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AI is rapidly becoming part of many aspects of daily life, with an impact that reaches all fields of research. We asked investigators to share their thoughts on how AI is changing immunology research, what is necessary to move forward, the potential and the pitfalls, and what will remain unchanged as the field journeys into a new era. [ABSTRACT FROM AUTHOR]

• Biomarkers are key to maximize clinical benefit of treatment with anti-CTLA4, anti-PD1 and anti-PDL1 drugs. • Genomic correlates of neoantigen load, such as defective mismatch repair and tumour mutation burden, are clinically applicable, but fail to completely explain differences in response patterns to immune checkpoint inhibitors. • HLA genotype, interferon expression and copy number variation are other promising biomarkers related to immune response pathways. • Somatic mutations in genes such as TP53 , PTEN , PBRM1 and ARID1A may also help identify responders to immunotherapy. Immune checkpoint inhibitors (ICI) aim to restore the immune system anti-tumor function by blocking two inhibitory axes: CTLA-4/CD28 and PD1/PDL1. ICI is established as a treatment option for multiple cancers, but their remarkable clinical impact is observed only in a fraction of patients. Together with their adverse effects and high cost, it's imperative to identify patients who are likely to benefit from this type of treatment. Genomic features represent promising candidates as predictive biomarkers of response to ICI, with agnostic FDA-approvals of an anti-PD1 drug for tumors with microsatellite instability and tumors with a high mutational burden. Other genomic markers are also emerging to help refine patient selection. In this review, we discuss recent progress in genomic biomarkers development and its challenges, with a focus on alterations in the neoantigen burden, immune, and oncogenic pathways. [ABSTRACT FROM AUTHOR]

Cancer immunotherapies — including therapeutic vaccines, adoptive cell transfer, oncolytic viruses, and immune checkpoint blockade — yield durable responses in many cancer types, but understanding of predictors of response is incomplete. Genomic characterization of human cancers has already contributed to the success of targeted therapies; in cancer immunotherapy, identification of tumor-specific antigens through whole-exome sequencing may be key to designing individualized, highly immunogenic therapeutic vaccines. Additionally, pre-treatment tumor mutational and gene expression signatures can predict which patients are most likely to benefit from cancer immunotherapy. Continued work in harnessing genomic, transcriptomic, and immunological data from clinical cohorts of immunotherapy-treated patients will bring the promises of precision medicine to immuno-oncology. [ABSTRACT FROM AUTHOR]

Monoclonal antibodies directed against cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), such as ipilimumab, yield considerable clinical benefit for patients with metastatic melanoma by inhibiting immune checkpoint activity, but clinical predictors of response to these therapies remain incompletely characterized. To investigate the roles of tumor-specific neoantigens and alterations in the tumor microenvironment in the response to ipilimumab, we analyzed whole exomes from pretreatment melanoma tumor biopsies and matching germline tissue samples from 110 patients. For 40 of these patients, we also obtained and analyzed transcriptome data from the pretreatment tumor samples. Overall mutational load, neoantigen load, and expression of cytolytic markers in the immune microenvironment were significantly associated with clinical benefit. However, no recurrent neoantigen peptide sequences predicted responder patient populations. Thus, detailed integrated molecular characterization of large patient cohorts may be needed to identify robust determinants of response and resistance to immune checkpoint inhibitors. [ABSTRACT FROM AUTHOR]

As a result of multiple technological and practical advances, high-throughput sequencing, known more commonly as "next-generation" sequencing (NGS), can now be incorporated into standard clinical practice. Whereas early protocols relied on samples that were harvested outside of typical clinical pathology workflows, standard formalin-fixed, paraffin-embedded specimens can more regularly be used as starting materials for NGS. Furthermore, protocols for the analysis and interpretation of NGS data, as well as knowledge bases, are being amassed, allowing clinicians to act more easily on genomic information at the point of care for patients. In parallel, new therapies that target somatically mutated genes identified through clinical NGS are gaining US Food and Drug Administration (FDA) approval, and novel clinical trial designs are emerging in which genetic identifiers are given equal weight to histology. For clinical oncology providers, understanding the potential and the limitations of DNA sequencing will be crucial for providing genomically driven care in this era of precision medicine. [ABSTRACT FROM AUTHOR]

Summary Toward development of a precision medicine framework for metastatic, castration-resistant prostate cancer (mCRPC), we established a multi-institutional clinical sequencing infrastructure to conduct prospective whole-exome and transcriptome sequencing of bone or soft tissue tumor biopsies from a cohort of 150 mCRPC affected individuals. Aberrations of AR , ETS genes, TP53 , and PTEN were frequent (40%–60% of cases), with TP53 and AR alterations enriched in mCRPC compared to primary prostate cancer. We identified new genomic alterations in PIK3CA/B , R-spondin, BRAF / RAF1 , APC , β-catenin, and ZBTB16/PLZF . Moreover, aberrations of BRCA2 , BRCA1 , and ATM were observed at substantially higher frequencies (19.3% overall) compared to those in primary prostate cancers. 89% of affected individuals harbored a clinically actionable aberration, including 62.7% with aberrations in AR, 65% in other cancer-related genes, and 8% with actionable pathogenic germline alterations. This cohort study provides clinically actionable information that could impact treatment decisions for these affected individuals. [ABSTRACT FROM AUTHOR]

An editorial is presented which addresses various aspects of the use of expanded germline (germ cells) testing in clinical oncology, and it mentions precision cancer medicine and discoveries in translational cancer research. A report in the same issue of the journal, which addresses a 410-gene tumor and germline molecular assay, is examined, along with genetic mutations in cancer patients and DNA repair genes.

Molecular profiling of tumors promises to advance the clinical management of cancer, but the benefits of integrating molecular data with traditional clinical variables have not been systematically studied. Here we retrospectively predict patient survival using diverse molecular data (somatic copy-number alteration, DNA methylation and mRNA, microRNA and protein expression) from 953 samples of four cancer types from The Cancer Genome Atlas project. We find that incorporating molecular data with clinical variables yields statistically significantly improved predictions (FDR < 0.05) for three cancers but those quantitative gains were limited (2.2-23.9%). Additional analyses revealed little predictive power across tumor types except for one case. In clinically relevant genes, we identified 10,281 somatic alterations across 12 cancer types in 2,928 of 3,277 patients (89.4%), many of which would not be revealed in single-tumor analyses. Our study provides a starting point and resources, including an open-access model evaluation platform, for building reliable prognostic and therapeutic strategies that incorporate molecular data. [ABSTRACT FROM AUTHOR]

Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a 'long tail' of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15 out of 16 patients. In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine. [ABSTRACT FROM AUTHOR]

Purpose: Off-label prescribing in oncology is common and unregulated. The aim of this study was to describe the off-label use of rituximab, a novel anti-CD20 antibody, among patients from a large proprietary insurance database to understand how frequently and appropriately off-label prescribing occurs for this medication. Patients and Methods: In this descriptive study, 11,232,642 patients were enrolled in the D2 Hawkeye commercial insurance database between 2001 and 2007, and 2,782 patients received rituximab. The main outcome measures were quantity and type of off-label usage, and expenditures for off-label usage. Results: Seven hundred five (25.3%) patients received rituximab for off-label indications, and of those, 332 (47.1%) received rituximab for uncertain or inadequate evidence-based diagnoses. Expenditures for off-label indications were 17.1% of expenditures for rituximab usage. Conclusion: The frequent use of rituximab for off-label indications should lead to improved postapproval surveillance of biologics by the US Food and Drug Administration, so that use can be adequately studied. This will also facilitate improved regulatory mechanisms to ensure evidence-based use. [ABSTRACT FROM AUTHOR]

Abstract: The high prevalence of Enterococcus faecalis in root canal treated teeth with post-treatment disease, as evidenced by both molecular and traditional culturing methods, suggests that this species may be a key player in endodontic treatment failure. This study aimed to detect virulence factors by phenotypic and western blotting tests, and virulence genes by PCR from 20 clinical strains of E. faecalis isolated from treated root canals of teeth with (10) or without (10) apical periodontitis. Moreover, genomic diversity of these strains was assessed by pulsed-field gel electrophoresis (PFGE) and rep-PCR. All 20 strains presented the gelE gene (gelatinase), but 10 of them did not hydrolyze gelatin. Seven of the 10 gelatinase-producing isolates were recovered from root canals with lesions, which suggests a role for this virulence factor in the pathogenesis of post-treatment disease. The esp gene was expressed only in cases where gelatinase production was negative. The other virulence genes were found in 90% (efaA and ace genes), 45% (agg gene) and 95% (cpd gene) of the E. faecalis isolates. As for PFGE and rep-PCR, no specific clonal type of E. faecalis was found in association with teeth with or without disease, revealing the interindividual clonal diversity of endodontic infections. [Copyright &y& Elsevier]

Summary: In this study, we standardized and evaluated a multiplex-PCR methodology using specific primers to identify Staphylococcus aureus, Staphylococcus epidermidis and Staphylococcus haemolyticus and their methicillin-resistance directly from blood cultures. Staphylococci clinical isolates (149) and control strains (16) previously identified by conventional methods were used to establish the multiplex PCR protocol. Subsequently, this methodology was evaluated using a fast and cheap DNA extraction protocol from 25 staphylococci positive blood cultures. A wash step of the pellet with 0.1% bovine serum albumin (BSA) solution was performed to reduce PCR inhibitors. Amplicons of 154bp (mecA gene), 271bp (S. haemolyticus mvaA gene) and 108 and 124bp (S. aureus and S. epidermidis species–specific fragments, respectively) were observed. Reliable results were obtained for 100% of the evaluated strains, suggesting that this new multiplex-PCR combined with an appropriate DNA-extraction method could be useful in the laboratory for fast and accurate identification of three staphylococci species and simultaneously their methicillin resistance directly in blood cultures. [Copyright &y& Elsevier]

Staphylococcus lugdunensis are unusually virulent coagulase-negative staphylococci associated with skin infections and endocarditis. We developed an accurate and simple PCR assay to identify S. lugdunensis isolates based on detection of the fbl gene, which encodes a fibrinogen-binding protein involved in pathogen adhesion. The PCR assay was established using 16 reference strains of different Staphylococcus species and further validated with a collection of 63 clinical staphylococcal isolates that were also phenotypically characterized. Reliable results for the detection of S. lugdunensis isolates were obtained for 100% of the strains evaluated, indicating that this PCR assay can be used in the routine of microbiology laboratories as one more tool for correct species differentiation. [ABSTRACT FROM AUTHOR]

Staphylococcus haemolyticus is the most frequently coagulase-negative Staphylococcus species associated with antimicrobial resistance isolated from nosocomial infections. We developed an accurate and simple multiplex PCR assay to identify methicillin-resistant S. haemolyticus (MRSH) isolates. We designed species-specific primers of the mvaA gene that encodes a 3-hydroxy-3-methylglutaryl coenzyme A involved in the mevalonate pathway of the microorganism. Simultaneously, mecA gene primers of methicillin resistance were also used. The PCR assay was established using 16 strains of different reference Staphylococcus species and validated with a collection of 147 clinical staphylococcal isolates that were also phenotypically characterized. Reliable results for the detection of MRSH isolates were obtained for 100% of the strains evaluated, showing that this PCR assay can be used for the routine microbiology laboratories. This is the first report using species-specific multiplex PCR to detect a single segment of S. haemolyticus associated with a segment of mecA gene. [ABSTRACT FROM AUTHOR]

Lake Nabugabo was a big bay of Lake Victoria before being separated from the latter by a sand bar about 4000 years ago. Whereas conductivity of Lake Victoria is 100 μScm−1 that of Nabugabo has been less than 30 μ cm−2 since the Cambridge Scientific Expedition, 1962. Dissolved calcium carbonate is below detectable levels although nitrate and phosphate are not significantly different from those of Lake Victoria. However, the total cations and anions are five times more in Lake Victoria than Nabugabo. Along the eastern, southern and south-western margins of the lake is an emergent swamp composed of different types of plants. In most places, Miscanthidium violaceum forms a floating platform of matted roots and rhizomes which border the open lake; it is associated with Sphagnum, a type of moss which normally grows in acidic and low-temperature conditions at very high altitudes and latitudes. Because of the presence of this moss, the Nabugabo swamps are sometimes called ‘ Sphagnum swamps’. Vossia cuspidata (hippo grass) is yet another emergent swamp plant in Lake Nabugabo, occurring in a number of isolated narrow mats stretching from a few metres to 0.5 km or longer along the edge of the emergent swamp. These floating mats are firmly anchored to the Micanthidium platform. Cyperus latifolia is another emergent-floating plant in Lake Nabugabo firmly anchored on to the Miscanthidium platform. Cyperus latifolia and V. cuspidata tend to grow side by side but in completely sheltered bays the former plant grows alone. Cyperus papyrus L. occurs in very few patches within the emergent swamp. In the interface zone along the emergent swamp, there are a number of euhydrophyte plant species: Nymphaea caerulea is the most dominant and widespread euhydrophyte species except in the eastern tip of the lake where it is replaced by Nymphaea lotus; interspersed among these lilies is Ceratophyllum demersum in certain bays which could either be water inlets or out-flows; Utricularia and Nymphoides indica are associated with monospecific stand of N. caerulea in the south-western end of the zone. [ABSTRACT FROM AUTHOR]

PURPOSE: There is significant interest in identifying complete responders to neoadjuvant chemotherapy (NAC) before radical cystectomy (RC) to potentially avoid removal of a pathologically benign bladder. However, clinical restaging after NAC is highly inaccurate. The objective of this study was to develop a next-generation sequencing–based molecular assay using urine to enhance clinical staging of patients with bladder cancer. METHODS: Urine samples from 20 and 44 patients with bladder cancer undergoing RC were prospectively collected for retrospective analysis for molecular correlate analysis from two clinical trials, respectively. The first cohort was used to benchmark the assay, and the second was used to determine the performance characteristics of the test as it correlates to responder status as measured by pathologic examination. RESULTS: First, to benchmark the assay, known mutations identified in the tissue (MT) of patients from the Accelerated Methotrexate, Vinblastine, Doxorubicin, Cisplatin trial (ClinicalTrials.gov identifier: NCT01611662, n = 16) and a cohort from University of California-San Francisco (n = 4) were cross referenced against mutation profiles from urine (MU). We then determined the correlation between MU persistence and residual disease in pre-RC urine samples from a second prospective clinical trial (The pT0 trial; ClinicalTrials.gov identifier: NCT02968732). Residual MU status correlated strongly with residual disease status (pT0 trial; n = 44; P =.0092) when MU from urine supernatant and urine pellet were assessed separately and analyzed in tandem. The sensitivity, specificity, PPV, and NPV were 91%, 50%, 86%, and 63% respectively, with an overall accuracy of 82% for this second cohort. CONCLUSION: MU are representative of MT and thus can be used to enhance clinical staging of urothelial carcinoma. Urine biopsy may be used as a reliable tool that can be further developed to identify complete response to NAC in anticipation of safe RC avoidance. [ABSTRACT FROM AUTHOR]

We report somatic mutations of RNF43 in over 18% of colorectal adenocarcinomas and endometrial carcinomas. RNF43 encodes an E3 ubiquitin ligase that negatively regulates Wnt signaling. Truncating mutations of RNF43 are more prevalent in microsatellite-unstable tumors and show mutual exclusivity with inactivating APC mutations in colorectal adenocarcinomas. These results indicate that RNF43 is one of the most commonly mutated genes in colorectal and endometrial cancers. [ABSTRACT FROM AUTHOR]

Lake Nabugabo interface zone, 10 km long, 10–50 m wide, 2 m deep, was dominated by Nymphaea caerulea except in the eastern tip that had Nymphaea lotus, while certain bays had Ceratophyllum demersum dominating. The south-western end of the zone had two small patches of Nymphoides indica. Electrical conductivity was very low, 17.8–38.2 μS cm−1. Chironomid larvae, over 50% occurrence, dominated food items for haplochromines; also consumed items included detritus, aufwuchs and, periodically, cladocerans. Absence of food item exceeding 50% relative abundance meant no feeding specialization. On the other hand, tilapiines seemed to specialize on chironomids. Résumé La zone d'interface du lac Nabugabo, de 10 km de long sur 10 à 50 mètres de large et 2 mètres de profondeur, était dominée par Nymphaea caeruleaà l'exception de la pointe est qui était occupée par Nymphaea lotus alors que dans certaines baies, c'est Ceratophyllum demersum qui domine. L'extrémité sud-ouest de la zone avait deux petites plages de Nymphoides indica. La conductivitéélectrique y était très faible, de 17.8 à 38.2 μ cm−2. Les larves de chironomides, représentant plus de 50%, dominaient dans l'alimentation des haplochromines qui consomment aussi des détritus, des aufwuchs et, périodiquement, des cladocères. L'absence d’élément alimentaire qui dépasse 50% d'abondance relative signifie qu'il n'y a pas de spécialisation alimentaire. D'autre part, les tilapiinés semblaient s’être spécialisés dans la consommation de chironomides. [ABSTRACT FROM AUTHOR]

The tumor immune microenvironment (TIME) plays key roles in tumor progression and response to immunotherapy. Previous studies have identified individual germline variants associated with differences in TIME. Here, we hypothesize that common variants associated with breast cancer risk or cancer-related traits, represented by polygenic risk scores (PRSs), may jointly influence immune features in TIME. We derived 154 immune traits from bulk gene expression profiles of 764 breast tumors and 598 adjacent normal tissue samples from 825 individuals with breast cancer in the Nurses' Health Study (NHS) and NHSII. Immunohistochemical staining of four immune cell markers were available for a subset of 205 individuals. Germline PRSs were calculated for 16 different traits including breast cancer, autoimmune diseases, type 2 diabetes, ages at menarche and menopause, body mass index (BMI), BMI-adjusted waist-to-hip ratio, alcohol intake, and tobacco smoking. Overall, we identified 44 associations between germline PRSs and immune traits at false discovery rate q < 0.25, including 3 associations with q < 0.05. We observed consistent inverse associations of inflammatory bowel disease (IBD) and Crohn disease (CD) PRSs with interferon signaling and STAT1 scores in breast tumor and adjacent normal tissue; these associations were replicated in a Norwegian cohort. Inverse associations were also consistently observed for IBD PRS and B cell abundance in normal tissue. We also observed positive associations between CD PRS and endothelial cell abundance in tumor. Our findings suggest that the genetic mechanisms that influence immune-related diseases are also associated with TIME in breast cancer. We investigated the germline genetic determinants of immune features in the breast tumor microenvironment. Our results reveal genetic links between tumor immune profiles, especially those related to interferon signaling, and autoimmune diseases. [ABSTRACT FROM AUTHOR]

PURPOSE: There is significant interest in identifying complete responders to neoadjuvant chemotherapy (NAC) before radical cystectomy (RC) to potentially avoid removal of a pathologically benign bladder. However, clinical restaging after NAC is highly inaccurate. The objective of this study was to develop a next-generation sequencing–based molecular assay using urine to enhance clinical staging of patients with bladder cancer. METHODS: Urine samples from 20 and 44 patients with bladder cancer undergoing RC were prospectively collected for retrospective analysis for molecular correlate analysis from two clinical trials, respectively. The first cohort was used to benchmark the assay, and the second was used to determine the performance characteristics of the test as it correlates to responder status as measured by pathologic examination. RESULTS: First, to benchmark the assay, known mutations identified in the tissue (MT) of patients from the Accelerated Methotrexate, Vinblastine, Doxorubicin, Cisplatin trial (ClinicalTrials.gov identifier: NCT01611662, n = 16) and a cohort from University of California-San Francisco (n = 4) were cross referenced against mutation profiles from urine (MU). We then determined the correlation between MU persistence and residual disease in pre-RC urine samples from a second prospective clinical trial (The pT0 trial; ClinicalTrials.gov identifier: NCT02968732). Residual MU status correlated strongly with residual disease status (pT0 trial; n = 44; P =.0092) when MU from urine supernatant and urine pellet were assessed separately and analyzed in tandem. The sensitivity, specificity, PPV, and NPV were 91%, 50%, 86%, and 63% respectively, with an overall accuracy of 82% for this second cohort. CONCLUSION: MU are representative of MT and thus can be used to enhance clinical staging of urothelial carcinoma. Urine biopsy may be used as a reliable tool that can be further developed to identify complete response to NAC in anticipation of safe RC avoidance. Presence or absence of tumor DNA in urine correlates with residual disease in cystectomy candidates [ABSTRACT FROM AUTHOR]

An introduction is presented in which the editor discusses various reports within the issue include tumor characterization's analytical and technological advances, genomic variant interpreation improvement, and precision cancer medicine effectiveness.

The author reflects on his experience with a patient who refused to have paracentesis administered on him. The patient, who had end-stage liver disease, had been experiencing abdominal pain and fevers yet refused to be examined. He recalls that the patient only submitted to treatment after his demand for jazz music by singer Perry Como was given. He adds that such an encounter with a patient emphasized the need for physicians to look at their patients as someone more than just a collection of parts that require treatment.

A personal narrative is presented which explore's the author experience on being a doctor.

Two letters to the editor and a response is presented referencing to an article about HIV screening which was published in the previous issue.

Background: Longitudinal data on key cancer outcomes for clinical research, such as response to treatment and disease progression, are not captured in standard cancer registry reporting. Manual extraction of such outcomes from unstructured electronic health records is a slow, resource-intensive process. Natural language processing (NLP) methods can accelerate outcome annotation, but they require substantial labeled data. Transfer learning based on language modeling, particularly using the Transformer architecture, has achieved improvements in NLP performance. However, there has been no systematic evaluation of NLP model training strategies on the extraction of cancer outcomes from unstructured text. Results: We evaluated the performance of nine NLP models at the two tasks of identifying cancer response and cancer progression within imaging reports at a single academic center among patients with non-small cell lung cancer. We trained the classification models under different conditions, including training sample size, classification architecture, and language model pre-training. The training involved a labeled dataset of 14,218 imaging reports for 1112 patients with lung cancer. A subset of models was based on a pre-trained language model, DFCI-ImagingBERT, created by further pre-training a BERT-based model using an unlabeled dataset of 662,579 reports from 27,483 patients with cancer from our center. A classifier based on our DFCI-ImagingBERT, trained on more than 200 patients, achieved the best results in most experiments; however, these results were marginally better than simpler "bag of words" or convolutional neural network models. Conclusion: When developing AI models to extract outcomes from imaging reports for clinical cancer research, if computational resources are plentiful but labeled training data are limited, large language models can be used for zero- or few-shot learning to achieve reasonable performance. When computational resources are more limited but labeled training data are readily available, even simple machine learning architectures can achieve good performance for such tasks. [ABSTRACT FROM AUTHOR]

Background: Breast cancer patients from the indigenous Arab population present much earlier than patients from Western countries and have traditionally been underrepresented in cancer genomics studies. The contribution of polygenic and Mendelian risk toward the earlier onset of breast cancer in the population remains elusive. Methods: We performed low-pass whole genome sequencing (lpWGS) and whole-exome sequencing (WES) from 220 female breast cancer patients unselected for positive family history from the indigenous Arab population. Using publicly available resources, we imputed population-specific variants and calculated breast cancer burden-sensitive polygenic risk scores (PRS). Variant pathogenicity was also evaluated on exome variants with high coverage. Results: Variants imputed from lpWGS showed high concordance with paired exome (median dosage correlation: 0.9459, Interquartile range: 0.9410–0.9490). After adjusting the PRS to the Arab population, we found significant associations between PRS performance in risk prediction and first-degree relative breast cancer history prediction (Spearman rho=0.43, p = 0.03), where breast cancer patients in the top PRS decile are 5.53 (95% CI 1.76–17.97, p = 0.003) times more likely also to have a first-degree relative diagnosed with breast cancer compared to those in the middle deciles. In addition, we found evidence for the genetic liability threshold model of breast cancer where among patients with a family history of breast cancer, pathogenic rare variant carriers had significantly lower PRS than non-carriers (p = 0.0205, Mann-Whitney U test) while for non-carriers every standard deviation increase in PRS corresponded to 4.52 years (95% CI 8.88–0.17, p = 0.042) earlier age of presentation. Conclusions: Overall, our study provides a framework to assess polygenic risk in an understudied population using lpWGS and identifies common variant risk as a factor independent of pathogenic variant carrier status for earlier age of onset of breast cancer among indigenous Arab breast cancer patients. [ABSTRACT FROM AUTHOR]

The article discusses how rare germline structural variants (SVs) are risk factors for pediatric solid tumors. The study analyzed germline genome sequencing from 1765 patients with solid tumors, their 943 unaffected parents, and 6665 adult controls. The research found that large SVs, gene-disrupting events, and alterations in chromatin domain boundaries were associated with an increased risk of pediatric solid tumors, particularly in neuroblastoma. The findings suggest that rare germline SVs play a modest yet meaningful role in the development of pediatric solid tumors, highlighting the importance of integrating SV analysis into clinical practice and research efforts. [Extracted from the article]

PURPOSE: Guidelines recommend somatic and germline testing for men with advanced prostate cancer (PCa). Barriers to widespread implementation result in underutilization of germline testing. Somatic testing alone risks missing pathogenic germline variants (PGVs). We sought to determine whether the addition of germline testing to tumor-only sequencing improves detection of PGVs in men with advanced PCa. Secondarily, we sought to define the added value of combining somatic and germline testing to optimize detection of clinically actionable alterations. PATIENTS AND METHODS: We analyzed results of independent germline testing and tumor-only sequencing from 100 men with advanced PCa from a prospective clinical trial (ClinicalTrials.gov identifier: NCT03328091). The primary outcome was the proportion of PGVs not reported with tumor-only sequencing. The secondary outcome was the association of locus-specific loss of heterozygosity for PGVs in homologous recombination genes with clinical-genomic features. RESULTS: In the 100 men who underwent germline testing and tumor-only sequencing, 24 PGVs were identified, 17 of which were clinically actionable, in 23 patients. Tumor-only sequencing failed to report four (17%) of the PGVs. One additional PGV (4.2%) had variant allele frequency on tumor-sequencing below the threshold for follow-up germline testing. When integrating tumor-only sequencing with germling testing results, 33% of patients harbored clinically actionable alterations. Rates of locus-specific loss of heterozygosity were higher for BRCA2 PGVs in castration-resistant PCa than PGVs in other homologous recombination genes in hormone-sensitive PCa (P =.029). CONCLUSION: Tumor-only sequencing failed to report more than 20% of PGVs in men with advanced PCa. These findings strongly support guideline recommendations for universal germline and somatic testing in this population. Combining tumor and germline sequencing doubled the chance of detecting a clinically actionable alteration. Tumor-only sequencing misses more than 20% of germline variants in men with advanced prostate cancer affirming guideline recommendations for universal germline testing. [ABSTRACT FROM AUTHOR]

The article describes the case of a 57-year old woman with metastatic anaplastic thyroid cancer who developed acquired resistance to everolimus after an 18-month response. Histological findings and computed tomographic (CT) scans in the patient are presented. The study explains the genomic mechanisms of sensitivity and acquired everolimus-resistance including the nonsense mutations in the tumor-suppressor gene TSC2 and mammalian target of tapamycin (mTOR) pathway.

PURPOSE: In metastatic triple-negative breast cancer (mTNBC), consistent biomarkers of immune checkpoint inhibitor (ICI) therapy benefit remain elusive. We evaluated the immune, genomic, and transcriptomic landscape of mTNBC in patients treated with ICIs. METHODS: We identified 29 patients with mTNBC treated with pembrolizumab or atezolizumab, either alone (n = 9) or in combination with chemotherapy (n = 14) or targeted therapy (n = 6), who had tumor tissue and/or blood available before ICI therapy for whole-exome sequencing. RNA sequencing and CIBERSORTx-inferred immune population analyses were performed (n = 20). Immune cell populations and programmed death-ligand 1 expression were assessed using multiplexed immunofluorescence (n = 18). Clonal trajectories were evaluated via serial tumor/circulating tumor DNA whole-exome sequencing (n = 4). Association of biomarkers with progression-free survival and overall survival (OS) was assessed. RESULTS: Progression-free survival and OS were longer in patients with high programmed death-ligand 1 expression and tumor mutational burden. Patients with longer survival also had a higher relative inferred fraction of CD8+ T cells, activated CD4+ memory T cells, M1 macrophages, and follicular helper T cells and enrichment of inflammatory gene expression pathways. A mutational signature of defective repair of DNA damage by homologous recombination was enriched in patients with both shorter OS and primary resistance. Exploratory analysis of clonal evolution among four patients treated with programmed cell death protein 1 blockade and a tyrosine kinase inhibitor suggested that clonal stability post-treatment was associated with short time to progression. CONCLUSION: This study identified potential biomarkers of response to ICIs among patients with mTNBC: high tumor mutational burden; presence of CD8+, CD4 memory T cells, follicular helper T cells, and M1 macrophages; and inflammatory gene expression pathways. Pretreatment deficiencies in the homologous recombination DNA damage repair pathway and the absence of or minimal clonal evolution post-treatment may be associated with worse outcomes. In patients with mTNBC, responses to ICI-containing therapies were associated with high TMB; the presence of CD8+, CD4 memory T cells, follicular helper T cells, and M1 macrophages; and inflammatory gene expression pathways. [ABSTRACT FROM AUTHOR]

More knowledge is needed regarding germline predisposition to Ewing sarcoma to inform biological investigation and clinical practice. Here, we evaluated the enrichment of pathogenic germline variants in Ewing sarcoma relative to other pediatric sarcoma subtypes, as well as patterns of inheritance of these variants. We carried out European-focused and pan-ancestry case-control analyses to screen for enrichment of pathogenic germline variants in 141 established cancer predisposition genes in 1,147 individuals with pediatric sarcoma diagnoses (226 Ewing sarcoma, 438 osteosarcoma, 180 rhabdomyosarcoma, and 303 other sarcoma) relative to identically processed cancer-free control individuals. Findings in Ewing sarcoma were validated with an additional cohort of 430 individuals, and a subset of 301 Ewing sarcoma parent-proband trios was analyzed for inheritance patterns of identified pathogenic variants. A distinct pattern of pathogenic germline variants was seen in Ewing sarcoma relative to other sarcoma subtypes. FANCC was the only gene with an enrichment signal for heterozygous pathogenic variants in the European Ewing sarcoma discovery cohort (three individuals, OR 12.6, 95% CI 3.0–43.2, p = 0.003, FDR = 0.40). This enrichment in FANCC heterozygous pathogenic variants was again observed in the European Ewing sarcoma validation cohort (three individuals, OR 7.0, 95% CI 1.7–23.6, p = 0.014), representing a broader importance of genes involved in DNA damage repair, which were also nominally enriched in individuals with Ewing sarcoma. Pathogenic variants in DNA damage repair genes were acquired through autosomal inheritance. Our study provides new insight into germline risk factors contributing to Ewing sarcoma pathogenesis. [ABSTRACT FROM AUTHOR]

Metastatic castration-resistant prostate cancers (mCRPCs) are treated with therapies that antagonize the androgen receptor (AR). Nearly all patients develop resistance to AR-targeted therapies (ARTs). Our previous work identified CREB5 as an upregulated target gene in human mCRPC that promoted resistance to all clinically approved ART. The mechanisms by which CREB5 promotes progression of mCRPC or other cancers remains elusive. Integrating ChIP-seq and rapid immunoprecipitation and mass spectroscopy of endogenous proteins, we report that cells overexpressing CREB5 demonstrate extensive reprogramming of nuclear protein-protein interactions in response to the ART agent enzalutamide. Specifically, CREB5 physically interacts with AR, the pioneering actor FOXA1, and other known co-factors of AR and FOXA1 at transcription regulatory elements recently found to be active in mCRPC patients. We identified a subset of CREB5/FOXA1 co-interacting nuclear factors that have critical functions for AR transcription (GRHL2, HOXB13) while others (TBX3, NFIC) regulated cell viability and ART resistance and were amplified or overexpressed in mCRPC. Upon examining the nuclear protein interactions and the impact of CREB5 expression on the mCRPC patient transcriptome, we found that CREB5 was associated with Wnt signaling and epithelial to mesenchymal transitions, implicating these pathways in CREB5/FOXA1-mediated ART resistance. Overall, these observations define the molecular interactions among CREB5, FOXA1, and pathways that promote ART resistance. [ABSTRACT FROM AUTHOR]

Radiation-associated muscle-invasive bladder cancers arising after prostate cancer radiotherapy have mutational evidence of radiation exposure but share many driver alterations with non–radiation-associated muscle-invasive bladder cancers. Muscle-invasive bladder cancer (MIBC) is a rare but serious event following definitive radiation for prostate cancer. Radiation-associated MIBC (RA-MIBC) can be difficult to manage given the challenges of delivering definitive therapy to a previously irradiated pelvis. The genomic landscape of RA-MIBC and whether it is distinct from non–RA-MIBC are unknown. To define mutational features of RA-MIBC and compare the genomic landscape of RA-MIBC with that of non–RA-MIBC. We identified patients from our institution who received radiotherapy for prostate cancer and subsequently developed MIBC. We performed whole exome sequencing of bladder tumors from RA-MIBC patients. Tumor genetic alterations including mutations, copy number alterations, and mutational signatures were identified and were compared with genetic features of non–RA-MIBC. We used the Kaplan-Meier method to estimate recurrence-free (RFS) and overall (OS) survival. We identified 19 RA-MIBC patients with available tumor tissue (n = 22 tumors) and clinical data. The median age was 76 yr, and the median time from prostate cancer radiation to RA-MIBC was 12 yr. The median RFS was 14.5 mo and the median OS was 22.0 mo. Compared with a cohort of non–RA-MIBC analyzed in parallel, there was no difference in tumor mutational burden, but RA-MIBCs had a significantly increased number of short insertions and deletions (indels) consistent with previous radiation exposure. We identified mutation signatures characteristic of APOBEC-mediated mutagenesis, aging, and homologous recombination deficiency. The frequency of mutations in many known bladder cancer genes, including TP53 , KDM6A , and RB1 , as well as copy number alterations such as CDKN2A loss was similar in RA-MIBC and non-RA-MIBC. We identified unique mutational properties that likely contribute to the distinct biological and clinical features of RA-MIBC. Bladder cancer is a rare but serious diagnosis following radiation for prostate cancer. We characterized genetic features of bladder tumors arising after prostate radiotherapy, and identify similarities with and differences from bladder tumors from patients without previous radiation. [ABSTRACT FROM AUTHOR]

Lysine acetylation (LysAc), a form of reversible protein posttranslational modification previously known only for histone regulation in plants, is shown to be widespread in Arabidopsis (Arabidopsis thaliana). Sixty-four Lys modification sites were identified on 57 proteins, which operate in a wide variety of pathways/processes and are located in various cellular compartments. A number of photosynthesis-related proteins are among this group of LysAc proteins, including photosystem II (PSII) subunits, light-harvesting chlorophyll a/b-binding proteins (LHCb), Rubisco large and small subunits, and chloroplastic ATP synthase (β-subunit). Using two-dimensional native green/sodium dodecyl sulfate gels, the loosely PSII-bound LHCb was separated from the LHCb that is tightly bound to PSII and shown to have substantially higher level of LysAc, implying that LysAc may play a role in distributing the LHCb complexes. Several potential LysAc sites were identified on eukaryotic elongation factor-1A (eEF-1A) by liquid chromatography/mass spectrometry and using sequence- and modification-specific antibodies the acetylation of Lys-227 and Lys-306 was established. Lys-306 is contained within a predicted calmodulin-binding sequence and acetylation of Lys-306 strongly inhibited the interactions of eEF-1A synthetic peptides with calmodulin recombinant proteins in vitro. These results suggest that LysAc of eEF-1A may directly affect regulatory properties and localization of the protein within time cell. Overall, these findings reveal the possibility that reversible LysAc may be an important and previously unknown regulatory mechanism of a large number of nonhistone proteins affecting a wide range of pathways and processes in Arabidopsis and likely in all plants. [ABSTRACT FROM AUTHOR]

This study demonstrates that germline mutations in the TP53 gene are likely to predispose men to prostate cancer. Current Li-Fraumeni syndrome screening guidelines should be updated to consider annual prostate cancer screening, and TP53 should be considered in germline prostate cancer susceptibility testing. Inherited germline TP53 pathogenic and likely pathogenic variants (g TP53) cause autosomal dominant multicancer predisposition including Li-Fraumeni syndrome (LFS). However, there is no known association of prostate cancer with gTP53. To determine whether gTP53 predisposes to prostate cancer. This multi-institutional retrospective study characterizes prostate cancer incidence in a cohort of LFS males and g TP53 prevalence in a prostate cancer cohort. We evaluated the spectrum of g TP53 variants and clinical features associated with prostate cancer. We identified 31 prostate cancer cases among 163 adult LFS males, including 26 of 54 aged ≥50 yr. Among 117 LFS males without prostate cancer at the time of genetic testing, six were diagnosed with prostate cancer over a median (interquartile range [IQR]) of 3.0 (1.3–7.2) yr of follow-up, a 25-fold increased risk (95% confidence interval [CI] 9.2–55; p < 0.0001). We identified g TP53 in 38 of 6850 males (0.6%) in the prostate cancer cohort, a relative risk 9.1-fold higher than that of population controls (95% CI 6.2–14; p < 0.0001; gnomAD). We observed hotspots at the sites of attenuated variants not associated with classic LFS. Two-thirds of available g TP53 prostate tumors had somatic inactivation of the second TP53 allele. Among g TP53 prostate cancer cases in this study, the median age at diagnosis was 56 (IQR: 51–62) yr, 44% had Gleason ≥8 tumors, and 29% had advanced disease at diagnosis. Complementary analyses of prostate cancer incidence in LFS males and g TP53 prevalence in prostate cancer cohorts suggest that g TP53 predisposes to aggressive prostate cancer. Prostate cancer should be considered as part of LFS screening protocols and TP53 considered in germline prostate cancer susceptibility testing. Inherited pathogenic variants in the TP53 gene are likely to predispose men to aggressive prostate cancer. [ABSTRACT FROM AUTHOR]

Bladder cancer is a genetically heterogeneous disease, and novel therapeutic strategies are needed to expand treatment options and improve clinical outcomes. Here, we identified a unique subset of urothelial tumors with focal amplification of the RAF1 (CRAF) kinase gene. RAF1-amplified tumors had activation of the RAF/MEK/ERK signaling pathway and exhibited a luminal gene expression pattern. Genetic studies demonstrated that RAF1-amplified tumors were dependent upon RAF1 activity for survival, and RAF1-activated cell lines and patient-derived models were sensitive to available and emerging RAF inhibitors as well as combined RAF plus MEK inhibition. Furthermore, we found that bladder tumors with HRAS- or NRAS-activating mutations were dependent on RAF1-mediated signaling and were sensitive to RAF1-targeted therapy. Together, these data identified RAF1 activation as a dependency in a subset making up nearly 20% of urothelial tumors and suggested that targeting RAF1-mediated signaling represents a rational therapeutic strategy. [ABSTRACT FROM AUTHOR]

The use of race in medicine has recently come to a reckoning,[1],[2] and the field of cancer genomics is not exempt from this critical introspection. Analysis was limited to tumors sequenced by Memorial Sloan Kettering (MSK) and Dana-Farber Cancer Institute (DFCI), as most evaluated tumor types in the GENIEv8.1 registry (66%) are captured by MSK/DFCI sequencing initiatives (Data Supplement). In primary CRC, Asian patients had significantly fewer mutations compared with White patients ( I P i =.01; Fig 1H). [Extracted from the article]

Intense neoadjuvant androgen deprivation therapy (ADT) before radical prostatectomy (RP) is an investigational approach to reduce recurrence rates in men with high-risk localized prostate cancer (PCa). The impact of germline DNA damage repair (gDDR) gene alterations on response to intense neoadjuvant ADT is not known. To evaluate the prevalence of gDDR alterations among men with localized PCa at high risk of recurrence and evaluate their impact on response to intense neoadjuvant ADT. We performed germline panel sequencing for 201 men with intermediate- and high-risk localized PCa from five randomized multicenter clinical trials of intense neoadjuvant ADT before RP. Intense neoadjuvant ADT followed by RP. The prevalence of pathogenic gDDR alterations and their association with exceptional pathologic response (complete response or minimal residual disease, defined as residual tumor with the largest cross-section dimension ≤5 mm) to intense neoadjuvant ADT and rates of post-RP biochemical recurrence. Pathogenic gDDR alterations were detected in 19 (9.5%) of the 201 PCa patients. The most frequently altered genes were BRCA2 (n = 6; 3.0%) and ATM (n = 4; 2.0%). Patients with gDDR alterations exhibited similar rates of exceptional pathologic response (26% vs 22%), pT3 disease (42% vs 53%), lymph node involvement (5.3% vs 10%), extraprostatic extension (35% vs 54%), and positive margins (5.3% vs 13%) to patients without gDDR alterations (all p > 0.05). The 3-yr biochemical recurrence–free survival was also similar at 45% (95% confidence interval 7.9–78%) for men with gDDR alterations and 55% (95% confidence interval 44–64%) for men without gDDR alterations. gDDR alterations are common among men with intermediate- and high-risk localized PCa. Men with gDDR alterations appear to have a comparable response to intense neoadjuvant ADT to that among men without gDDR alterations and should not be excluded from consideration for this treatment approach. Intense therapy to inhibit the production of androgen hormones (eg, testosterone) before surgery may minimize the risk of cancer recurrence for men with high-risk localized prostate cancer. Inherited mutations in certain DNA repair genes are associated with particularly high rates of recurrence. We found that men with these mutations respond equally well to this intense androgen inhibition before surgery as men without the mutations. We identified pathogenic germline DNA damage repair (gDDR) alterations in 10% of men with localized high-risk prostate cancer. Despite their association with aggressive disease, we observed comparable pathologic response rates to intense neoadjuvant androgen deprivation therapy before prostatectomy for men with versus without gDDR alterations. [ABSTRACT FROM AUTHOR]

PURPOSE: To inform precision oncology, methods are needed to use electronic health records (EHRs) to identify patients with cancer who are experiencing clinical inflection points, consistent with worsening prognosis or a high propensity to change treatment, at specific time points. Such patients might benefit from real-time screening for clinical trials. METHODS: Using serial unstructured imaging reports for patients with solid tumors or lymphoma participating in a single-institution precision medicine study, we trained a deep neural network natural language processing (NLP) model to dynamically predict patients' prognoses and propensity to start new palliative-intent systemic therapy within 30 days. Model performance was evaluated using Harrell's c-index (for prognosis) and the area under the receiver operating characteristic curve (AUC; for new treatment and new clinical trial enrollment). Associations between model outputs and manual annotations of cancer progression were also evaluated using the AUC. RESULTS: A deep NLP model was trained and evaluated using 302,688 imaging reports for 16,780 patients. In a held-out test set of 34,770 reports for 1,952 additional patients, the model predicted survival with a c-index of 0.76 and initiation of new treatment with an AUC of 0.77. Model-generated prognostic scores were associated with annotation of cancer progression on the basis of manual EHR review (n = 1,488 reports for 110 patients with lung or colorectal cancer) with an AUC of 0.78, and predictions of new treatment were associated with annotation of cancer progression on the basis of manual EHR review with an AUC of 0.84. CONCLUSION: Training a deep NLP model to identify clinical inflection points among patients with cancer is feasible. This approach could identify patients who may benefit from real-time targeted clinical trial screening interventions at health system scale. [ABSTRACT FROM AUTHOR]

In primary CRC, Asian patients had significantly fewer mutations compared with White patients ( I P i =.01; Fig 1H). Analysis was limited to tumors sequenced by Memorial Sloan Kettering (MSK) and Dana-Farber Cancer Institute (DFCI), as most evaluated tumor types in the GENIEv8.1 registry (66%) are captured by MSK/DFCI sequencing initiatives (Data Supplement). The use of race in medicine has recently come to a reckoning,[1],[2] and the field of cancer genomics is not exempt from this critical introspection. [Extracted from the article]