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While whole genome sequencing (WGS) of cell-free DNA (cfDNA) holds enormous promise for detection of molecular residual disease (MRD), its performance is limited by WGS error rate. Here we introduce AccuScan, an efficient cfDNA WGS technology that enables genome-wide error correction at single read-level, achieving an error rate of 4.2 × 10−7, which is about two orders of magnitude lower than a read-centric de-noising method. The application of AccuScan to MRD demonstrated analytical sensitivity down to 10−6 circulating variant allele frequency at 99% sample-level specificity. AccuScan showed 90% landmark sensitivity (within 6 weeks after surgery) and 100% specificity for predicting relapse in colorectal cancer. It also showed 67% sensitivity and 100% specificity in esophageal cancer using samples collected within one week after surgery. When AccuScan was applied to monitor immunotherapy in melanoma patients, the circulating tumor DNA (ctDNA) levels and dynamic profiles were consistent with clinical outcomes. Overall, AccuScan provides a highly accurate WGS solution for MRD detection, empowering ctDNA detection at parts per million range without requiring high sample input or personalized reagents. Synopsis: A novel approach, named AccuScan, was developed for molecular residual disease (MRD) detection and immunotherapy monitoring. This technology uses whole genome sequencing (WGS) with single-read error correction for circulating tumor DNA (ctDNA) analysis. AccuScan reduced WGS error rate to less than 5 × 10−7, enabling an ultralow limit of detection for circulating tumor variant allele frequency down to the parts-per-million (PPM) range. When applied to MRD detection, AccuScan achieved 90% landmark sensitivity and 100% specificity in post-surgical colorectal cancer patients. AccuScan showed high sensitivity and specificity for MRD detection in esophageal cancer and for immunotherapy monitoring in melanoma patients. AccuScan established a simple, white blood cell-free workflow for tumor-specific variant identification and tumor-informed MRD detection. A novel approach, named AccuScan, was developed for molecular residual disease (MRD) detection and immunotherapy monitoring. This technology uses whole genome sequencing (WGS) with single-read error correction for circulating tumor DNA (ctDNA) analysis. [ABSTRACT FROM AUTHOR]

Summary: Immune‐related toxicities, otherwise known as immune‐related adverse events (irAEs), occur in a substantial fraction of cancer patients treated with immune checkpoint inhibitors (ICIs). Ranging from asymptomatic to life‐threatening, ICI‐induced irAEs can result in hospital admission, high‐dose corticosteroid treatment, ICI discontinuation, and in some cases, death. A deeper understanding of the factors underpinning severe irAE development will be essential for improved irAE prediction and prevention, toward maximizing the benefits and safety profiles of ICIs. In recent work, we applied mass cytometry, single‐cell RNA sequencing, single‐cell V(D)J sequencing, bulk RNA sequencing, and bulk T‐cell receptor (TCR) sequencing to identify pretreatment determinants of severe irAE development in patients with advanced melanoma. Across 71 patients separated into three cohorts, we found that two baseline features in circulation—elevated activated CD4 effector memory T‐cell abundance and TCR diversity—are associated with severe irAE development, independent of the affected organ system within 3 months of ICI treatment initiation. Here, we provide an extended perspective on this work, synthesize and discuss related literature, and summarize practical considerations for clinical translation. Collectively, these findings lay a foundation for data‐driven and mechanistic insights into irAE development, with the potential to reduce ICI morbidity and mortality in the future. [ABSTRACT FROM AUTHOR]

BRAF inhibitors improve melanoma patient survival, but resistance invariably develops. Here we report the discovery of a novel BRAF mutation that confers resistance to PLX4032 employing whole-exome sequencing of drug-resistant BRAF V600K melanoma cells. We further describe a new screening approach, a genome-wide piggy Bac mutagenesis screen that revealed clinically relevant aberrations ( N-terminal BRAF truncations and CRAF overexpression). The novel BRAF mutation, a Leu505 to His substitution ( BRAF L505H), is the first resistance-conferring second-site mutation identified in BRAF mutant cells. The mutation replaces a small nonpolar amino acid at the BRAF- PLX4032 interface with a larger polar residue. Moreover, we show that BRAF L505H, found in human prostate cancer, is itself a MAPK-activating, PLX4032-resistant oncogenic mutation. Lastly, we demonstrate that the PLX4032-resistant melanoma cells are sensitive to novel, next-generation BRAF inhibitors, especially the 'paradox-blocker' PLX8394, supporting its use in clinical trials for treatment of melanoma patients with BRAF-mutations. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented related to the growth of clone cells of human melanocytes from single cells.

BRAFV600E/K is a frequent mutationally active tumor-specific kinase in melanomas that is currently targeted for therapy by the specific inhibitor PLX4032. Our studies with melanoma tumor cells that are BRAFV600E/K and BRAFWT showed that, paradoxically, while PLX4032 inhibited ERK1/2 in the highly sensitive BRAFV600E/K, it activated the pathway in the resistant BRAFWT cells, via RAF1 activation, regardless of the status of mutations in NRAS or PTEN. The persistently active ERK1/2 triggered downstream effectors in BRAFWT melanoma cells and induced changes in the expression of a wide-spectrum of genes associated with cell cycle control. Furthermore, PLX4032 increased the rate of proliferation of growth factor-dependent NRAS Q61L mutant primary melanoma cells, reduced cell adherence and increased mobility of cells from advanced lesions. The results suggest that the drug can confer an advantage to BRAFWT primary and metastatic tumor cells in vivo and provide markers for monitoring clinical responses. [ABSTRACT FROM AUTHOR]

Presents abstracts of studies on pigment cells. Genetics and genomics of pigment type-switching; Expression and regulatory elements of the human melanocortin 1 receptor; Maturation and degradation of tyrosinase in the early secretory pathway.

Reviews the regulation of normal melanocyte proliferation. Synergism among mitogens in vitro; Overview of mitogens in tissues and cells; Description of melanocyte mitogens during development.

To proliferate in vitro, normal melanocytes, unlike normal fibroblasts, require specific growth factors in addition to those supplied in serum. The substances that promote melanocyte proliferation, such as 12-O-tetradecanoyl-phorbol-13-acetate (TPA) and stimulators of cyclic adenosine monophosphate (cAMP), also promote pigmentation. Consequently, cell division and expression of at least some differentiated functions are not mutually exclusive for melanocytes. At present, the only known natural growth factor that can replace TPA in normal human melanocyte cultures is basic fibroblast growth factor (bFGF). Like TPA, bFGF is effective, most of the time, only in the presence of added cAMP. Some preparations of bFGF, however, may have a highly labile, intrinsinc cAMP stimulatory activity. It is thus possible that bFGF can assume two forms, dependent on and independent of cAMP stimulatory activity. Alternatively, a second factor may exist in pituitary glands that co-purifies with bFGF but deteriorates with storage. Abnormal melanocytes in culture, such as those derived from dysplastic nevi and primary melanomas, depend on the specific factors (bFGF and cAMP), whereas melanocytes from metastatic melanomas do not [ABSTRACT FROM AUTHOR]

The BULT melanoma originated at Brown University as a spontaneous, small black nodule on the tail of an adult female mouse of the LT/Ch strain. Histological examination of a portion of the tumor indicated that it was intradermal and consisted predominantly of heavily melanized, ovoid to fusiform cells with melanin-laden macrophages scattered among them. The BULT melanoma has been maintained in LT/Ch mice for approximately 5 years by periodic transplantation, at first subcutaneously on the flanks and, more recently, intramuscularly in the hind legs. The shift in transplantation site was made following a marked decline in the growth of subcutaneous grafts. The transplants have retained the uniform deep-black melanization and general histology of the primary melanoma. Numerous melanosomes at all stages of development are found within the melanoma cells. DOPA-positive cytoplasmic vesicles are abundant. Occasional autophagic vacuoles containing clusters of melanosomes are also present. A few metastases from the transplanted melanoma have been observed in lymph nodes and on one occasion in the lungs. When grown in vitro, BULT melanoma cells do not require special growth promoting agents (e.g., TPA; cAMP) in order to proliferate. The BULT melanoma differs in one or more respects from each of the other three transplantable spontaneous mouse melanomas widely used in cancer research. In addition, it arose in a strain of mice characterized by the spontaneous death of melanocytes while the latter are engaged in synthesizing eumelanin within hair follicles. Karyotypic analysis of cultured cells showed a modal chromosome number of 68 with a range of 58-72 chromosomes. [ABSTRACT FROM AUTHOR]

Pmel 17 cDNA clones, isolated from wild-type and si/si murine melanocytes, were sequenced and compared. A single nucleotide (A) insertion was found in the putative cytoplasmic tail of the si/si Pmel 17 cDNA clone. This insertion is predicted to alter the last 24 amino acids at the C-terminus and to extend the Pmel 17 protein by 12 residues. The mutation was confirmed by the sequence of the PCR-amplified genomic region including the mutation site. Silver Pmel 17 was not recognized by antibodies directed toward the C-terminal amino acids of wild-type Pmel 17, indicating a defect in this region. These results indicate that silver Pmel 17 protein has a major defect at the carboxyl terminus. [ABSTRACT FROM AUTHOR]

In this article, the author focuses on the professional life of Melanoma Research Foundation acting chair Meenhard Herlyn. He commends Herlyn's contribution to the melanoma field which includes the establishment of the Society for Melanoma Research in 2004. He relates that Herlyn grew up on a farm in Northern Germany and studied in the Veterinary Medical School in Hannover, Germany. He believes that Herlyn represents the voice of melanoma research.