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IMPORTANCE: Persistent radiation-induced alopecia (pRIA) and its management have not been systematically described. OBJECTIVE: To characterize pRIA in patients with primary central nervous system (CNS) tumors or head and neck sarcoma. DESIGN, SETTING, AND PARTICIPANTS: A retrospective cohort study of patients from January 1, 2011, to January 30, 2019, was conducted at 2 large tertiary care hospitals and comprehensive cancer centers. Seventy-one children and adults diagnosed with primary CNS tumors or head and neck sarcomas were evaluated for pRIA. MAIN OUTCOMES AND MEASURES: The clinical and trichoscopic features, scalp radiation dose-response relationship, and response to topical minoxidil were assessed using standardized clinical photographs of the scalp, trichoscopic images, and radiotherapy treatment plans. RESULTS: Of the 71 patients included (median [range] age, 27 [4-75] years; 51 female [72%]), 64 (90%) had a CNS tumor and 7 (10%) had head and neck sarcoma. Alopecia severity was grade 1 in 40 of 70 patients (56%), with localized (29 of 54 [54%]), diffuse (13 of 54 [24%]), or mixed (12 of 54 [22%]) patterns. The median (range) estimated scalp radiation dose was 39.6 (15.1-50.0) Gy; higher dose (odds ratio [OR], 1.15; 95% CI, 1.04-1.28) and proton irradiation (OR, 5.7; 95% CI, 1.05-30.8) were associated with greater alopecia severity (P < .001), and the dose at which 50% of patients were estimated to have severe (grade 2) alopecia was 36.1 Gy (95% CI, 33.7-39.6 Gy). Predominant trichoscopic features included white patches (16 of 28 [57%]); in 15 patients, hair-shaft caliber negatively correlated with scalp dose (correlation coefficient, −0.624; P = .01). The association between hair density and scalp radiation dose was not statistically significant (−0.381; P = .16). Twenty-eight of 34 patients (82%) responded to topical minoxidil, 5% (median follow-up, 61 [interquartile range, 21-105] weeks); 4 of 25 (16%) topical minoxidil recipients with clinical images improved in severity grade. Two patients responded to hair transplantation and 1 patient responded to plastic surgical reconstruction. CONCLUSIONS AND RELEVANCE: Persistent radiation-induced alopecia among patients with primary CNS tumors or head and neck sarcomas represents a dose-dependent phenomenon that has distinctive clinical and trichoscopic features. The findings of this study suggest that topical minoxidil and procedural interventions may have benefit in the treatment of pRIA.

Tobacco smoking causes lung cancer1–3, a process that is driven by more than 60 carcinogens in cigarette smoke that directly damage and mutate DNA4,5. The profound effects of tobacco on the genome of lung cancer cells are well-documented6–10, but equivalent data for normal bronchial cells are lacking. Here we sequenced whole genomes of 632 colonies derived from single bronchial epithelial cells across 16 subjects. Tobacco smoking was the major influence on mutational burden, typically adding from 1,000 to 10,000 mutations per cell; massively increasing the variance both within and between subjects; and generating several distinct mutational signatures of substitutions and of insertions and deletions. A population of cells in individuals with a history of smoking had mutational burdens that were equivalent to those expected for people who had never smoked: these cells had less damage from tobacco-specific mutational processes, were fourfold more frequent in ex-smokers than current smokers and had considerably longer telomeres than their more-mutated counterparts. Driver mutations increased in frequency with age, affecting 4–14% of cells in middle-aged subjects who had never smoked. In current smokers, at least 25% of cells carried driver mutations and 0–6% of cells had two or even three drivers. Thus, tobacco smoking increases mutational burden, cell-to-cell heterogeneity and driver mutations, but quitting promotes replenishment of the bronchial epithelium from mitotically quiescent cells that have avoided tobacco mutagenesis.

To our knowledge, this is the largest study investigating mutational profiles of renal cell carcinoma brain metastases (BMs) and the only such study with annotated intracranial outcomes. Stereotactic radiosurgery (SRS) provides durable in-field local control of BMs, and recognition of pseudoprogression following SRS is crucial to ensuring appropriate management. The incidence of PI3Kpathway alterations are enriched in BM+ patients compared with BM– patients and warrants further investigation.

ABSTRACTAmino acid sequence variation in protein therapeutics requires close monitoring during cell line and cell culture process development. A cross-functional team of Pfizer colleagues from the Analytical and Bioprocess Development departments worked closely together for over 6 years to formulate and communicate a practical, reliable sequence variant (SV) testing strategy with state-of-the-art techniques that did not necessitate more resources or lengthen project timelines. The final Pfizer SV screening strategy relies on next-generation sequencing (NGS) and amino acid analysis (AAA) as frontline techniques to identify mammalian cell clones with genetic mutations and recognize cell culture process media/feed conditions that induce misincorporations, respectively. Mass spectrometry (MS)-based techniques had previously been used to monitor secreted therapeutic products for SVs, but we found NGS and AAA to be equally informative, faster, less cumbersome screening approaches. MS resources could then be used for other purposes, such as the in-depth characterization of product quality in the final stages of commercial-ready cell line and culture process development. Once an industry-wide challenge, sequence variation is now routinely monitored and controlled at Pfizer (and other biopharmaceutical companies) through increased awareness, dedicated cross-line efforts, smart comprehensive strategies, and advances in instrumentation/software, resulting in even higher product quality standards for biopharmaceutical products.

IMPORTANCE: Lung cancer is the leading cause of cancer-related mortality in the United States and worldwide. As systemic therapies improve, patients with lung cancer live longer and thus are at increased risk for brain metastases. Understanding how prognosis varies across this heterogeneous patient population is essential to individualize care and design future clinical trials. OBJECTIVE: To update the current Diagnosis-Specific Graded Prognostic Assessment (DS-GPA) for patients with non–small-cell lung cancer (NSCLC) and brain metastases. The DS-GPA is based on data from patients diagnosed between 1985 and 2005, and we set out to update it by incorporating more recently reported gene and molecular alteration data for patients with NSCLC and brain metastases. This new index is called the Lung-molGPA. DESIGN, SETTING, AND PARTICIPANTS: This is a multi-institutional retrospective database analysis of 2186 patients diagnosed between 2006 and 2014 with NSCLC and newly diagnosed brain metastases. The multivariable analyses took place between December 2015 and May 2016, and all prognostic factors were weighted for significance by hazard ratios. Significant factors were included in the updated Lung-molGPA prognostic index. MAIN OUTCOMES AND MEASURES: The main outcome was survival. Multiple Cox regression was used to select and weight prognostic factors in proportion to their hazard ratios. Log rank tests were used to compare adjacent classes and to compare overall survival for adenocarcinoma vs nonadenocarcinoma groups. RESULTS: The original DS-GPA was based on 4 factors found in 1833 patients with NSCLC and brain metastases diagnosed between 1985 and 2005: patient age, Karnofsky Performance Status, extracranial metastases, and number of brain metastases. The patients studied for the creation of the DS-GPA had a median survival of 7 months from the time of initial treatment of brain metastases. To design the updated Lung-molGPA, we analyzed data from 2186 patients from 2006 through 2014 with NSCLC and newly diagnosed brain metastases (1521 adenocarcinoma and 665 nonadenocarcinoma). Significant prognostic factors included the original 4 factors used in the DS-GPA index plus 2 new factors: EGFR and ALK alterations in patients with adenocarcinoma (mutation status was not routinely tested for nonadenocarcinoma). The overall median survival for the cohort in the present study was 12 months, and those with NSCLC-adenocarcinoma and Lung-molGPA scores of 3.5 to 4.0 had a median survival of nearly 4 years. CONCLUSIONS AND RELEVANCE: In recent years, patient survival and physicians’ ability to predict survival in NSCLC with brain metastases has improved significantly. The updated Lung-molGPA incorporating gene alteration data into the DS-GPA is a user-friendly tool that may facilitate clinical decision making and appropriate stratification of future clinical trials.

Drug resistance is an almost inevitable consequence of cancer therapy and ultimately proves fatal for the majority of patients. In many cases, this is the consequence of specific gene mutations that have the potential to be targeted to resensitize the tumor. The ability to uniformly saturate the genome with point mutations without chromosome or nucleotide sequence context bias would open the door to identify all putative drug resistance mutations in cancer models. Here, we describe such a method for elucidating drug resistance mechanisms using genome-wide chemical mutagenesis allied to next-generation sequencing. We show that chemically mutagenizing the genome of cancer cells dramatically increases the number of drug-resistant clones and allows the detection of both known and novel drug resistance mutations. We used an efficient computational process that allows for the rapid identification of involved pathways and druggable targets. Such a priori knowledge would greatly empower serial monitoring strategies for drug resistance in the clinic as well as the development of trials for drug-resistant patients.

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFYgene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes—both single copy and amplified—on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

Antibody–drug conjugates have transformed the treatment of HER2+ breast and other cancers. Unfortunately, the CNS remains a sanctuary site for many such patients in part due to poor macromolecule penetration across the blood–brain tumor barrier. Trastuzumab deruxtecan (T-DXd), a high-payload antibody–drug conjugate, was recently found to improve progression-free survival in HER2+ breast cancer patients versus prior-generation trastuzumab emtansine, prompting us to evaluate CNS activity in a woman with brain-only metastatic disease. T-DXd achieved complete response despite heavy pretreatment. Three persistent, previously-irradiated lesions were biopsy-proven to represent treatment effect. Subsequent recurrence occurred upon treatment holiday; partial response was observed with rechallenge. This case suggests T-DXd is active in HER2+ breast cancer brain metastases and supports further prospective evaluation.

SUMMARY Aims:To describe results of melanoma brain metastases (BM) treated with whole-brain radiation (WBRT). Methods:Retrospective review of patients with melanoma BM treated with WBRT divided into two groups based on the timing of WBRT (at BM diagnosis or recurrence). Results:We identified 61 patients with melanoma BM who received WBRT. For the group treated at diagnosis (n = 39): median overall survival was 3 months; best radiographic response included one partial response, ten stable disease, 18 progressive disease, and ten no follow-up imaging. For the group treated at recurrence (n = 22): median overall survival was 3 months; best radiographic response was three partial response, four stable disease, eight progressive disease, and seven no follow-up imaging. Conclusion:WBRT activity was limited; however, its role in symptom palliation is unclear.

SUMMARYThe standard of care for malignant gliomas is maximal surgical cytoreduction followed by concurrent chemoradiation and adjuvant chemotherapy with temozolomide. Chemotherapy adds a modest improvement in overall survival. Unfortunately, tumor recurrence is the rule and typically occurs at the initial site of disease. Salvage reirradiation may be a useful approach in selected patients with recurrent glioblastoma. Image-guided technology coupled with highly conformal treatment planning techniques have allowed the safe delivery of high-dose radiotherapy in the setting of tumor recurrence. Defining the optimal combination of hypofractionated stereotactic radiotherapy with chemotherapy is under investigation. In this perspective, we examine the role of image guidance in malignant gliomas.

We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Trev is a DNA trace editor and viewer, which is available free for UNIX and Microsoft Windows platforms. It can read all the commonly used file formats, including the new, compact ZTR files.

Advances in sequencing technology have boosted population genomics and made it possible to map the positions of transcription factor binding sites (TFBSs) with high precision. Here we investigate TFBS variability by combining transcription factor binding maps generated by ENCODE, modENCODE, our previously published data and other sources with genomic variation data for human individuals and Drosophila isogenic lines.

Background: Bronchial-associated lymphoid tissue (BALT) lymphoma, an indolent marginal zone lymphoma, is a rare clinical entity with only few published reports on its optimal management and treatment outcome. In the absence of a well established standard of care, different treatment options are available including surgery, radiation, chemotherapy, immunotherapy or merely observation. We analyzed a large cancer center’s experience with the management of BALT lymphoma patients during the last 12 years. Patients and Methods: Nineteen cases of BALT lymphoma were identified from a database of 175 cases of MALT lymphoma pathologically confirmed at our center. We retrospectively reviewed the clinical data and treatment results. Results: There were 12 (63%) men and 7 (37%) women with a median age of 68 years (range 37–81 years). Seven (37%) patients were asymptomatic at diagnosis and were diagnosed after radiologic studies ordered either for routine evaluation or for pre-operative clearance showed unexpected abnormalities. The 12 (63%) symptomatic patients had non-specific pulmonary complaints such as cough, shortness of breath, or dyspnea on exertion. One patient had B symptoms (significant unintentional weight loss). Twelve patients (63%) had unilateral lung involvement and 7 (37%) had bilateral involvement on chest CT. Twelve patients had FDG-PET scans at the time of diagnosis and all had FDG uptake in pathologically confirmed sites of disease with a median SUV of 3.2 (range 1.3–26). Five patients (26%) had radiographically enlarged hilar or mediastinal lymph nodes including 1 with pathologically confirmed transformation to diffuse large B-cell lymphoma in a mediastinal lymph node and 1 with progression to a supraclavicular lymph node. Fifteen patients (79%) had stage I or II disease limited to their thorax. One patient had previously treated MALT of the bilateral orbits, 1 patient was also found to have MALT involving her small bowel, 1 patient also had bone marrow involvement, and 1 patient had extensive disease involving not only lung parenchyma but also mediastinal lymph nodes, and bilateral axillary, supraclavicular, and cervical lymph nodes. Ten patients were treated with surgery alone (8 had wedge resections, 2 had lobectomies). Six received chemotherapy alone and 2 had rituximab alone. One received radiation (RT) alone. With a median follow-up of 28 months (range 11–146 months), no patients were lost to follow-up. At 5 years, overall survival was 91% and disease free survival was 42%. At latest follow-up all patients were alive with the exception of one patient who died of his disease (the patient who had extensive lung parenchymal disease and lymphadenopathy) and 8 patients (42%) were without evidence of any disease after RT(1), chemotherapy(2), or surgery(5). Conclusion: In one of the largest series of BALT lymphoma patients with complete follow-up, we document good response to local treatment and overall excellent prognosis. Of interest, BALT lymphoma lesions are PET-positive and thus are similar to lung cancer lesions. Limited lesions may be safely resected and patients remain disease-free, but even some patients with unresectable disease respond to chemotherapy and are rendered disease-free or stable.