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To investigate germline predisposition in lymphoma, we performed whole-exome sequencing and discovered a novel variant (c.817-1GT) in programmed cell death 1 ligand 2 (PD-L2) in a family with early-onset lymphomas and other cancers. The variant was present in the proband with follicular lymphoma and his son with Hodgkin's lymphoma. It was in the terminal splice acceptor site of PD-L2 and embedded in a putative enhancer of Janus kinase 2 (JAK2) and programmed cell death 1 ligand (PD-L1). We also found that gene expression of PD-L2, PD-L1, and JAK2 was significantly increased. Using 3' rapid amplification of cDNA ends (3' RACE), we detected an abnormal PD-L2 transcript in the son. Thus, the c.817-1GT variant may result in the elevated PD-L2 expression due to the abnormal PD-L2 transcript and the elevated PD-L1 and JAK2 expression due to increased enhancer activity of PD-L1 and JAK2. The PD-L2 novel variant likely underlies the genetic etiology of the lymphomas in the family. As PD-L2 plays critical roles in tumor immunity, identification of PD-L2 as a germline predisposition gene may inform personalized immunotherapy in lymphoma patients.

The extent and importance of functional heterogeneity and crosstalk between tumor cells is poorly understood. Here, we describe the generation of clonal populations from a patient-derived ovarian clear cell carcinoma model which forms malignant ascites and solid peritoneal tumors upon intraperitoneal transplantation in mice. The clonal populations are engineered with secreted Gaussia luciferase to monitor tumor growth dynamics and tagged with a unique DNA barcode to track their fate in multiclonal mixtures during tumor progression. Only one clone, CL31, grows robustly, generating exclusively malignant ascites. However, multiclonal mixtures form large solid peritoneal metastases, populated almost entirely by CL31, suggesting that transient cooperative interclonal interactions are sufficient to promote metastasis of CL31. CL31 uniquely harbors ERBB2 amplification, and its acquired metastatic activity in clonal mixtures is dependent on transient exposure to amphiregulin, which is exclusively secreted by non-tumorigenic clones. Amphiregulin enhances CL31 mesothelial clearance, a prerequisite for metastasis. These findings demonstrate that transient, ostensibly innocuous tumor subpopulations can promote metastases via “hit-and-run” commensal interactions., Cooperative interactions among tumor cells may have important implications for metastasis. Here, the authors examined the spatio-temporal nature of interactions among clonal populations of ovarian carcinoma cells and found that transient interactions cells can promote metastases via commensal interactions.

To interrogate functional heterogeneity and crosstalk between tumor cells, we generated clonal populations from a patient-derived ovarian clear cell carcinoma model which forms malignant ascites and solid peritoneal tumors upon intraperitoneal transplantation in mice. The clonal populations were engineered with secreted Gaussia luciferase to monitor tumor growth dynamics and tagged with a unique DNA barcode to track their fate in multiclonal mixtures during tumor progression. Only one clone, CL31, grew robustly, generating exclusively malignant ascites. However, multiclonal mixtures formed large solid peritoneal metastases, populated almost entirely by CL31, suggesting that transient cooperative interclonal interactions were sufficient to promote metastasis of CL31. CL31 uniquely harbored ERBB2 amplification, and its acquired metastatic trait was dependent on transient exposure to amphiregulin, which was exclusively secreted by non-tumorigenic clones. Amphiregulin enhanced CL31 mesothelial clearance, a prerequisite for metastasis. These findings demonstrate that transient, ostensibly innocuous tumor subpopulations can promote metastases via “hit- and-run” commensal interactions.

Metastasis is a complex biological process that has been difficult to delineate in human colorectal cancer (CRC) patients. A major obstacle in understanding metastatic lineages is the extensive intra-tumor heterogeneity at the primary and metastatic tumor sites. To address this problem, we developed a highly multiplexed single-cell DNA sequencing approach to trace the metastatic lineages of two CRC patients with matched liver metastases. Single-cell copy number or mutational profiling was performed, in addition to bulk exome and targeted deep-sequencing. In the first patient, we observed monoclonal seeding, in which a single clone evolved a large number of mutations prior to migrating to the liver to establish the metastatic tumor. In the second patient, we observed polyclonal seeding, in which two independent clones seeded the metastatic liver tumor after having diverged at different time points from the primary tumor lineage. The single-cell data also revealed an unexpected independent tumor lineage that did not metastasize, and early progenitor clones with the “first hit” mutation in APC that subsequently gave rise to both the primary and metastatic tumors. Collectively, these data reveal a late-dissemination model of metastasis in two CRC patients and provide an unprecedented view of metastasis at single-cell genomic resolution.

Aberrant expression of microRNAs (miRNAs) and the enzymes that control their processing have been reported in multiple biological processes including primary and metastatic tumours1–6, but the mechanisms governing this are not clearly understood. Here we show that TAp63, a p53 family member, suppresses tumorigenesis and metastasis, and coordinately regulates Dicer and miR-130b to suppress metastasis. Metastatic mouse and human tumours deficient in TAp63 express Dicer at very low levels, and we found that modulation of expression of Dicer and miR-130b markedly affected the metastatic potential of cells lacking TAp63. TAp63 binds to and transactivates the Dicer promoter, demonstrating direct transcriptional regulation of Dicer by TAp63. These data provide a novel understanding of the roles of TAp63 in tumour and metastasis suppression through the coordinate transcriptional regulation of Dicer and miR-130b and may have implications for the many processes regulated by miRNAs.

Vemurafenib and dabrafenib selectively inhibit the v-Raf murine sarcoma viral oncogene homolog B1 (BRAF) kinase, resulting in high response rates and increased survival in melanoma. Approximately 22% of individuals treated with vemurafenib develop cutaneous squamous cell carcinoma (cSCC) during therapy. The prevailing explanation for this is drug-induced paradoxical ERK activation, resulting in hyperproliferation. Here we show an unexpected and novel effect of vemurafenib/PLX4720 in suppressing apoptosis through the inhibition of multiple off-target kinases upstream of c-Jun N-terminal kinase (JNK), principally ZAK. JNK signaling is suppressed in multiple contexts, including in cSCC of vemurafenib-treated patients, as well as in mice. Expression of a mutant ZAK that cannot be inhibited reverses the suppression of JNK activation and apoptosis. Our results implicate suppression of JNK-dependent apoptosis as a significant, independent mechanism that cooperates with paradoxical ERK activation to induce cSCC, suggesting broad implications for understanding toxicities associated with BRAF inhibitors and for their use in combination therapies. DOI: http://dx.doi.org/10.7554/eLife.00969.001, eLife digest Over 50% of melanomas, a highly lethal form of skin cancer, carry mutations in a gene called BRAF. The BRAF gene encodes an enzyme that helps to regulate the proliferation of cells, but mutations in this gene lead to the excessive proliferation that is seen in cancer. Clinical trials have shown that a drug called vemurafenib can be used to treat patients who carry the mutated BRAF genes and go on to develop melanoma, but around one fifth of these patients developed another type of skin cancer called cSCC (cutaneous squamous cell carcinoma). The cSCC tumors often develop in areas where the sun has damaged the patient’s skin, and it is thought that their growth is then accelerated by vemurafenib activating another enzyme, ERK, which causes the excessive proliferation of skin cells. Vin et al. have now found that vemurafenib might also cause cSCC tumors by blocking another signaling pathway. The experiments were performed in human cells and also in mice, and the results were then verified in human cSCC samples. Cells that are exposed to UV radiation usually die, but when treated with vemurafenib, some 70% of the cells that would have died instead survived. The stress from the UV radiation activates the JNK signaling pathway, which causes the irradiated cells to die. However, Vin et al. found that cSCC cells had very low levels of JNK signaling because treatment with vemurafenib had the unintended effect of inhibiting three enzymes that are needed to fully activate the JNK signaling pathway. Vin et al. estimate that suppression of JNK signaling and cell death is responsible for about 17.6 to 40% of the effect on cSCC growth seen in melanoma patients, with activation of the ERK pathway accounting for the rest. These unexpected findings suggest that combining vemurafenib treatment with radiation or chemotherapy should be done with caution as these effects could affect their efficacy. It also suggests that future drugs should be designed in a way that avoids these types of effects by making sure they do not inhibit important ‘off-target’ enzymes. DOI: http://dx.doi.org/10.7554/eLife.00969.002

Metastatic colorectal cancer (mCRC) is a devastating disease with only 11% 5-year survival rate for stage IV patients. The genomic basis of metastasis has been difficult to study, in part due to the extensive intratumor heterogeneity at both the primary and metastatic tumor sites. Previous studies have applied bulk next-generation sequencing (NGS) methods, which have limited ability to resolve intratumor heterogeneity. To address this problem, we developed a highly-multiplexed single cell DNA sequencing method that combines flow-sorting of single nuclei, multiple-displacement-amplification, low-input library preparation, library barcoding, targeted capture and NGS to generate high-coverage data from single tumor cells. To increase throughput, we performed targeted single-cell DNA sequencing using a panel of 201-cancer genes to analyze single cells from primary tumors and liver metastases from two mCRC patients. In each patient, we sequenced 90 single tumor cells from the primary and metastatic tumor, to delineate the clonal architecture of the tumor and reconstruct their phylogenetic lineages. In addition, we sequenced populations of tumor cells at high coverage depth (200X). Our data identified a large number of nonsynonymous mutations that evolved in the root nodes during the earliest stages of primary tumor evolution and were maintained in all single cells during the clonal expansion of the tumor mass. We also identified a small number of mutations that were specific to the liver metastases, which are likely to play an important role in metastatic dissemination. Using the single cell data, we constructed phylogenetic trees, which revealed branched evolution at both organ sites. Collectively, our data suggest that both mCRC patients are consistent with a late-dissemination model, in which the primary tumors evolved for a long period of time prior to the dissemination of clones to distant organ sites. This model has important clinical implications, by suggesting that surgical intervention or therapeutic treatment of the primary CRC tumor can prevent metastasis, since single tumor cells do not disseminate at the earliest stages of tumor growth Citation Format: Marco L. Leung, Anna Casasent, Yong Wang, Emi Sei, Nicholas Navin. Single-cell DNA sequencing identifies a late dissemination model in metastatic colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 157.

Human breast cancers often display intratumor genomic heterogeneity. This clonal diversity confounds the clinical diagnosis and basic research of cancer, because single samples may not represent that tumor as a whole. Sequencing breast tumor cohorts en masse has identified many prevalent mutations, but has limited ability for resolving subclonal diversity. Here, we developed a whole-genome and exome single-cell sequencing approach (Nuc-Seq) using G2/M cells. To validate our method, we applied Nuc-Seq to sequence the whole genomes of two single cells from a genetically monoclonal breast cancer cell line (SK-BR-3) at high coverage depth (61X ± 5 sem, n=2) and breadth (83.70% ± 3.40 sem, n=2) to detect somatic mutations. Our analysis suggests that Nuc-Seq generates low allelic dropout rates (9.73% ± 2.19%) and low false positive error rates for point mutations (FPR = 1.24e-6). We then applied this method to sequence single normal and tumor cells from an estrogen-receptor positive breast cancer and a triple-negative ductal carcinoma at base-pair resolution. In parallel, we performed single cell copy number profiling. In both tumors, we observed a large number of rare variants that were not detected by sequencing the bulk tumor en masse. In contrast, we find that single cell copy number profiles are highly similar. Our data suggest that aneuploid rearrangements occurred early in tumor evolution and remained highly stable as the tumor mass expanded. In contrast we find that point mutations evolved gradually, generating extensive clonal diversity. Many of the diverse mutations were shown to occur at low frequencies (0.03 -10%) in the tumor mass by targeted duplex sequencing. Mathematical modeling suggests that the triple-negative tumor cells have an increased mutation rate (13.3X), while the ER+ tumor cells do not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer. Citation Format: Yong Wang, Nicholas Navin, Jill Waters, Marco Leung, Anna Unruh, Xiuqing Shi, Whijae Roh, Ken Chen, Paul Scheet, Selina Vattathil, Han Liang, Asha Multani, Hong Zhang, Funda Meric-Bernstam, Franziska Michor, Rui Zhao. Single cell genome sequencing reveals clonal stability and diversity in breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-310. doi:10.1158/1538-7445.AM2014-LB-310

The roles of microRNAs (miRNAs) and the miRNA processing machinery in the regulation of stem cell biology are not well understood. Here, we show that the p53 family member and p63 isoform, ΔNp63, is a critical transcriptional activator of a co-factor pivotal for miRNA processing, DGCR8. This regulation is important in the terminal differentiation of adult keratinocytes and likely of other cells. Loss of ΔNp63 or DGCR8 induces pluripotency in these cells. Generation of a conditional ΔNp63 knock-out mouse model with the help of a Cre-LoxP system led to the development of mice with single layered fragile and disorganized epidermis. Analysis of the skin with immunohistochemistry and immmunofluorescence exhibit aberrant expression of differentiation markers like keratin 5,14,10, loricrin and filaggrin, suggesting a defect in terminal differentiation and BrdU incorporation assay suggested hyperproliferation and self-renewal. Further characterization of stem cell marker expression in the epidermal cells from these embryos was found to be high. Chromatin immunoprecipitation assay and luciferase assays demonstrated the transcriptional activation of the DGCR8 promoter by ΔNp63. Overexpression of DGCR8 in the epidermal cells with the help of a lentiviral doxycycline inducible DGCR8 construct forced these cells to undergo differentiation as validated by in vitro differentiation assay and teratoma formation assay. These cells were also capable of generating chimeras when injected into blastocysts. Lentiviral knock-down of ΔNp63 or DGCR8 in normal human epidermal keratinocytes led to the development of induced pluripotent stem cells capable of forming teratomas as analyzed by differentiation markers AFP, MyoD and Nestin for various lineages like endoderm, mesoderm and ectoderm respectively. Low expression of key miRNAs in ΔNp63 deficient cells results in the failure to repress genes required for stem cell pluripotency, Oct4, Sox2, and Nanog. Strikingly, ΔNp63-/- epidermal cells display profound defects in terminal differentiation and express markers and miRNAs of pluripotency at levels comparable to those in embryonic stem cells. Moreover, these cells can differentiate into multiple cell fates in vitro and in vivo. We found that human primary keratinocytes depleted of ΔNp63 or DGCR8 become pluripotent. For the first time we demonstrate a novel role for ΔNp63 in the transcriptional regulation of DGCR8 to maintain stem cell pluripotency. Importantly, our findings identify a simple method of generating human induced pluripotent stem cells through the knockdown of a single gene. Citation Format: Deepavali Chakravarti, Xiaohua Su, Minsoon Cho, Young Jin Gi, Ashley Benham, Cristian Coarfa, Avinashnarayan Venkatanarayan, Jennifer Alana, Chad Creighton, weimin Xiao, Marco Leung, Harina Vin, Io Long Chan, Arianexys Aquino, Nicole Müller, Jan Parker-Thornburg, Kenneth Y. Tsai, Preethi H. Gunarante, Elsa R. Flores. Induced pluripotency in adult keratinocytes through downregulation of ΔNp63 or DGCR8. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1119. doi:10.1158/1538-7445.AM2013-1119

8537 Background: The advent of targeted therapy has revolutionized the treatment of cancer. The mutant BRAFV600E protein is found in over 50% of melanomas and thyroid carcinomas, resulting in elevated kinase activity, increased mitogen-activated protein kinase (MAPK) pathway signaling, and cell proliferation. Vemurafenib and PLX4720 were designed to selectively inhibit the BRAF kinase, and clinical trials of vemurafenib in metastatic melanoma have demonstrated a response rate of over 50% and an overall survival advantage over standard dacarbazine therapy. Approximately 20-30% of individuals treated with vemurafenib develop cutaneous squamous cell carcinoma (cSCC) highlighting the importance of understanding toxicities associated with this drug. Paradoxical ERK activation in BRAF wild-type, RAS-mutant cells is thought to be the major mechanism by which this occurs, as evidenced by the presence of RAS mutations in 60% of such lesions. Methods: Using a combination of BRAF-wild-type cSCC cell lines, primary human keratinocytes, as well as a UV mouse model of cSCC and human cSCC samples, we identified novel effects of BRAFi on apoptosis. Results: Here we show an unexpected and novel effect of vemurafenib and PLX4720 in suppressing apoptosis through the inhibition of multiple off-target kinases. JNK signaling and apoptosis are suppressed in cSCC lesions arising in vemurafenib-treated patients as well as in irradiated mouse skin. This occurs independently of paradoxical ERK signaling and in the presence of MEK inhibitor. Treatment with PLX4720 greatly accelerates the development of UV-induced cSCC in mice without Ras mutations. Kinome screening identified ZAK and MKK4 (MEK4 / MAP2K4) kinases as inhibited by vemurafenib, leading to suppression of MKK4 and MKK7 (MAP2K7) phosphorylation. Knockdown of inhibited off-target kinases recapitulates these anti-apoptotic effects of vemurafenib. Conclusions: Our results implicate suppression of JNK signaling, independent of ERK activation, as an additional, complementary mechanism of adverse effects of vemurafenib. This has broad implications for combination therapies with other modalities that induce apoptosis and for the long-term use of vemurafenib in the adjuvant setting.