Genome evolution in the allotetraploid frog Xenopus laevis

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ???fossil??? transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.ope

Abstract P4-07-01: Tumor expression and microenvironment in HER2-positive breast cancer before and on HER2-targeted therapy: Analysis of microarray expression data from the TRIO-US B07 trial

Abstract Background: Neoadjuvant HER2-targeted therapy in combination with chemotherapy is a standard treatment approach for early-stage HER2-positive breast cancer. Proposed biomarkers to predict pathologic complete response (pCR), and thereby inform which patients may benefit from de-escalation of therapy, include expression-based subtyping and immune enrichment scores. Little is known about how tumors and their microenvironment may change with HER2-targeted therapy alone, and whether these changes may predict outcome. Methods: The TRIO-US B07 phase II trial randomized 128 participants with stage I-III HER2-positive breast cancer to trastuzumab (N=34), lapatinib (N=36), or the combination (N=58) for three weeks, followed by six cycles of docetaxel and carboplatin with continued HER2-targeted therapy. Fresh-frozen core biopsies of the tumor prior to therapy (N=110) and after 14-21 days of HER2-targeted therapy alone (N=89) were collected, and RNA was extracted and subjected to Agilent Whole Human Genome 44K 2-color chip. The pre-treatment tumor RNA was normalized against a mixed breast tumor reference, and the on-treatment tumor RNA against the matched pre-treatment sample. Absolute intrinsic molecular subtyping was used to determine intrinsic subtype, the iC10 expression-based classifier to determine integrative subtype, gene set enrichment analysis (GSEA) to assess signature changes across treatment, single-sample GSEA to compare individual gene signature scores between tumors, and CIBERSORT to quantify immune cell populations before and on treatment. Results: Primary trial results have been reported previously and showed a pCR rate of 47% with trastuzumab, 25% with lapatinib, and 52% with the combination. Prior to treatment, 56% of tumors classified as the HER2-enriched intrinsic subtype and 78% as the iC5 integrative subtype. HER2-enriched tumors trended toward a higher rate of pCR relative to other intrinsic subtypes (50% vs 33%, P=0.12), as did iC5 tumors relative to other integrative subtypes (48% vs 25%, P=0.08). However, in multivariate analysis, HER2 FISH ratio (P=0.04) and hormone receptor status (P=0.02), each associated themselves with intrinsic and integrative subtype, proved the most valuable in predicting pCR, with little information added by expression-based subtyping. Immune cell signatures correlated with pCR in the trastuzumab-containing arms only. Of 65 gene signatures tested, 47 changed across HER2-targeted therapy with false discovery rate < 0.1, driven by decreasing tumor proliferation, increasing immune cell signatures, and increasing stromal cell/epithelial mesenchymal transition signatures. Quantification of immune cell populations suggested the immune changes were both anti-tumor (CD8+ T cells) and pro-tumor (M2 macrophages). Intrinsic subtype changed in 54% of tumors (79% of these converting to normal-like) and integrative subtype changed in 26%. Change in subtype, proliferation, or immune infiltration with targeted therapy did not correlate with pCR. A higher proportion of tumors treated with trastuzumab alone maintained their proliferation (42%), compared with lapatinib alone (20%; P=0.16) or the combination (16%; P=0.04). Conclusions: In the TRIO-US B07 study, the biomarkers most predictive of response to neoadjuvant HER2-targeted therapy were hormone receptor status in combination with HER2 FISH ratio. Multiple changes in the tumor and its microenvironment occurred with HER2-targeted therapy, but these changes did not predict pCR. Tumors treated with lapatinib tended to decrease proliferation more than tumors treated with trastuzumab, despite trastuzumab being more effective in preventing recurrence, an observation with implications for window of opportunity studies. Citation Format: Jennifer L. Caswell-Jin, Katherine L. McNamara, Judy Dering, Hsiao-Wang Chen, Robert Dichmann, Alejandra Perez, Ravindranath Patel, Eran Kotler, Jason J. Zoeller, Joan S. Brugge, Michael F. Press, Dennis J. Slamon, Christina Curtis, Sara A. Hurvitz. Tumor expression and microenvironment in HER2-positive breast cancer before and on HER2-targeted therapy: Analysis of microarray expression data from the TRIO-US B07 trial [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-07-01

Phase Ib/II single-arm trial evaluating the combination of everolimus, lapatinib and capecitabine for the treatment of HER2-positive breast cancer with brain metastases (TRIO-US B-09).

BackgroundImproving outcomes for patients with human epidermal growth factor 2-positive (HER2+) central nervous system (CNS) metastases remains an unmet clinical need. This trial evaluated a novel combination of everolimus, lapatinib and capecitabine for this disease.MethodsPatients with trastuzumab-pretreated, HER2+ breast cancer brain metastasis without prior therapy with a mammalian target of rapamycin (mTOR) inhibitor were eligible. Patients received lapatinib and everolimus daily (continuously) and capecitabine twice daily (d1-14) in 21-d cycles. The primary endpoint was the 12-week CNS objective response rate (ORR). Secondary endpoints included safety, progression-free survival (PFS), overall survival (OS), best CNS ORR and extra-CNS ORR.ResultsA total of 19 participants were enrolled and treated with ⩾1 dose of the study drug. The median age was 58.5 years, the median number of therapies for metastatic breast cancer was 2.5 (0-11). Pretrial, 74% of participants had received prior lapatinib, capecitabine or both. A total of 63% had received previous CNS radiation or surgical resection and CNS radiation. The maximum tolerated doses were lapatinib at 1000 mg, everolimus at 10 mg, and capecitabine at 1000 mg/m2. Phase II proceeded with capecitabine at 750 mg/m2 due to better tolerability. The most common grade 3/4 adverse events were mucositis (16%), diarrhea, fatigue, and hypokalemia (11% each). Of 11 participants evaluable for 12-week CNS ORR, 3 (27%) had partial response and 7 (64%) had stable disease. The best CNS ORR in eligible participants was 28% (5/18). The median PFS and OS were 6.2 and 24.2 months, respectively.ConclusionsThis novel triplet combination of lapatinib, everolimus, and capecitabine is well tolerated and yielded a 27% response rate in the CNS at 12 weeks in heavily pretreated participants. Larger studies are warranted to further evaluate this regimen.Trial registrationClinicalTrials.gov: NCT01783756. Registered 05 February 2013, https://clinicaltrials.gov/ct2/show/NCT01783756

Phase Ib/II single-arm trial evaluating the combination of everolimus, lapatinib and capecitabine for the treatment of HER2-positive breast cancer with brain metastases (TRIO-US B-09)

Background: Improving outcomes for patients with human epidermal growth factor 2-positive (HER2+) central nervous system (CNS) metastases remains an unmet clinical need. This trial evaluated a novel combination of everolimus, lapatinib and capecitabine for this disease. Methods: Patients with trastuzumab-pretreated, HER2+ breast cancer brain metastasis without prior therapy with a mammalian target of rapamycin (mTOR) inhibitor were eligible. Patients received lapatinib and everolimus daily (continuously) and capecitabine twice daily (d1–14) in 21-d cycles. The primary endpoint was the 12-week CNS objective response rate (ORR). Secondary endpoints included safety, progression-free survival (PFS), overall survival (OS), best CNS ORR and extra-CNS ORR. Results: A total of 19 participants were enrolled and treated with ⩾1 dose of the study drug. The median age was 58.5 years, the median number of therapies for metastatic breast cancer was 2.5 (0–11). Pretrial, 74% of participants had received prior lapatinib, capecitabine or both. A total of 63% had received previous CNS radiation or surgical resection and CNS radiation. The maximum tolerated doses were lapatinib at 1000 mg, everolimus at 10 mg, and capecitabine at 1000 mg/m 2 . Phase II proceeded with capecitabine at 750 mg/m 2 due to better tolerability. The most common grade 3/4 adverse events were mucositis (16%), diarrhea, fatigue, and hypokalemia (11% each). Of 11 participants evaluable for 12-week CNS ORR, 3 (27%) had partial response and 7 (64%) had stable disease. The best CNS ORR in eligible participants was 28% (5/18). The median PFS and OS were 6.2 and 24.2 months, respectively. Conclusions: This novel triplet combination of lapatinib, everolimus, and capecitabine is well tolerated and yielded a 27% response rate in the CNS at 12 weeks in heavily pretreated participants. Larger studies are warranted to further evaluate this regimen. Trial registration: ClinicalTrials.gov: NCT01783756. Registered 05 February 2013, https://clinicaltrials.gov/ct2/show/NCT0178375

Pathologic and molecular responses to neoadjuvant trastuzumab and/or lapatinib from a phase II randomized trial in HER2-positive breast cancer (TRIO-US B07).

In this multicenter, open-label, randomized phase II investigator-sponsored neoadjuvant trial with funding provided by Sanofi and GlaxoSmithKline (TRIO-US B07, Clinical Trials NCT00769470), participants with early-stage HER2-positive breast cancer (N = 128) were recruited from 13 United States oncology centers throughout the Translational Research in Oncology network. Participants were randomized to receive trastuzumab (T; N = 34), lapatinib (L; N = 36), or both (TL; N = 58) as HER2-targeted therapy, with each participant given one cycle of this designated anti-HER2 therapy alone followed by six cycles of standard combination chemotherapy with the same anti-HER2 therapy. The primary objective was to estimate the rate of pathologic complete response (pCR) at the time of surgery in each of the three arms. In the intent-to-treat population, we observed similar pCR rates between T (47%, 95% confidence interval [CI] 30-65%) and TL (52%, 95% CI 38-65%), and a lower pCR rate with L (25%, 95% CI 13-43%). In the T arm, 100% of participants completed all protocol-specified treatment prior to surgery, as compared to 69% in the L arm and 74% in the TL arm. Tumor or tumor bed tissue was collected whenever possible pre-treatment (N = 110), after one cycle of HER2-targeted therapy alone (N = 89), and at time of surgery (N = 59). Higher-level amplification of HER2 and hormone receptor (HR)-negative status were associated with a higher pCR rate. Large shifts in the tumor, immune, and stromal gene expression occurred after one cycle of HER2-targeted therapy. In contrast to pCR rates, the L-containing arms exhibited greater proliferation reduction than T at this timepoint. Immune expression signatures increased in all arms after one cycle of HER2-targeted therapy, decreasing again by the time of surgery. Our results inform approaches to early assessment of sensitivity to anti-HER2 therapy and shed light on the role of the immune microenvironment in response to HER2-targeted agents

The Genome of the Western Clawed Frog Xenopus tropicalis

The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes over 20,000 protein-coding genes, including orthologs of at least 1,700 human disease genes. Over a million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like other tetrapods, the genome contains gene deserts enriched for conserved non-coding elements. The genome exhibits remarkable shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage