Human Biology Publications

Chromosome length and gene density contribute to micronuclear membrane stability

Life Sci Alliance

2022 Anna Mammel; Amanda Gunn; Emily Hatch

Micronuclei are derived from missegregated chromosomes and frequently lose membrane integrity, leading to DNA damage, innate immune activation, and metastatic signaling. Here, we demonstrate that two characteristics of the trapped chromosome, length and gene density, are key contributors to micronuclei membrane stability and determine the timing of micronucleus rupture. We demonstrate that these results are not due to chromosome-specific differences in spindle position or initial protein recruitment during post-mitotic nuclear envelope assembly. Micronucleus size strongly correlates with lamin B1 levels and nuclear pore density in intact micronuclei, but, unexpectedly, lamin B1 levels do not completely predict nuclear lamina organization or membrane stability. Instead, small gene-dense micronuclei have decreased nuclear lamina gaps compared to large micronuclei, despite very low levels of lamin B1. Our data strongly suggest that nuclear envelope composition defects previously correlated with membrane rupture only partly explain membrane stability in micronuclei. We propose that an unknown factor linked to gene density has a separate function that inhibits the appearance of nuclear lamina gaps and delays membrane rupture until late in the cell cycle.

HIV-1 Vif gained breadth in APOBEC3G specificity after cross-species transmission of its precursors

J Virol

2021 Nicholas Chesarino; Michael Emerman

APOBEC3G (A3G) is a host-encoded cytidine deaminase that potently restricts retroviruses, such as HIV-1, and depends on its ability to package into virions. As a consequence of this, HIV-1 protein Vif has evolved to antagonize human A3G by targeting it for ubiquitination and subsequent degradation. There is an ancient arms-race between Vif and A3G highlighted by amino acids 128 and 130 in A3G that have evolved under positive selection due to Vif-mediated selective pressure in Old World primates. Nonetheless, not all possible amino acid combinations at these sites have been sampled by nature and it is not clear the evolutionary potential of species to resist Vif antagonism. To explore the evolutionary space of positively selected sites in the Vif-binding region of A3G, we designed a combinatorial mutagenesis screen to introduce all 20 amino acids at sites 128 and 130. Our screen uncovered mutants of A3G with several interesting phenotypes, including loss of antiviral activity and resistance of Vif antagonism. However, HIV-1 Vif exhibited remarkable flexibility in antagonizing A3G 128 and 130 mutants, which significantly reduces viable Vif resistance strategies for hominid primates. Importantly, we find that broadened Vif specificity was conferred through Loop 5 adaptations that were required for cross-species adaptation from Old World monkey A3G to hominid A3G. Our evidence suggests that Vif adaptation to novel A3G interfaces during cross-species transmission may train Vif towards broadened specificity that can further facilitate cross-species transmissions and raise the barrier to host resistance. Importance APOBEC3G (A3G) is an antiviral protein that potently restricts retroviruses like HIV. In turn, the HIV-1 protein Vif has evolved to antagonize A3G through degradation. Two rapidly evolving sites in A3G confer resistance to unadapted Vif and act as a barrier to cross-species transmission of retroviruses. We recently identified a single amino acid mutation in an SIV Vif that contributed to the cross-species origins of SIV infecting chimpanzee, and ultimately the HIV-1 pandemic. This mutation broadened specificity of this Vif to both antagonize the A3G of its host while simultaneously overcoming the A3G barrier in the great apes. In this work, we explore the evolutionary space of human A3G at these rapidly evolving sites to understand if the broadened Vif specificity gained during cross-species transmission confers an advantage to HIV-1 Vif in its host-virus arms race with A3G.

Genomic attributes of homology-directed DNA repair deficiency in metastatic prostate cancer

JCI Insight

2021 Ilsa Coleman; Gavin Ha; Colin Pritchard; Payel Chatterjee; Eva Corey; Navonil De Sarkar; Emily Kohlbrenner; Peter Nelson; Radhika Patel; Talina Nunez; Stephen Salipante; Michael Schweizer; Brian Hanratty; Ruth Dumpit; Sander Frank; Sayan Dasgupta; Jared Lucas; Robert Montgomery; Colm Morrissey; Lisa Ang; Michael Haffner

Cancers with homology-directed DNA repair (HRR) deficiency exhibit high response rates to poly(ADP-ribose) polymerase inhibitors (PARPi) and platinum chemotherapy. Though mutations disrupting BRCA1 and BRCA2 associate with HRR deficiency (HRRd), patterns of genomic aberrations and mutation signatures may be more sensitive and specific indicators of compromised repair. Here, we evaluated whole-exome sequences from 418 metastatic prostate cancers (mPCs) and determined that one-fifth exhibited genomic characteristics of HRRd that included Catalogue Of Somatic Mutations In Cancer mutation signature 3. Notably, a substantial fraction of tumors with genomic features of HRRd lacked biallelic loss of a core HRR-associated gene, such as BRCA2. In this subset, HRRd associated with loss of chromodomain helicase DNA binding protein 1 but not with mutations in serine-protein kinase ATM, cyclin dependent kinase 12, or checkpoint kinase 2. HRRd genomic status was strongly correlated with responses to PARPi and platinum chemotherapy, a finding that supports evaluating biomarkers reflecting functional HRRd for treatment allocation.

Machine learning modeling of genome-wide copy number alteration signatures reliably predicts IDH mutational status in adult diffuse glioma

Acta Neuropathol Commun

2021 Patrick Cimino; Linda Shapiro; Eric Holland

Knowledge of 1p/19q-codeletion and IDH1/2 mutational status is necessary to interpret any investigational study of diffuse gliomas in the modern era. While DNA sequencing is the gold standard for determining IDH mutational status, genome-wide methylation arrays and gene expression profiling have been used for surrogate mutational determination. Previous studies by our group suggest that 1p/19q-codeletion and IDH mutational status can be predicted by genome-wide somatic copy number alteration (SCNA) data alone, however a rigorous model to accomplish this task has yet to be established. In this study, we used SCNA data from 786 adult diffuse gliomas in The Cancer Genome Atlas (TCGA) to develop a two-stage classification system that identifies 1p/19q-codeleted oligodendrogliomas and predicts the IDH mutational status of astrocytic tumors using a machine-learning model. Cross-validated results on TCGA SCNA data showed near perfect classification results. Furthermore, our astrocytic IDH mutation model validated well on four additional datasets (AUC = 0.97, AUC = 0.99, AUC = 0.95, AUC = 0.96) as did our 1p/19q-codeleted oligodendroglioma screen on the two datasets that contained oligodendrogliomas (MCC = 0.97, MCC = 0.97). We then retrained our system using data from these validation sets and applied our system to a cohort of REMBRANDT study subjects for whom SCNA data, but not IDH mutational status, is available. Overall, using genome-wide SCNAs, we successfully developed a system to robustly predict 1p/19q-codeletion and IDH mutational status in diffuse gliomas. This system can assign molecular subtype labels to tumor samples of retrospective diffuse glioma cohorts that lack 1p/19q-codeletion and IDH mutational status, such as the REMBRANDT study, recasting these datasets as validation cohorts for diffuse glioma research.

Evaluating the Outcomes of Active Surveillance in Grade Group 2 Prostate Cancer: Prospective Results From the Canary PASS Cohort

J Urol

2021 Yingye Zheng; Menghan Liu; Peter Nelson; Lisa Newcomb; Kehao Zhu; Daniel Lin

INTRODUCTION: Active Surveillance (AS) for grade group 2 (GG2) patients is not yet well-defined. We sought to compare clinical outcomes of men with GG1 and GG2 prostate cancer undergoing AS in a large prospective North American cohort. METHODS: Participants were prospectively enrolled in an AS study with protocol-directed follow up at 10 centers in the US and Canada. We evaluated time from diagnosis to biopsy grade reclassification and time to treatment. In men treated after initial surveillance, adverse pathology (AP) and recurrence were also analyzed. RESULTS: At diagnosis, 154 (9%) had GG2 and 1574 (91%) had GG1. Five-year reclassification rates were similar between GG2 or GG1 (30% vs 37%, p=0.11). However, more patients with GG2 were treated at 5 years (58% vs 34%, p <0.001) and GG at diagnosis was associated with time to treatment (HR=1.41; p=0.01). Treatment rates were similar in patients who reclassified during AS, but in patients who did not reclassify, those diagnosed with GG2 underwent definitive treatment more often than GG1 (5-year treatment rates 52% and 12%, p <0.0001). In participants who underwent RP after initial surveillance, the adjusted risk of AP was similar (HR=1.26; p=0.4). Biochemical recurrence (BCR) within 3 years of treatment for GG2 and GG1 patients was 6% for both groups. CONCLUSIONS: In patients on active surveillance, the rate of definitive treatment is higher after an initial diagnosis of GG2 than GG1. Adverse pathology after RP and short-term BCR after definitive treatment were similar between GG2 and GG1.

Inherited TP53 Variants and Risk of Prostate Cancer

Eur Urol

2021 Robert Montgomery; Peter Nelson; Heather Cheng; Brian Shirts; Marianne Dubard-Gault; Roman Gulati; Colin Pritchard

BACKGROUND: Inherited germline TP53 pathogenic and likely pathogenic variants (gTP53) cause autosomal dominant multicancer predisposition including Li-Fraumeni syndrome (LFS). However, there is no known association of prostate cancer with gTP53. OBJECTIVE: To determine whether gTP53 predisposes to prostate cancer. DESIGN, SETTING, AND PARTICIPANTS: This multi-institutional retrospective study characterizes prostate cancer incidence in a cohort of LFS males and gTP53 prevalence in a prostate cancer cohort. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We evaluated the spectrum of gTP53 variants and clinical features associated with prostate cancer. RESULTS AND LIMITATIONS: We identified 31 prostate cancer cases among 163 adult LFS males, including 26 of 54 aged 50yr. 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 gTP53 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 gTP53 prostate tumors had somatic inactivation of the second TP53 allele. Among gTP53 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. CONCLUSIONS: Complementary analyses of prostate cancer incidence in LFS males and gTP53 prevalence in prostate cancer cohorts suggest that gTP53 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. PATIENT SUMMARY: Inherited pathogenic variants in the TP53 gene are likely to predispose men to aggressive prostate cancer.

Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1

Sci Signal

2021 Sitapriya Moorthi; Shriya Kamlapurkar; April Lo; Alice Berger; Kristin Holmes

[Figure: see text].

Metagenomic analysis to identify novel infectious agents in systemic anaplastic large cell lymphoma

Infect Agent Cancer

2021 Susan Bullman

Systemic anaplastic large cell lymphoma (ALCL) is a rare CD30-expressing T-cell non-Hodgkin lymphoma. Risk of systemic ALCL is highly increased among immunosuppressed individuals. Because risk of cancers associated with viruses is increased with immunosuppression, we conducted a metagenomic analysis of systemic ALCL to determine whether a known or novel pathogen is associated with this malignancy. Total RNA was extracted and sequenced from formalin-fixed paraffin-embedded tumor specimens from 19 systemic ALCL cases (including one case from an immunosuppressed individual with human immunodeficiency virus infection), 3 Epstein-Barr virus positive diffuse large B-cell lymphomas (DLBCLs) occurring in solid organ transplant recipients (positive controls), and 3 breast cancers (negative controls). We used a pipeline based on the Genome Analysis Toolkit (GATK)-PathSeq algorithm to subtract out human RNA reads and map the remaining RNA reads to microbes. No microbial association with ALCL was identified, but we found Epstein-Barr virus in the DLBCL positive controls and determined the breast cancers to be negative. In conclusion, we did not find a pathogen associated with systemic ALCL, but because we analyzed only one ALCL tumor from an immunosuppressed person, we cannot exclude the possibility that a pathogen is associated with some cases that arise in the setting of immunosuppression.

Elimination of fluorescent protein immunogenicity permits modeling of metastasis in immune-competent settings

Cancer Cell

2022 Erica Goddard; Cyrus Ghajar; Jinxiang Dai; Candice Grzelak; Jeanna Kim; Ryann Shor; Slobodan Beronja; Andrea Lim; Emma Lederer; Kamya Rajaram


Molecular and Pathology Features of Colorectal Tumors and Patient Outcomes Are Associated with Fusobacterium nucleatum and Its Subspecies animalis

Cancer Epidemiol Biomarkers Prev

2022 Susan Bullman; Yi Lin; Jiayin Zheng; Amanda Phipps; Robert Steinfelder; Wei Sun; Barbara Banbury; Polly Newcomb; Conghui Qu; Li Hsu; Tabitha Harrison

BACKGROUND: Fusobacterium nucleatum activates oncogenic signaling pathways and induces inflammation to promote colorectal carcinogenesis. METHODS: We characterized F nucleatum and its subspecies in colorectal tumors and examined associations with tumor characteristics and colorectal cancer (CRC) specific survival. We conducted deep sequencing of nusA, nusG, and bacterial 16s rRNA genes in tumors from 1,994 CRC patients and assessed associations between F nucleatum presence and clinical characteristics, CRC-specific mortality, and somatic mutations. RESULTS: F nucleatum, which was present in 10.3% of tumors, was detected in a higher proportion of right-sided and advanced-stage tumors-particularly subspecies animalis. Presence of F nucleatum was associated with higher CRC-specific mortality (hazard ratio [HR], 1.97; P=0.0004). This association was restricted to non-hypermutated, microsatellite-stable tumors (HR, 2.13; P=0.0002) and those who received chemotherapy (HR = 1.92, CI: 1.07-3.45, p-value = 0.029). Only F nucleatum subspecies animalis, the main subspecies detected (65.8%), was associated with CRC-specific mortality (HR, 2.16; P=0.0016)-subspecies vincentii and nucleatum were not (HR, 1.07, P=0.86). Additional adjustment for tumor stage suggests that the effect of F nucleatum on mortality is partly driven by a stage shift. Presence of F nucleatum was associated with microsatellite instable tumors, tumors with POLE exonuclease domain mutations, ERBB3 mutations, and suggestively associated with TP53 mutations. CONCLUSIONS: F nucleatum, and particularly subspecies animalis, was associated with a higher CRC-specific mortality and specific somatic mutated genes. IMPACT: Our findings identify the F nucleatum subspecies animalis as negatively impacting CRC mortality which may occur through a stage shift and its effect on chemoresistance.