and P=0.0437). Acquired/secondary mutations at baseline were observed in cohort A, including V564F/I (3/24 and 5/24) and N549K/H (5/24 and 5/24); favorable anti-tumor activity was noted despite these resistant mutations, consistent with preclinical data. Conclusions: Tinengotinib has shown promising anti-tumor efficacy in CCA pts with FGFR fusion after prior FGFR i and in those with primary FGFR mutations. An ongoing randomized phase III study will investigate tinengotinib vs. chemotherapy in FGFR inhibitor refractory CCA (NCT05948475). Clinical trial information: NCT04919642 .

Clinical landscape of cell free DNA alterations in patients with advanced biliary tract cancer treated with targeted therapies.

626 Background: Although 40% of patients (pts) with advanced biliary tract cancer (BTC) harbor actionable alterations amenable to targeted therapy (TT), tumor genotyping can be challenging due to limited tissue and other factors. Next generation sequencing (NGS) of cell free DNA (cfDNA) may aid in prognostication, identification of TT opportunities, and characterization of acquired resistance mechanisms to TT. Methods: cfDNA was collected prospectively in pts with BTC treated at MSK from 2016-2023. Samples were analyzed using a CLIA-approved, cfDNA targeted NGS assay (MSK-ACCESS). When available, matched tumor samples were analyzed using an FDA-authorized targeted NGS assay (MSK-IMPACT). Objectives included evaluating association of cfDNA genomic alteration variant allele frequency (VAF) with outcomes and description of genomic features identified on cfDNA at resistance to TT. Results: N=170 BTC pts (intrahepatic cholangiocarcinoma [CCA], n=121; extrahepatic CCA, n=29, gallbladder cancer, n=20) underwent cfDNA genotyping, comprising 270 samples overall. A majority of pts (146/170, 86%) had locally advanced or metastatic disease. OncoKB level 1/2 alterations were identified in 19% of pts overall. Pts with treatment-naïve locally advanced or metastatic BTC whose baseline detected cfDNA genomic alterations were VAFhigh (defined as > median VAFmax across all samples, n=60) had significantly worse median PFS (4.5 (95% CI 2.2-6.5) vs. 11.8 (95% CI 5.4-18.4) months, (HR 2.7, p=0.002) and OS (14.1 (95% CI 5.4-19.9) vs. 32.0 (95% CI 13.8-39.9) months, HR 3.1, p=0.002)) to first line treatment. Serial cfDNA was available from 28 pts who received TT. Emergent RAS isoform alterations were identified at resistance in 7/25 (28%) pts who received BRAF-, FGFR-, or HER2-directed TT. These included 3/5 pts who received BRAF/MEK TT for BRAF V600E+ BTC (emergent KRAS G12D in 1, NRAS Q61K in 1, polyclonal KRAS G12D, G12V, G13D in 1), 2/13 pts who received FGFR TT for FGFR2 fusion+ BTC (KRAS Q61H in 1, NRAS Q61R in 1), and 2/7 pts who received HER2 TT for ERBB2-amplified BTC (KRAS G12C in 1, KRAS amp in 1). Serial cfDNA also revealed canonical FGFR2 resistance mutations in 3 pts who received FGFR TT, as well as loss of index ERBB2 amp in 2, acquired ERBB2 resistance mutation in 1, acquired MYC amp in 2, and MET amp in 1 pt who received HER2 TT. Conclusions: cfDNA NGS in pts with BTC may assist with prognostication in advanced disease and can identify novel patterns of resistance, including frequent emergence of RAS alterations at resistance across multiple TTs. These may identify therapeutic opportunities for KRAS- and NRAS-directed therapeutics in development, and underscore the importance of serial cfDNA profiling.

TYRA-430: First reversible FGFR4/3 inhibitor designed to overcome current challenges in FGF19-driven hepatocellular carcinoma treatment.

583 Background: Hepatocellular carcinoma (HCC) is an aggressive malignancy that accounts for approximately 80-90% of all primary liver cancers and is projected to become the third leading cause of cancer-related mortality by 2030. Previous work demonstrated that human Fibroblast Growth Factor 19 (FGF19) was overexpressed in 20-30% of HCC, thereby exerting an oncogenic effect via signaling through its cognate receptors FGFR4, FGFR3, and the co-receptor Klotho b (KLB). Multiple selective covalent FGFR4 inhibitors have been clinically evaluated in FGF19-overexpressing HCC. However, selective inhibition of FGFR4 alone was insufficient and resulted in low response rates and limited duration, likely due to redundant signaling through FGFR3. Here we describe the first report on the preclinical profile of TYRA-430, a first-in-class reversible FGFR4/3 inhibitor. Methods: The preclinical profile of TYRA-430 was assessed in vitro in HCC cellular assays and in vivo in mouse xenograft models. The in vitro potency was assessed by measuring cell viability using Cell Titer-Glo 2.0 Luminescent assay. Percentage of tumor growth inhibition (TGI) was used as a measure to evaluate in vivo efficacy of TYRA-430. Results: TYRA-430 exhibited potency against Ba/F3 cells dependent on wildtype FGFR3 and FGFR4, as well as the known Cys552 and Val550 gatekeeper (GK) resistance mutations in FGFR4. In vitro data showed that TYRA-430 displayed superior potency over the reversible multi-kinase inhibitors sorafenib and lenvatinib, and the covalent FGFR4 inhibitors fisogatinib (BLU-554) and roblitinib (FGF401) in KLB/FGF-19/FGFR3/4 driven models of HCC (Hep3B, HuH-7, and JHH-7 cells). Furthermore, in a human HuH-7 HCC xenograft model in nu/nu mice, TYRA-430 achieved 96% tumor growth inhibition (TGI), compared to 75% TGI for lenvatinib and 86% TGI for FGF401. Additionally, in the GA180 FGF19-driven gastric cancer PDX model, TYRA-430 demonstrated superior efficacy with 93% tumor growth inhibition (TGI), compared to 56% TGI achieved by roblitinib. Conclusions: TYRA-430 was active and potent in multiple KLB/FGF-19/FGFR3/4 models of human hepatocellular carcinoma in vitro and in vivo . Moreover, TYRA-430 displayed potent activity against known FGFR4 resistance mutations compared to covalent FGFR4-specific inhibitors in the clinic. TYRA-430 will be investigated in a Phase 1 clinical trial in hepatocellular carcinoma and other advanced solid tumors.

Clostridioides difficile hypervirulent strain ST1 isolated from clinical stool specimens obtained from three Provinces in South Africa

Clostridioides difficile infection is a serious healthcare-associated infection linked to antimicrobial use. The severity of the disease can be associated with hypervirulent ribotypes such as RT027. The study aimed to investigate the molecular epidemiology and genomic characteristics of C. difficile isolates from private and public healthcare settings in South Africa. One hundred clinical stool specimens were cultured on cycloserine-cefoxitin-fructose agar. Conventional multiplex polymerase chain reaction (M-PCR) assays were conducted for isolate identification and detection of toxin genes. Genomic characteristics of the isolates were determined using whole genome sequencing (WGS) and data was analysed using pubMLST, EnteroBase, Pathogenwatch and CARD. One hundred clinically presumptive C. difficile positive stool specimens were collected, of which 62% (62/100) were confirmed as C. difficile by M-PCR assay. Among the 62 identified C. difficile isolates, 97% (60/62) were toxigenic, with the most dominant toxin profile being A+B+CDT+according to the M-PCR assay. The results showed that 93% (40/43) of the WGS analysed C. difficile strains clustered into clades 1 to 5. These 40 strains were categorized into 16 sequence types (STs), with ST1 (clade 2) being the most prevalent, representing 45% (18/40), this strain is an RT027-associated strain previously epidemic hypervirulent strain. One major cluster (n=18) comprising ST1 strains was identified in Gauteng Province and all the isolates associated with this cluster showed the same resistome (antimicrobial resistance genes and mutations: CDD-1, aac (6')-Ie-aph (2″)-Ia, PnimBG and Thr82Ile). The study also identified one strain as ST11, this strain is well known for its zoonotic potential, and two strains were identified as ST37 known as an epidemic strain. Strains from public healthcare settings exhibited genetic similarity, while those from private settings showed greater genetic diversity. The study reported, for the first time, hypervirulent strains ST1 in Africa and ST11 in South Africa, with a minimum spanning tree indicating an ongoing ST1 outbreak.

INSIGHT: A phase 3, randomized, open-label study of ripretinib vs sunitinib in patients with advanced gastrointestinal stromal tumor previously treated with imatinib with KIT exon 11 + 17/18 mutations.

TPS848 Background: Gastrointestinal stromal tumor (GIST) is the most common gastrointestinal sarcoma, with approximately 80% of cases driven by KIT mutations. Most patients (pts) with advanced GIST experience disease progression following first-line treatment with imatinib due to KIT secondary resistance mutations occurring most commonly in the ATP-binding pocket (exons 13/14) and/or activation loop (exons 17/18). Sunitinib is approved as second-line therapy for advanced GIST. Ripretinib is a switch-control tyrosine kinase inhibitor approved for pts with GIST who received prior treatment with 3 or more kinase inhibitors, including imatinib. In the INTRIGUE phase 3 study (NCT03673501) in second-line therapy for advanced GIST, ripretinib was not superior to sunitinib in terms of progression-free survival (PFS); however, a more favorable safety profile was observed with ripretinib vs sunitinib (Bauer S et al. J Clin Oncol . 2022). Exploratory mutational analysis from INTRIGUE using baseline circulating tumor DNA (ctDNA) demonstrated that pts harboring primary KIT exon 11 mutations with secondary resistance mutations exclusively in KIT exons 17/18 derived PFS benefit with ripretinib vs sunitinib (median, 14.2 vs 1.5 months; HR, 0.22; 95% CI, 0.11 to 0.44; nominal P <0.0001; Heinrich MC et al. Nat Med . 2024). Here, we describe an ongoing phase 3 study for pts with advanced GIST previously treated with imatinib harboring KIT exon 11 + 17/18 mutations. Methods: INSIGHT (NCT05734105) is a phase 3, randomized, open-label study designed to evaluate the efficacy of ripretinib vs sunitinib in pts with advanced GIST previously treated with imatinib and who harbor KIT exon 11 + 17/18 mutations. Eligible pts must be ≥18 years old with histologically confirmed GIST and co-occurring KIT exon 11 + 17/18 mutations confirmed by ctDNA analysis. Pts must also have advanced disease with ≥1 measurable lesion per modified Response Evaluation Criteria in Solid Tumors (mRECIST) v1.1, radiologic progression on imatinib, and an Eastern Cooperative Oncology Group performance status ≤2. Key exclusion criteria include a KIT exon 9, 13, or 14 mutation confirmed via ctDNA analysis at screening and prior treatment with another line of therapy in addition to imatinib for advanced GIST. A total of 54 pts will be randomized (2:1) to receive ripretinib 150 mg once daily (QD; continuous) or sunitinib 50 mg QD (4 weeks on/2 weeks off) in 6-week cycles. The primary endpoint is PFS by independent radiologic review (IRR) per mRECIST v1.1; key secondary endpoints are objective response rate by IRR using mRECIST v1.1 and overall survival. Safety and patient-reported outcome measures will also be assessed. Pts randomized to the sunitinib arm may cross over to the ripretinib arm upon disease progression. This abstract was originally presented at ASCO 2023. Clinical trial information: NCT05734105 .

From challenges to solutions: A review of fourth-generation EGFR tyrosine kinase inhibitors to overcome the C797S triple mutation in non-small cell lung cancer.

This Review discusses recent advancements in the development of fourth-generation "Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors (EGFR-TKIs)" targeting resistance mutations, with an emphasis on the C797S mutation in "Non-small Cell Lung Cancer (NSCLC)". While first, second, and third-generation EGFR-TKIs have made significant progress in overcoming EGFR kinase resistance, the emergence of the EGFR-C797S mutation poses a substantial challenge, particularly in the context of resistance to Osimertinib. Fourth-generation TKIs are classified into ATP-competitive, allosteric, and ortho-allosteric inhibitors, with the goal of enhancing specificity for mutant EGFR while minimizing off-target effects on wild-type EGFR to reduce toxicity. This Review provides a detailed analysis of structural modifications and their impact on drug potency and selectivity, with the aim of improving efficacy against resistant NSCLC. Preclinical and early-phase clinical trials of these inhibitors are promising, though further optimization of pharmacokinetic and safety profiles is crucial for future clinical success. This work offers key insights for medicinal chemists in the design and development of fourth-generation EGFR inhibitors to address drug-resistant mutations in NSCLC.

Evaluation of a next generation sequencing assay for Hepatitis B antiviral drug resistance on the oxford nanopore system.

Next-generation sequencing (NGS) for Hepatitis B virus (HBV) antiviral resistance (AVR) testing is a highly sensitive diagnostic method, able to detect low-level mutant subpopulations. Our clinical virology laboratory previously transitioned from DNA hybridization (INNO-LiPA) to NGS, initially with the GS Junior System and subsequently the MiSeq. The Oxford Nanopore Technology (ONT) sequencing system was evaluated for HBV resistance testing, with regards to sequencing accuracy and turn-around time. We performed amplicon sequencing of the HBV polymerase gene from patient plasma and external quality assessment (EQA) samples on the MiSeq Reagent Nano Kit v2 and GridION ONT with R10.4.1 flowcells. Mutational analysis and genotyping were performed by DeepChek®Assay-HBV (version 2.0). A total of 49 patient samples and 15 EQA samples were tested on both the MiSeq and ONT. There was high agreement for both patient and EQA samples between the MiSeq and ONT systems, with regards to total drug resistance mutations detected and total patient sample agreement, 68/70 (97 %) and 47/49 (96 %), respectively. The ONT NGS platform provided accurate HBV AVR results, with improved turn-around times. Sequencing error rates at AVR codons were below 1 %.

Peak part 1 summary: A phase 3, randomized, open-label, multicenter clinical study of bezuclastinib (CGT9486) and sunitinib combination versus sunitinib in patients with gastrointestinal stromal tumors (GIST).

826 Background: After initial response to first line therapy with imatinib, GISTs commonly progress due to secondary resistance mutations in KIT. As the KIT mutation targeting profiles of bezuclastinib (type I TKI) and sunitinib are distinct, when combined they inhibit a broad spectrum of secondary KIT mutations. Herein we report extended experience of patients treated with 2 nd line combination bezuclastinib and sunitinib, including response assessment and safety. Methods: Peak (NCT05208047), a global randomized Phase 3, open-label study, aims to evaluate efficacy and safety of bezuclastinib + sunitinib vs sunitinib in GIST pts with imatinib intolerance or resistance. In Part 1a of the 3-part study, the dose of an optimized formulation of bezuclastinib was escalated in serial cohorts to achieve a target exposure comparable to that achieved at the RP2D established in the prior Phase 1b/2a study. Part 1b evaluated the interaction between bezuclastinib + sunitinib. Key inclusion: adult with locally advanced, metastatic and/or unresectable GIST, ≥1 measurable lesion according to modified RECIST v1.1, and ECOG PS 0 to 2. Part 1 completed enrollment in Apr 2023. Based upon PK and safety, a dose of bezuclastinib 600 mg QD + sunitinib 37.5 mg QD was selected for Part 2. All Part 1 data reported herein are as of Aug 2023; updated safety and efficacy will be presented. Results: Part 1 has completed enrollment with 19 pts in Part 1a and 23 in 1b. In Part 1a, Cohort 1 included 5 pts starting at bezuclastinib 300 mg QD + sunitinib 37.5 mg QD; Cohort 2 included 14 pts at bezuclastinib 600 mg QD + sunitinib 37.5 mg QD. Pt characteristics in Part 1a+1b: median age - 60 yrs (range: 33-77); 81% men; 98% ECOG PS 0-1; 98% metastatic and 2% locally advanced. The majority of TEAEs were low grade and reversible with low rate (38%) of Grade 3+ events. There were limited (24%) dose reductions and infrequent (n=2) discontinuations due to TEAEs. Three pts experienced serious AEs possibly associated with study medications. In pts evaluable for response (received ≥1 cycle of study treatment and had assessments at baseline and post-baseline [n=40]), the objective response rate (ORR) was 20% (6 confirmed PRs, 2 unconfirmed PRs). Data remain immature to estimate median PFS for Part 1 pts. In a subset of pts with prior imatinib only (n=6), the closest approximation for pts enrolling in Part 2, the ORR was 33% (2 confirmed PRs). The majority of 2nd-line pts remain on treatment past 12 months. Conclusions: Data from Peak Part 1 show an encouraging safety and tolerability profile generally consistent with published sunitinib monotherapy experience. ORR in evaluable pts from Part 1 was 20%; ORR in 2 nd line pts was 33%. Part 2 of the Peak study is actively enrolling pts globally at the selected dose of bezuclastinib 600 mg QD + sunitinib 37.5 mg QD versus sunitinib 37.5 mg QD. Clinical trial information: NCT05208047 .

P-1344. Molecular Characterization of Daptomycin Non-susceptible Staphylococcus aureus

Abstract Background Staphylococcus aureus (SA) is the leading cause of bacteremia in hospitalized patients. With limited therapeutic options, increasing use of daptomycin (DAP) has resulted in the emergence of DAP non-susceptible (DNS) SA strains. Nevertheless, the mechanisms of resistance in DNS SA are not fully understood. Proposed mechanisms include genetic and phenotypic changes affecting the cell membrane and cell wall. However, studies have been limited to single pairs of isolates or isolates that are laboratory derived. Methods We performed whole-genome sequencing (WGS) on clinically obtained SA blood isolates at Henry Ford Health, a comprehensive, integrated, health care organization in Southeast Michigan from 2005-2023. DNS was defined as MIC >1. Sequencing libraries were created using QIAseq FX DNA Library Kit (Qiagen, USA) according to manufacturer’s instructions and sequenced on NovaSeq 6000 (Illumina, San Diego, USA). FastQ files were further analyzed for the presence of genetic variations using a WGS bioinformatic pipeline based on de novo assembly. Results We sequenced 199 SA isolates from 59 patients, of which 88 (44%) were DNS. 43 (73%) patients had multiple isolates, whereas 16 (27%) only had one. All DNS isolates except one were MRSA. 46 (52%) DNS isolates had amino acid substitution in the MprF and 2 (2%) in the cls genes, which are known to be associated with DNS. 10 (11%) DNS isolates were found to have substitutions (S829L and L406I) in the MprF gene that have not been previously reported. Mutations in cls, rpoB, rpoC, walK and agrA genes were also detected. All isolates with known mutations were exposed to DAP prior to development of DNS. 30 (34%) DNS isolates did not have mutations associated with resistance. Of these, only 13 (43%) had prior exposure to DAP, 9 (30%) were only exposed to vancomycin, and 11 (37%) were not exposed to any antibiotics. ST5 and ST8 were the most common sequence types. Conclusion In this study involving a large number of clinical SA isolates, the majority of patients who developed DNS due to MprF mutations were exposed to DAP, likely due to selection pressure. However, more than one-third of DNS isolates did not exhibit resistance mutations. Further studies are needed to identify other mechanisms of DAP resistance, especially in those with no prior antibiotic exposure. Disclosures Marcus Zervos, MD, Johnson and johnson: Grant/Research Support|Moderna: Grant/Research Support

The status of pyrethroid resistance mutation frequencies in Varroa destructor populations in the most important beekeeping areas of Türkiye

The Varroa destructor (hereafter referred to as Varroa) is a major pest of honeybees that is generally controlled using pyrethroid-based acaricides. However, resistance to these insecticides has become a growing problem, driven by the acquisition of knockdown resistance (kdr) mutations in the mite’s voltage-gated sodium channel (vgsc) gene. Resistance mutations in the vgsc gene, such as the L925V mutation, can confer resistance to pyrethroids like flumethrin and tau-fluvalinate. Monitoring genotypic resistance through molecular mutation screening is crucial for tracking and mitigating resistance spread. In this study, the frequency of resistance mutations in the vgsc was examined using a Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) approach in Varroa populations sampled throughout the Mediterranean, Aegean, and Black Sea regions of Türkiye. Considering all the samples analyzed, the results demonstrated a mean resistance allele frequency of 83.29%, indicating a relatively high frequency of resistant alleles. We observed 94.58%, 85.71%, and 69.58% resistant allele frequencies in populations sampled from the Mediterranean, Aegean, and Black Sea regions, respectively, in our study. The results of our investigation demonstrated substantial regional variations in the frequencies of resistant alleles among Varroa populations throughout Türkiye, with notably elevated resistance levels observed in the Mediterranean and Aegean regions. Due to the significant resistance mutation frequency differences between both provinces and regions, long-term monitoring of resistance alleles and the planning of regional control strategies are required for effective control of this pest.

Characterization of Bozitinib as a potential therapeutic agent for MET-amplified gastric cancer

Hyperactive c-Met signaling pathway caused by altered MET is a common mechanism underlying gastric cancer and represents an attractive target for the treatment of gastric cancer with MET alterations. However, no c-Met kinase inhibitors are currently approved specifically for the treatment of c-Met-amplified gastric cancer. Recently, bozitinib, a highly selective c-Met kinase inhibitor, has shown remarkable potency in selectively inhibiting MET-altered non-small cell lung cancer and secondary glioblastoma. In this study, we investigate the antitumor activity of bozitinib against MET-amplified gastric cancer and elucidate its molecular mechanism. Bozitinib demonstrates a strong effect on MET-amplified gastric cancer cells by blocking the c-Met signaling pathway, leading to the inhibition of cell proliferation and survival, as well as the induction of G0/G1 phase arrest and apoptosis. Structurally, bozitinib is optimally embedded in the ATP pocket of c-Met and firmly binds via an extensive interaction network. In addition, bozitinib efficiently inhibits c-Met resistance-conferring mutations G1163R and Y1230H, although its potency is significantly decreased against the D1228N and Y1230C mutations. Overall, our study reveals the molecular mechanism of bozitinib against c-Met, highlights its ability to overcome acquired resistance mutations, and provides valuable insights into further design and improvement of selective c-Met inhibitors.

The southern house mosquito Culex quinquefasciatus in Abu Dhabi, UAE, is developing resistance to deltamethrin insecticide

Culex quinquefasciatus is a widely spread mosquito species that poses a significant public health threat in many countries. This insect vector is present in the United Arab Emirates (UAE), yet no studies have been conducted on its resistance to any insecticide group. Research shows that controlling mosquitoes is crucial to eliminating mosquito-borne diseases, but when these vectors develop insecticide resistance, the situation can escalate dangerously out of control. This study aimed to identify a knockdown resistance (kdr) mutation L1014F using molecular tools. Additionally, it aimed to assess deltamethrin resistance using the Centers for Disease Control and Prevention (CDC) bottle bioassay. We screened Cx. quinquefasciatus adults (N = 174) for the presence of the mutation using allele-specific PCR (AS-PCR) and DNA sequencing. We detected the mutation and found the kdr allele in all the sampled locations. Furthermore, the CDC bottle bioassay revealed deltamethrin resistance from only one sampling location. To our knowledge, this is the first report of insecticide resistance in Cx. quinquefasciatus in the UAE. Our findings show the need for continued insecticide resistance monitoring for effective mosquito control in the UAE.

Case report: A panorama gene profile of ovarian cancer metastasized to axillary lymph node

BackgroundOvarian cancer is among the most lethal gynecologic malignancies, with a high proportion of patients diagnosed at advanced stages, leading to poor survival outcomes. Axillary lymph node metastasis from ovarian cancer is extremely rare and the mechanism is still unclear.MethodsA comprehensive set of clinical and gynecologic oncology assessments were performed, including ultrasound, mammography, MRI, transvaginal ultrasound, and tissue staining. To unravel the carcinogenesis, the next-generation sequencing (NGS) was performed.ResultsConventional examinations and imaging suggested the presence of both occult breast cancer and ovarian cancer. However, immunohistochemical staining confirmed the diagnosis of high-grade serous ovarian carcinoma. Further analysis of NGS identified two novel missense mutations, D326E in BTK (Bruton’s tyrosine kinase) at SH2 domain and D251E in EPHA5 (EPH receptor A5), along with other known cancer- associated mutations. These mutations, particularly the novel missense mutations, may lead to metastasis to the axillary lymph nodes and drug resistance. Therefore, based on these findings, the chemotherapy regimen was adjusted accordingly.ConclusionThis is the first report on the panorama gene profile of ovarian cancer metastasis to axillary lymph node and we found two novel mutations (BTK pD326E and EPHA5 pD251E). This study unraveled the potential mechanism of genetic mutation for tumor metabolism, drug resistance, and metastasis.

Defective HIV-1 DNA pol sequences are not associated with HIV-1 DNA levels and drive most APOBEC-context drug resistance mutations.

The specificity of HIV-1 DNA genotypic resistance tests (GRTs) is hampered by the detection of the APOBEC-context drug resistance mutations (AC DRMs), usually harboured by replication-incompetent proviruses. We sought factors associated with defective sequences in the HIV-1 pol region. In addition, AC DRMs and their link with defective sequences were investigated. We included ART-treated patients with viral suppression or plasma viral load (VL) lower than 200 copies/mL, who underwent HIV-1 DNA genotyping, with successful sequencing of protease (PR), reverse transcriptase (RT) and integrase (IN) regions. Sequencing was performed using either the Sanger method or the Sentosa® NGS approach with a 20% cut-off. All hypermutated sequences and/or those containing at least one stop codon were considered defective. A total of 613 HIV-1 DNA GRTs were analysed. Defective sequences were identified for 186 samples (30.3%) including 65 PR sequences, 92 RT sequences and 65 IN sequences. No association, including HIV-1 DNA levels, was found with the detection of defective pol sequences. A total of 226 AC DRMs were recorded in all sequences. Most of these mutations (78%) were harboured by defective sequences. AC DRMs did not emerge in the plasma viral population, and likely do not impact the virological response to ART. Defectives pol sequences were not associated with HIV-1 DNA levels and harboured most of the AC DRMs. Such mutations likely have no clinical impact, and should not be reported in routine practice. Consensus guidelines for reporting HIV-1 DNA GRTs are needed, especially for the assessment and management of AC DRMs.

Multiplex digital PCR enables sensitive detection of resistance to BTK inhibitors.

The advent of BTK inhibitors has been transformative in the management of patients with chronic lymphocytic leukemia or other B-cell lymphoproliferative disorders. However, emergence of BTK or PLCG2 mutations lead to resistance to these compounds and are now a growing concern in clinical practice. Assessing BTK mutations is now becoming a priority to guide the therapeutic decision at further relapse. To this end, targeted next-generation sequencing (NGS) is a valid tool, but lack of sensitivity and the required time for delivering results remain major challenges. Digital PCR could be more sensitive but is also limited by the number of mutations that can be screened. We here overcame these challenges by multiplexing digital PCR (mdPCR) in three assays that can cover 96% of ibrutinib-resistant cases. We investigated a cohort of 28 patients progressing on ibrutinib and for whom NGS revealed BTK mutations (C481S, C481F and C481R) and/or PLCG2 R665W mutation. Overall, 49 mutations were detected by NGS and 68 by mdPCR. We found mdPCR to bemore sensitive than NGS, particularly at low allelic frequencies, making it more suitable for the detection and quantification of small mutated clones. Thus, mdPCR offers high sensitivity, is expected to be more rapid and cost-effective than NGS in detecting resistance mutations to improve the therapeutic choice at relapse after exposure to BTK inhibitors.

ACQUIRED MUTATIONS IN PATIENTS WITH RELAPSED/REFRACTORY CLL WHO PROGRESSED IN THE ALPINE STUDY.

Some CLL patients who develop progressive disease (PD) during treatment with covalent Bruton tyrosine kinase inhibitors (cBTKi) acquire pathway resistance mutations in BTK or PLCG2. Here, we report gene mutation data from paired baseline and PD peripheral blood samples from 52 patients (zanubrutinib, n=24; ibrutinib, n=28) who, at an early median follow-up time of 25.7 months, progressed on zanubrutinib or ibrutinib treatment in the ALPINE trial (NCT03734016). No BTK mutations were observed at baseline; at PD, eight patients (zanubrutinib, n=5, ibrutinib, n=3) acquired a total of 17 BTK mutations. Among BTK mutations, 82.4% (zanubrutinib, n=11/14; ibrutinib, n=3/3) were at C481. Non-C481 mutations were detected in 12.5% (3/24) of zanubrutinib-treated patients (L528W: n=2, cancer cell fraction [CCF]=9.58% and 17.6%; A428D, n=1, CCF=37.03%); these were not detected in ibrutinib-treated patients. At baseline, 48/52 patients had ≥1 driver gene mutation/s, most frequently in: NOTCH1 (n=21), TP53 (n=19), BRAF (n=10), SF3B1 (n=8), and ATM (n=8). At PD, acquired driver gene mutations were observed in one zanubrutinib-treated patient (TP53, XPO1) and five ibrutinib-treated patients (TP53, n=1 patient; SETD2, n=1; SF3B1, n=1; ASXL1, n=2). Baseline driver gene mutations were not associated with later development of BTK mutations, but patients with ≥2 baseline driver gene mutations were more likely to acquire BTK mutations at PD. In conclusion, patients in this data set had a short treatment duration and a low incidence of BTK mutations, suggesting that mechanisms other than BTK/PLCG2 mutations are driving most instances of early PD. NCT03734016.

Design, Synthesis, and SAR of Covalent KIT and PDGFRA Inhibitors─Exploring Their Potential in Targeting GIST.

Gastrointestinal stromal tumors (GIST), driven by KIT and PDGFRA mutations, are the most common mesenchymal tumors of the gastrointestinal tract. Although tyrosine kinase inhibitors (TKIs) have advanced treatment, resistance mutations and off-target toxicity limit their efficacy. This study develops covalent TKIs targeting drug-resistant GIST through structure-based design, synthesis, and biological evaluation. SAR studies provided key insights into mutant KIT and PDGFRA interactions, and the first crystal structure of PDGFRA bound to a covalent inhibitor is reported. These findings highlight the promise of covalent inhibitors for overcoming resistance and advancing safer, more effective therapies for advanced GIST.

Prevalence of drug resistance mutations in low-level viremia patients under antiretroviral therapy in Southwestern China: a cross-sectional study.

This study aimed to evaluate the prevalence and characteristics of drug resistance mutations (DRMs) in patients with low-level viremia (LLV) in Southwestern China, as it has become a growing challenge in AIDS clinical practice. This cross-sectional study was performed in Yunnan Province, Southwestern China. LLV was defined as 50-999 copies/mL of plasma viral load with antiretroviral therapy (ART) for at least 6 months. HIV-1 DRM detection used validated in-house protocol. A total of 470 sequences were obtained, and 13 HIV-1 genotypes were identified, among which CRF08_BC (47.5%), CRF07_BC (22.3%) and CRF01_AE (10.0%) subtypes were the most prevalent. The overall prevalence of DRMs was 45.7% (215/470), and the prevalence of DRMs to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs) was 39.4% (185/470), 20.6% (97/470) and 5.3% (25/470), respectively. The most common NNRTI-associated mutations were K103N (16.0%), E138A (6.6%), V179D (6.6%) and P225H (4.9%), and those in NRTIs were M184V (17.0%), D67N (3.4%) and K65R (3.0%). PI-associated mutations were infrequent, occurring in less than 1.8% of cases. The prevalence of NNRTI-associated mutations (K101E and Y188C) was found to be statistically significant among various LLV groups. Additionally, significant variations were observed in the prevalence of NNRTI-associated mutations (V106I, V106M, E138A and P225H), NRTI-associated mutation (K65R) and PI-associated mutations (L33F and Q58E) across different subtypes. The prevalence of DRMs in ART-experienced patients with LLV was high, and HIV-1 genotypes exhibited diversity in Yunnan Province. These findings indicate that regular DRM monitoring during LLV episodes was essential for effective clinical treatment and management in this region.

Ganciclovir Resistance-Linked Mutations in the HCMV UL97 Gene: Sanger Sequencing Analysis in Samples from Transplant Recipients at a Tertiary Hospital in Southern Brazil.

Background/Objectives: Human cytomegalovirus (HCMV) DNAemia remains a significant concern for transplant recipients, largely due to mutations in the viral genome that may lead to antiviral-resistant strains. Mutations in the UL97 gene are frequently associated with resistance to ganciclovir (GCV), highlighting the importance of early mutation detection to effectively manage viremia. This study aimed to optimize a Sanger sequencing protocol for analyzing GCV resistance-linked mutations in the HCMV UL97 gene from plasma samples of transplant patients treated at Hospital de Clínicas de Porto Alegre, Rio Grande do Sul, Brazil. Methods: A nested-PCR approach combined with a touchdown PCR method was employed to enhance the sensitivity and specificity of the sequencing analysis. Results: The study sample included various transplants, encompassing solid organ and bone marrow recipients. Among 16 sequenced samples, 8 exhibited nucleotide substitutions resulting in amino acid changes. Notably, the A594V and C603W mutations, associated with GCV resistance, were identified in four samples. Additionally, three mutations with unknown phenotypic impact (P509L, A628T, and H662Y) and two viral polymorphisms (N510S and D605E) were detected. Furthermore, double peaks in the Sanger electropherograms, indicative of mixed viral populations of HCMV were observed in seven samples. Conclusions: The optimized Sanger sequencing protocol provides a cost-effective solution for detecting GCV resistance mutations in HCMV UL97 among transplant recipients. This approach could improve the understanding of HCMV strain dynamics and serve as a valuable tool for long-term patient monitoring, particularly within resource-constrained settings such as the public health systems of middle-income countries.