Lab validation of an ultrasensitive ctDNA pan-cancer MRD assay using whole-genome sequencing

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Background: Minimal residual disease (MRD) monitoring using liquid biopsy for solid tumors requires a highly sensitive and specific assay that can overcome the limitation of low abundance cfDNA in a standard blood draw. We developed a whole-genome sequencing (WGS)-based assay to detect the presence of circulating tumor DNA (ctDNA) in plasma. The C2i assay is a tumor-informed assay that uses personalized tumor signature, advanced noise models, and artificial intelligence (AI) modalities to interrogate plasma for the presence of ctDNA longitudinally. Methods: The C2i test was developed in accordance with CAP/CLIA and New York state validation principles. We used contrived samples to establish analytical validation of the assay performance, which was then validated with a large clinical cohort of early-stage patients across various cancer types. Briefly, aggregated tumor signatures derived from cancer cell lines were fragmented and spiked into a contrived healthy plasma pool; the mixed samples were used to assess the presence of tumor DNA signature down to tumor fractions of 10e-4. Positive samples are identified by tumor-derived variants detected above the noise levels. Noise modeling was established using a panel of normal (PON) approach. We assessed the analytical sensitivity, specificity, and accuracy using 348 contrived samples derived from five different cancer cell lines. Reproducibility and precision were assessed with multiple replicates, and statistical concordance was reported. This validation was complemented by a cohort of 200 patients and ̃1000 plasma samples across a variety of cancer types including, NSCLC, MIBC, CRC, GBM, Breast Cancer, and a mixture of other cancer types. Results: Cancer cell lines, representing the five most prevalent disease indications, used for determining analytical sensitivity are as follows: CRC HT-29, Breast SK-BR3, Bladder HT-1376, Lung HCI-H526, and Prostate LNCaP. The cell line DNA was enzymatically fragmented and size-selected to mimic ctDNA. This ctDNA was spiked into cfDNA extracted from healthy volunteers at various dilution levels, varying from 10e0 to 10e-4. The 95% probability of detecting ctDNA was established at 10e-4. The reproducibility of tumor signature between replicates was assessed to be greater than 90%. The assay was performed using both normal and maximum input amounts. These performance estimates were then validated on a cohort of plasma collected from early-stage (stage I-III) patients across various cancer types. Conclusions: C2i MRD test is an ultrasensitive pan-cancer MRD monitoring assay used in several clinical trials across the world. We present an extensive analytical and clinical validation of the assay supporting its high performance.

Development of multifunctional metabolic synergists to suppress the evolution of resistance against pyrethroids in insects that blood feed on humans

BACKGROUND

Pyrethroids are the insecticides of choice when exposure to humans is likely, such as occurs in vector and public-health-related control programs. Unfortunately, the pyrethroids share a common resistance mechanism with dichlorodiphenyltrichloroethane (DDT), knockdown resistance (kdr), and prior extensive use of DDT has predisposed the pyrethroids to cross-resistance via kdr. Given the widespread occurrence of kdr, the use of synergists with pyrethroids is considered to be prudent to guard against the selection of multiply resistant insects.

RESULTS

3-Phenoxybenzyl hexanoate (PBH) was synthesized as a multifunctional pyrethroid synergist that, besides being a surrogate substrate for sequestration/hydrolytic carboxylesterases, now also functions as a substrate for oxidative xenobiotic metabolism. The addition of PBH to permethrin-treated females of the ISOP450 strain of Culex pipiens quinquefasciatus resulted in a threefold increase in synergism, as judged by the synergistic ratio. Similarly, PBH synergized the action of deltamethrin sixfold on females of the common bed bug, Cimex lectularius, and was 2.8-fold more synergistic than piperonyl butoxide (PBO).

CONCLUSIONS

PBH synergized the action of both type I and type II pyrethroids in a mosquito vector (Cx. p. quinquefasciatus) and in a public-health pest, C. lectularius, respectively, indicating a broad spectrum of action on blood-feeding insects. PBH appears to have residual properties similar to permethrin and is itself non-toxic, unlike PBO, and therefore should be compatible with existing pyrethroid formulations used for insecticide-treated nets and home/residential sprays.

Comparison of the transcriptional profiles of head and body lice

Head and body lice are both blood-feeding parasites of humans although only the body louse is a potent disease vector. In spite of numerous morphological and life history differences, head and body lice have recently been hypothesized to be ecotypes of the same species. We took a comparative genomics approach to measure nucleotide diversity by comparing expressed sequence tag data sets from head and body lice. A total of 10 771 body louse and 10 770 head louse transcripts were predicted from a combined assembly of Roche 454 and Illumina sequenced cDNAs from whole body tissues collected at all life stages and during pesticide exposure and bacterial infection treatments. Illumina reads mapped to the 10 775 draft body louse gene models from the whole genome assembly predicted nine presence/absence differences, but PCR confirmation resulted in a single gene difference. Read per million base pair estimates indicated that 14 genes showed significant differential expression between head and body lice under our treatment conditions. One novel microRNA was predicted in both lice species and 99% of the 544 transcripts from Candidatus riesia indicate that they share the same endosymbiont. Overall, few differences exist, which supports the hypothesis that these two organisms are ecotypes of the same species.

Ivermectin acts as a posteclosion nymphicide by reducing blood feeding of human head lice (Anoplura: Pediculidae) that hatched from treated eggs

The 0.5% ivermectin topical cream formulation was not directly ovicidal to treated eggs of head lice, as hatchability was not decreased. Nevertheless, the percent of hatched lice from treated eggs that took a blood meal significantly decreased (80-95%) compared with lice that hatched from untreated eggs and all treated lice died within 48 h of hatching, including those that fed. Dilutions of ivermectin formulation of 0.15 and 0.2 microg/ml, which were topically applied to 0-8 d old eggs, were not lethal to lice at 24 h posteclosion. However, 9 and 16% less lice fed when hatched from these treated eggs, respectively. Total [3H] inulin ingested by untreated first instars significantly increased over a 48 h feeding interval but was significantly less in instars that hatched from eggs receiving the 0.15 (36% less) and 0.2 (55% less) microg/ml ivermectin treatments compared with placebo. The reduced feeding that occurred after the 0.15 and 0.2 microg/ml ivermectin treatments occurred in the absence of mortality and suggests a unique mode of action of ivermectin on feeding that is separate from the mode of action of ivermectin leading to mortality. Failure of hatched instars to take a blood meal after egg treatments with formulated ivermectin is likely responsible for its action as a posteclosion nymphicide.

Simplify, simplify: Lifestyle and compact genome of the body louse provide a unique functional genomics opportunity

The body louse, with its recently sequenced genome, is now primed to serve as a powerful model organism for addressing fundamental questions relating to how insects interact with their environment. One characteristic of the body louse that facilitates this research is the size of its genome-the smallest insect genome sequenced to date. This diminutive genome must nonetheless control an organism that senses and responds to its environment, reacting to threats of corporal and genomic integrity. Additionally, the body louse transmits several important human diseases compared to its very close relative, the head louse, which does not. Therefore, these two organisms comprise an excellent model system for studying molecular mechanisms associated with vector competence. To understand more fully the development of vector/pathogen interactions, we have developed an in vitro bioassay system and determined that the body louse genome appears to contain the genes necessary for RNAi. The body louse will therefore be useful for determining the set of conditions permissive to the evolution of vector competence.

Decreased detoxification genes and genome size make the human body louse an efficient model to study xenobiotic metabolism

The human body louse, Pediculus humanus humanus, has one of the smallest insect genomes, containing ∼10 775 annotated genes. Annotation of detoxification [cytochrome P450 monooxygenase (P450), glutathione-S-transferase (GST), esterase (Est) and ATP-binding cassette transporter (ABC transporter)] genes revealed that they are dramatically reduced in P. h. humanus compared to other insects except for Apis mellifera. There are 37 P450, 13 GST and 17 Est genes present in P. h. humanus, approximately half the number found in Drosophila melanogaster and Anopheles gambiae. The number of putatively functional ABC transporter genes in P. h. humanus and Ap. mellifera are the same (36) but both have fewer than An. gambiae (44) or Dr. melanogaster (65). The reduction of detoxification genes in P. h. humanus may be a result of this louse's simple life history, in which it does not encounter a wide variety of xenobiotics. Neuronal component genes are highly conserved across different insect species as expected because of their critical function. Although reduced in number, P. h. humanus still retains at least a minimum repertoire of genes known to confer metabolic or toxicokinetic resistance to xenobiotics (eg Cyp3 clade P450s, Delta GSTs, B clade Ests and B/C subfamily ABC transporters), suggestive of its high potential for resistance development.

Biochemical and molecular analysis of deltamethrin resistance in the common bed bug (Hemiptera: Cimicidae)

This study establishes deltamethrin resistance in a common bed bug, Cimex lectularius L., population collected from New York City (NY-BB). The NY-BB population was 264-fold more resistant to 1% deltamethrin in contact bioassay compared with an insecticide-susceptible population collected in Florida (FL-BB). General esterase, glutathione S-transferase, and 7-ethoxycoumarin O-deethylase activities of NY-BB were not statistically different from those of FL-BB. cDNA fragments that encoded the open reading frame of voltage-sensitive sodium channel alpha-subunit genes from the FL-BB and NY-BB populations, respectively, were obtained by homology probing polymerase chain reaction (PCR) and sequenced. Sequence alignment of the internal and 5' and 3' rapid amplification of cDNA ends (RACE) fragments generated a 6500-bp cDNA sequence contig, which was composed of a 6084-bp open reading frame (ORF) encoding 2027 amino acid residues and 186-bp 5' and 230-bp 3' untranslated regions (5' and 3' UTRs, respectively). Sequence comparisons of the open reading frames of the alpha-subunit genes identified two point mutations (V419L and L925I) that were presented only in the NY-BB population. L925I, located the intracellular loop between IIS4 and IIS5, has been previously found in a highly pyrethroid-resistant populations of whitefly (Bemisia tabaci). V419L, located in the IS6 transmembrane segment, is a novel mutation. A Val to Met mutation at the corresponding position of the bed bug V419, however, has been identified in the tobacco budworm as a kdr-type mutation. This evidence suggests that the two mutations are likely the major resistance-causing mutations in the deltamethrin-resistant NY-BB through a knockdown-type nerve insensitivity mechanism.

Determination of permethrin resistance allele frequency of human head louse populations by quantitative sequencing

A quantitative sequencing (QS) protocol that detects the frequencies of sodium channel mutations (M815I, T917I, and L920F) responsible for knockdown resistance in permethrin-resistant head lice (Pediculus humanus capitis De Geer) was tested as a population genotyping method for use as a preliminary resistance monitoring tool. Genomic DNA fragments of the sodium channel a-subunit gene that encompass the three mutation sites were polymerase chain reaction (PCR)-1 amplified from individual head lice with either resistant or susceptible genotypes, and combined in various ratios to generate standard DNA template mixtures for QS. After sequencing, the signal ratios between resistant and susceptible nucleotides were calculated and plotted against the corresponding resistance allele frequencies. Quadratic regression coefficients of the plots were close to 1, demonstrating that the signal ratios are highly correlated with the resistance allele frequencies. Resistance allele frequencies predicted by QS, using either "pooled DNA" (DNA extracted from individual louse specimens and pooled) or "pooled specimen DNA" (DNA simultaneously extracted from multiple louse specimens), agreed well with those determined by individual sequencing, confirming the reliability and accuracy of QS as a population genotyping method and validating our approach of using the pooled specimen DNA as the DNA template for QS. Our protocol for QS was determined to be highly reliable for the prediction of resistance allele frequencies higher than approximately 7.4% at the 95% confidence level. According to the resistance allele frequencies determined by QS, pyrethroid resistance varies substantially among different geographical regions, emphasizing the importance of early resistance detection and proper management strategies.

A new ivermectin formulation topically kills permethrin-resistant human head lice (Anoplura: Pediculidae)

This study examines the effectiveness of a new ivermectin formulation for the topical treatment of the human head louse, Pediculus humanus capitis De Geer (Anoplura: Pediculidae). Permethrin-resistant lice originally obtained from south Florida and maintained on an in vitro rearing system were 100% susceptible to ivermectin formulations by using a semiclinical hair tuft bioassay. The formulation was 100% effective at killing lice using 1, 0.5, and 0.25% ivermectin concentrations after 10-min exposures. As judged by the lethal time (LT)50 and LT95 values, 0.5% formulated ivermectin was 3.8 and 3.2 times faster at killing lice, respectively, than 0.5% nonformulated ivermectin, indicating that the formulation may facilitate the penetration of ivermectin into the louse. The hair tuft-based bioassay in conjunction with the in vitro rearing system provides a standardized method to assess the comparative efficacy of pediculicide formulations in a reproducible format that mimics the exposure scenario that occurs on the human scalp.

Body lice and head lice (Anoplura: Pediculidae) have the smallest genomes of any hemimetabolous insect reported to date

The human body louse, Pediculus humanus humanus L. (Anoplura: Pediculidae), is a vector of several diseases, including louse-borne epidemic typhus, relapsing fever, and trench fever, whereas the head louse, Pediculus humanus capitis De Geer (Anoplura: Pediculidae), is more a pest of social concern. Sequencing of the body louse genome has recently been proposed and undertaken by National Human Genome Research Institute. One of the first steps in understanding an organism's genome is to determine its genome size. Here, using flow cytometry determinations, we present evidence that body louse genome size is 104.7 +/- 1.4 Mb for females and 108.3 +/- 1.1 Mb for males. Our results suggest that head lice also have a small genome size, of similar size to the body louse. Thus, Pediculus lice have one of the smallest genome sizes known in insects, suggesting it may be a suitable choice as a minimal hemimetabolous genome.