Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases

Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, which include >400 terabytes of data from 1087 subjects, are now available to the research community via the NIMH Data Archive (NDA) and are described here.

Identifying Phased Mutations and Complex Rearrangements in Human Prostate Cancer Cell Lines through Linked-Read Whole-Genome Sequencing

A limited number of cell lines have fueled the majority of preclinical prostate cancer research, but their genomes remain incompletely characterized. Here, we utilized whole-genome linked-read sequencing for comprehensive characterization of phased mutations and rearrangements in the most commonly used cell lines in prostate cancer research including PC3, LNCaP, DU145, CWR22Rv1, VCaP, LAPC4, MDA-PCa-2b, RWPE-1, and four derivative castrate-resistant (CR) cell lines LNCaP_Abl, LNCaP_C42b, VCaP-CR, and LAPC4-CR. Phasing of mutations allowed determination of "gene-level haplotype" to assess whether genes harbored heterozygous mutations in one or both alleles. Phased structural variant analysis allowed identification of complex rearrangement chains consistent with chromothripsis and chromoplexy. In addition, comparison of parental and derivative CR lines revealed previously known and novel genomic alterations associated with the CR phenotype.

IMPLICATIONS

This study therefore comprehensively characterized phased genomic alterations in the commonly used prostate cancer cell lines, providing a useful resource for future prostate cancer research.

Abstract 2198: Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines

Prostate cancer research has relied on a limited number of prostate cancer cell lines despite decades of effort in establishing them from human prostate cancers. These cell lines thus represent precious resources for in vitro and in vivo preclinical studies of prostate cancer and have fueled many advances in the field. While there has been tremendous effort in characterizing their molecular profiles and genomic features, comprehensive whole genome sequencing with allelic phasing of genomic alterations has not been undertaken to date. Here, we utilized powerful whole genome linked-read sequencing of high molecular weight DNA (>60Kbp) from eight common prostate cancer cell lines as well as four castrate resistant (CR) subclones derived from three of those cell lines. Long range information enabled assembly of mutations (single nucleotide variants-SNVs and small indels) and structural variants (SVs) across the genome into large phased blocks. This allowed accounting of multiple mutations within a given gene to assess whether they were present on a single allele, or on opposite alleles, to assess the “allelic status” of phased mutations. Using this phased mutational analysis, we found that in cell lines with microsatellite instability (MSI; LNCaP, LAPC4, DU145, CWR22Rv1), 10-20% of a priori defined driver genes are inactivated by at least two heterozygous mutations on opposite alleles. Overall, MSI cell lines had higher levels of mutations and fewer SVs than those that were microsatellite stable (MSS; PC3, VCaP). The phased SV analysis allowed identification of complex rearrangement chains consistent with chromothripsis (PC3, DU145) and chromoplexy (VCAP, LnCAP-C42b), including reconstruction of the complex chained TMPRSS2-ERG rearrangement in VCaP. Additionally, comparison of parental and CR subclones revealed previously known as well as several novel genomic alterations that were associated with the CR subclones, including chromosome 8 amplification (in LNCaP-Abl and LAPC4-CR), further androgen receptor amplification amongst a host of increased complex SVs (in VCAP-CR), SWI/SNF mutations and increased complex SVs (in LNCAP-C42b), CDK12 biallelic loss and numerous tandem duplications (in LAPC4-CR). This study therefore comprehensively characterizes allelically phased genomic alterations in the commonly used prostate cancer cell lines and provides a useful resource for future cancer research.

Citation Format: Minh-Tam Pham, Harshath Gupta, Anuj Gupta, Ajay Vaghasia, Alyza M. Skaist, McKinzie A. Garrison, Roshan Chikamarne, Sarah J. Wheelan, William G. Nelson, Srinivasan Yegnasubramanian. Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2198.

Abstract P4-22-11: Combined targeted therapies for advanced triple negative breast cancer: A phase II trial of nab-paclitaxel and bevacizumab followed by maintenance targeted therapy with bevacizumab and erlotinib

Background: Chemotherapy remains the mainstay of therapy for patients with metastatic triple negative breast cancer (TNBC). We hypothesized that the addition of biologic agents targeting key pathways (bevacizumab targeting angiogenesis and erlotinib directed against EGFR) may prolong progression free survival (PFS) and offer a novel treatment strategy free from chemotherapy for patients with metastatic TNBC.

Methods: Patients with TNBC receiving initial therapy for metastatic disease were eligible for this multicenter phase II trial (NCT00733408) conducted at an academic center and affiliated, community practice sites. Induction therapy included nab-paclitaxel 100 mg/m2 IV Qweek (wk) and Bevacizumab 10 mg/kg IV Q2wks x 24 weeks. Patients free of progression at 24 wks began maintenance therapy with bevacizumab 10 mg/kg IV Q2wks and erlotinib 150 mg po daily until progression with radiographic assessment every 8 wks. Primary objective was PFS with secondary objectives of response rate, overall survival (OS) and safety. All eligible patients were included in the analysis of PFS and OS. Response was evaluated among patients with measurable disease by RECIST 1.1 with central review. Patients with inadequate disease assessments were coded as non-responders. Kaplan-Meier method was used to estimate PFS and OS with patients censored at date of last tumor assessment (PFS) or date of last follow up (OS).

Results: From April 2009 – December 2015, 58 patients (median age 54, range 33-83) were enrolled; 56 (97%) had measurable disease, and all had metastatic TNBC by local assessment. 33 (57%) patients completed induction; 22 (38%) came off study during induction; 3 (5%) continue on maintenance therapy. 4 patients discontinued therapy prior to first assessment. As of June 8, 2016, 53 patients (91%) have progressed. Median follow up for surviving patients is 14.5 months (range 4.1-65.4). Median PFS is 7.7 months (95% CI 5.7, 9.5). Of 56 patients with measurable disease, 38 (66%) had partial response (PR); 10 (17%) with stable disease for clinical benefit rate (CBR) of 86%. Median OS is 18.2 months (95% CI 16.3, 24.5). Most common grade 3-4 toxicities during induction were neutropenia [17 (29%), 1 grade 4], fatigue [13 (22%), all grade 3], leukopenia [7 (12%), all grade 3], and neuropathy [7 (12%), all grade 3]. Rash was most common ≥ grade 3 toxicity during maintenance [4 (7%), grade 3]. One patient experienced clinical CHF during maintenance month 16 requiring bevacizumab discontinuation. Conclusions: Nab-paclitaxel and bevacizumab followed by maintenance targeted therapy with bevacizumab and erlotinib was well tolerated. While the observed PFS did not meet pre-specified criteria of interest, the majority of patients experienced clinical benefit (86%) with 30 (57%) receiving maintenance targeted therapy. Correlative studies are ongoing. Supported by Genentech (OSI4266s), Celegene (AX-CL-BRST-PI-003828) and Janssen.

Citation Format: Specht JM, Gadi VK, Gralow JR, Korde LA, Linden HM, Salazar LG, Rodler ET, Cundy A, Buening BJ, Baker KK, Redman MW, Kurland BF, Garrison MA, Smith JC, vanHaelst C, Anderson JE. Combined targeted therapies for advanced triple negative breast cancer: A phase II trial of nab-paclitaxel and bevacizumab followed by maintenance targeted therapy with bevacizumab and erlotinib [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-22-11.

NMR-monitored titration of acid-stress bacterial chaperone HdeA reveals that Asp and Glu charge neutralization produces a loosened dimer structure in preparation for protein unfolding and chaperone activation

HdeA is a periplasmic chaperone found in several gram-negative pathogenic bacteria that are linked to millions of cases of dysentery per year worldwide. After the protein becomes activated at low pH, it can bind to other periplasmic proteins, protecting them from aggregation when the bacteria travel through the stomach on their way to colonize the intestines. It has been argued that one of the major driving forces for HdeA activation is the protonation of aspartate and glutamate side chains. The goal for this study, therefore, was to investigate, at the atomic level, the structural impact of this charge neutralization on HdeA during the transition from near-neutral conditions to pH 3.0, in preparation for unfolding and activation of its chaperone capabilities. NMR spectroscopy was used to measure pKa values of Asp and Glu residues and monitor chemical shift changes. Measurements of R2/R1 ratios from relaxation experiments confirm that the protein maintains its dimer structure between pH 6.0 and 3.0. However, calculated correlation times and changes in amide protection from hydrogen/deuterium exchange experiments provide evidence for a loosening of the tertiary and quaternary structures of HdeA; in particular, the data indicate that the dimer structure becomes progressively weakened as the pH decreases. Taken together, these results provide insight into the process by which HdeA is primed to unfold and carry out its chaperone duties below pH 3.0, and it also demonstrates that neutralization of aspartate and glutamate residues is not likely to be the sole trigger for HdeA dissociation and unfolding.

Within- versus cross-channel mechanisms in detection of envelope phase disparity

These experiments were designed to examine the mechanism of detection of phase disparity in the envelopes of two sinusoidally amplitude-modulated (AM) sinusoids. Specifically, they were performed to determine whether detection of envelope phase disparity was consistent with processing within a single channel in which the AM tones were simply added. In the first condition, with an 8-Hz modulation frequency, phase-disparity thresholds increased sharply with an initial increase in separation of the carrier frequencies. They then remained approximately constant when the separation was an octave or above. In the second condition, with carrier pairs of 1 and 2 kHz or 1 and 3.2 kHz and a modulation frequency of 8 Hz, thresholds were little affected as the level of one carrier was decreased relative to the other. With a modulation frequency of 128 Hz, for most subjects there was more of an effect of level disparity on thresholds. In the third condition, when the modulation frequency was 8 Hz, subjects showed relatively constant thresholds whether the signals were presented monotically, dichotically, or dichotically with low- and high-pass noise. Dichotic thresholds were typically higher than monotic when the modulation frequency was 128 Hz. These results suggest that it is not necessary to have information available within a single additive channel to detect envelope phase disparity. In certain circumstances, a comparison across channels may be used to detect such disparities.