Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E Rood, Orr Ashenberg, Ethan Cerami, Robert J Coffey, Emek Demir, Li Ding, Edward D Esplin, James M Ford, Jeremy Goecks, Sharmistha Ghosh, Joe W Gray, Justin Guinney, Sean E Hanlon, Shannon K Hughes, Shelley E Hwang, Christine A Iacobuzio-Donahue, Judit Jané-Valbuena, Bruce E Johnson, Ken S Lau, Tracy Lively, Sarah A Mazzilli, Dana Pe'er, Sandro Santagata, Alex K Shalek, Denis Schapiro, Michael P Snyder, Peter K Sorger, Avrum E Spira, Sudhir Srivastava, Kai Tan, Robert B West, and Elizabeth H Williams. 2020. “The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.” Cell, 181, 2, Pp. 236-249.Abstract
Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types. This effort complements both ongoing efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at a single point in time. Generating single-cell, multiparametric, longitudinal atlases and integrating them with clinical outcomes should help identify novel predictive biomarkers and features as well as therapeutically relevant cell types, cell states, and cellular interactions across transitions. The resulting tumor atlases should have a profound impact on our understanding of cancer biology and have the potential to improve cancer detection, prevention, and therapeutic discovery for better precision-medicine treatments of cancer patients and those at risk for cancer.
Mary Speir, Cameron J Nowell, Alyce A Chen, Joanne A O'Donnell, Isaac S Shamie, Paul R Lakin, Akshay A D'Cruz, Roman O Braun, Jeff J Babon, Rowena S Lewis, Meghan Bliss-Moreau, Inbar Shlomovitz, Shu Wang, Louise H Cengia, Anca I Stoica, Razq Hakem, Michelle A Kelliher, Lorraine A O'Reilly, Heather Patsiouras, Kate E Lawlor, Edie Weller, Nathan E Lewis, Andrew W Roberts, Motti Gerlic, and Ben A Croker. 2020. “Ptpn6 inhibits caspase-8- and Ripk3/Mlkl-dependent inflammation.” Nat Immunol, 21, 1, Pp. 54-64.Abstract
Ptpn6 is a cytoplasmic phosphatase that functions to prevent autoimmune and interleukin-1 (IL-1) receptor-dependent, caspase-1-independent inflammatory disease. Conditional deletion of Ptpn6 in neutrophils (Ptpn6) is sufficient to initiate IL-1 receptor-dependent cutaneous inflammatory disease, but the source of IL-1 and the mechanisms behind IL-1 release remain unclear. Here, we investigate the mechanisms controlling IL-1α/β release from neutrophils by inhibiting caspase-8-dependent apoptosis and Ripk1-Ripk3-Mlkl-regulated necroptosis. Loss of Ripk1 accelerated disease onset, whereas combined deletion of caspase-8 and either Ripk3 or Mlkl strongly protected Ptpn6 mice. Ptpn6 neutrophils displayed increased p38 mitogen-activated protein kinase-dependent Ripk1-independent IL-1 and tumor necrosis factor production, and were prone to cell death. Together, these data emphasize dual functions for Ptpn6 in the negative regulation of p38 mitogen-activated protein kinase activation to control tumor necrosis factor and IL-1α/β expression, and in maintaining Ripk1 function to prevent caspase-8- and Ripk3-Mlkl-dependent cell death and concomitant IL-1α/β release.
Akshay A D'Cruz, Mary Speir, Meghan Bliss-Moreau, Sylvia Dietrich, Shu Wang, Alyce A Chen, Mathilde Gavillet, Arshed Al-Obeidi, Kate E Lawlor, James E Vince, Michelle A Kelliher, Razq Hakem, Manolis Pasparakis, David A Williams, Maria Ericsson, and Ben A Croker. 2018. “The pseudokinase MLKL activates PAD4-dependent NET formation in necroptotic neutrophils.” Sci Signal, 11, 546.Abstract
Neutrophil extracellular trap (NET) formation can generate short-term, functional anucleate cytoplasts and trigger loss of cell viability. We demonstrated that the necroptotic cell death effector mixed lineage kinase domain-like (MLKL) translocated from the cytoplasm to the plasma membrane and stimulated downstream NADPH oxidase-independent ROS production, loss of cytoplasmic granules, breakdown of the nuclear membrane, chromatin decondensation, histone hypercitrullination, and extrusion of bacteriostatic NETs. This process was coordinated by receptor-interacting protein kinase-1 (RIPK1), which activated the caspase-8-dependent apoptotic or RIPK3/MLKL-dependent necroptotic death of mouse and human neutrophils. Genetic deficiency of RIPK3 and MLKL prevented NET formation but did not prevent cell death, which was because of residual caspase-8-dependent activity. Peptidylarginine deiminase 4 (PAD4) was activated downstream of RIPK1/RIPK3/MLKL and was required for maximal histone hypercitrullination and NET extrusion. This work defines a distinct signaling network that activates PAD4-dependent NET release for the control of methicillin-resistant (MRSA) infection.
Meghan Bliss-Moreau, Alyce A Chen, Akshay A D'Cruz, and Ben A Croker. 2017. “A motive for killing: effector functions of regulated lytic cell death.” Immunol Cell Biol, 95, 2, Pp. 146-151.Abstract
Immunological responses activated by pathogen recognition come in many guises. The proliferation, differentiation and recruitment of immune cells, and the production of inflammatory cytokines and chemokines are central to lifelong immunity. Cell death serves as a key function in the resolution of innate and adaptive immune responses. It also coordinates cell-intrinsic effector functions to restrict infection. Necrosis was formally considered a passive form of cell death or a consequence of pathogen virulence factor expression, and necrotic tissue is frequently associated with infection. However, there is now emerging evidence that points to a role for regulated forms of necrosis, such as pyroptosis and necroptosis, driving inflammation and shaping the immune response.
Alyce A Chen, Tarik Gheit, Marco Stellin, Valentina Lupato, Giacomo Spinato, Roberto Fuson, Anna Menegaldo, Sandrine Mckay-Chopin, Elisa Dal Cin, Giancarlo Tirelli, Maria Cristina Da Mosto, Massimo Tommasino, and Paolo Boscolo-Rizzo. 2017. “Oncogenic DNA viruses found in salivary gland tumors.” Oral Oncol, 75, Pp. 106-110.Abstract
BACKGROUND: Previous investigations studying the association of DNA viruses with salivary gland tumors (SGTs) have led to conflicting results. The aim of this study was to determine the prevalence of different DNA viruses by using a highly sensitive assay in a multi-center series of over 100 fresh frozen salivary gland samples. METHODS: DNA was isolated from 84 SGTs (80 parotid tumors and 4 submandibular gland tumors) and 28 normal salivary tissue samples from 85 patients in Northeast Italy. Using a highly sensitive type-specific multiplex genotyping assay, we analyzed the samples for the presence of DNA from 62 different viruses including 47 papillomaviruses, 10 polyomaviruses, and 5 herpesviruses. RESULTS: We observed a high prevalence of beta human papillomavirus DNA in malignant tumors. In contrast, polyomavirus DNA was present in benign, malignant, and non-tumor control samples. Most striking was the significant distribution of herpesvirus DNA in the SGT samples, in particular the high prevalence of Epstein-Barr type 1 and type 2 DNA in Warthin's tumor samples. CONCLUSION: Our data provides evidence for the presence of DNA viruses in SGTs. Mechanistic studies are needed to further attribute tumor formation to these viruses.
Xinping Yang, Jasmin Coulombe-Huntington, Shuli Kang, Gloria M Sheynkman, Tong Hao, Aaron Richardson, Song Sun, Fan Yang, Yun A Shen, Ryan R Murray, Kerstin Spirohn, Bridget E Begg, Miquel Duran-Frigola, Andrew MacWilliams, Samuel J Pevzner, Quan Zhong, Shelly A Trigg, Stanley Tam, Lila Ghamsari, Nidhi Sahni, Song Yi, Maria D Rodriguez, Dawit Balcha, Guihong Tan, Michael Costanzo, Brenda Andrews, Charles Boone, Xianghong J Zhou, Kourosh Salehi-Ashtiani, Benoit Charloteaux, Alyce A Chen, Michael A Calderwood, Patrick Aloy, Frederick P Roth, David E Hill, Lilia M Iakoucheva, Yu Xia, and Marc Vidal. 2016. “Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.” Cell, 164, 4, Pp. 805-17.Abstract
While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms" are functionally divergent (i.e., "functional alloforms").
Alyce A Chen, Tarik Gheit, Silvia Franceschi, Massimo Tommasino, and Gary M Clifford. 2015. “Human Papillomavirus 18 Genetic Variation and Cervical Cancer Risk Worldwide.” J Virol, 89, 20, Pp. 10680-7.Abstract
UNLABELLED: Human papillomavirus 18 (HPV18) is the second most carcinogenic HPV type, after HPV16, and it accounts for approximately 12% of squamous cell carcinoma (SCC) as well as 37% of adenocarcinoma (ADC) of the cervix worldwide. We aimed to evaluate the worldwide diversity and carcinogenicity of HPV18 genetic variants by sequencing the entire long control region (LCR) and the E6 open reading frame of 711 HPV18-positive cervical samples from 39 countries, taking advantage of the International Agency for Research on Cancer biobank. A total of 209 unique HPV18 sequence variants were identified that formed three phylogenetic lineages (A, B, and C). A and B lineages each divided into four sublineages, including a newly identified candidate B4 sublineage. The distribution of lineages varied by geographical region, with B and C lineages found principally in Africa. HPV18 (sub)lineages were compared between 453 cancer cases and 236 controls, as well as between 81 ADC and 160 matched SCC cases. In region-stratified analyses, there were no significant differences in the distribution of HPV18 variant lineages between cervical cancer cases and controls or between ADC and SCC. In conclusion, our findings do not support the role of HPV18 (sub)lineages for discriminating cancer risk or explaining why HPV18 is more strongly linked with ADC than SCC. IMPORTANCE: This is the largest and most geographically/ethnically diverse study of the genetic variation of HPV18 to date, providing a comprehensive reference for phylogenetic classification of HPV18 sublineages for epidemiological and biological studies.
Alyce A Chen, Daniëlle AM Heideman, Debby Boon, Zigui Chen, Robert D Burk, Hugo De Vuyst, Tarik Gheit, Peter JF Snijders, Massimo Tommasino, Silvia Franceschi, and Gary M Clifford. 2014. “Human papillomavirus 33 worldwide genetic variation and associated risk of cervical cancer.” Virology, 448, Pp. 356-62.Abstract
Human papillomavirus (HPV) 33, a member of the HPV16-related alpha-9 species group, is found in approximately 5% of cervical cancers worldwide. The current study aimed to characterize the genetic diversity of HPV33 and to explore the association of HPV33 variants with the risk for cervical cancer. Taking advantage of the International Agency for Research on Cancer biobank, we sequenced the entire E6 and E7 open reading frames of 213 HPV33-positive cervical samples from 30 countries. We identified 28 HPV33 variants that formed 5 phylogenetic groups: the previously identified A1, A2, and B (sub)lineages and the novel A3 and C (sub)lineages. The A1 sublineage was strongly over-represented in cervical cases compared to controls in both Africa and Europe. In conclusion, we provide a classification system for HPV33 variants based on the sequence of E6 and E7 and suggest that the association of HPV33 with cervical cancer may differ by variant (sub)lineage.
Alyce A Chen, Daniëlle AM Heideman, Debby Boon, Tarik Gheit, Peter JF Snijders, Massimo Tommasino, Silvia Franceschi, and Gary M Clifford. 2014. “Human papillomavirus 45 genetic variation and cervical cancer risk worldwide.” J Virol, 88, 8, Pp. 4514-21.Abstract
UNLABELLED: Human papillomavirus 45 (HPV45) is a member of the HPV18-related alpha-7 species and accounts for approximately 5% of all cervical cancer cases worldwide. This study evaluated the genetic diversity of HPV45 and the association of HPV45 variants with the risk of cervical cancer by sequencing the entire E6 and E7 open reading frames of 300 HPV45-positive cervical samples from 36 countries. A total of 43 HPV45 sequence variants were identified that formed 5 phylogenetic sublineages, A1, A2, A3, B1, and B2, the distribution of which varied by geographical region. Among 192 cases of cervical cancer and 101 controls, the B2 sublineage was significantly overrepresented in cervical cancer, both overall and in Africa and Europe separately. We show that the sequence analysis of E6 and E7 allows the classification of HPV45 variants and that the risk of cervical cancer may differ by HPV45 variant sublineage. IMPORTANCE: This work describes the largest study to date of human papillomavirus 45 (HPV45)-positive cervical samples and provides a comprehensive reference for phylogenetic classification for use in epidemiological studies of the carcinogenicity of HPV45 genetic variants, particularly as our findings suggest that the B2 sublineage of HPV45 is associated with a higher risk of cervical cancer.
Jean-Damien Combes, Alyce A Chen, and Silvia Franceschi. 2014. “Prevalence of human papillomavirus in cancer of the oropharynx by gender.” Cancer Epidemiol Biomarkers Prev, 23, 12, Pp. 2954-8.Abstract
Oropharyngeal cancer (OPC) is more frequent in men than women mainly due to the heavier and longer duration of smoking in men. Human papillomavirus (HPV) has a role in the rising incidence of OPC in the United States and other high-income countries. To determine whether there is a difference in the proportion of HPV-attributable OPC between men and women, we systematically retrieved HPV prevalence data from 63 studies reporting separately on OPC by gender. The male/female (M/F) ratios of HPV prevalence in OPC across different countries and the corresponding M/F ratios of cumulative lung cancer risk (a proxy for smoking) were compared. The United States had the highest M/F ratios of HPV prevalence in OPC (1.5). The lowest M/F ratios (≤0.7) were found in Asia and some European countries (e.g., France). The countries in which the M/F ratio of HPV prevalence in OPC was ≥1.0 had the most similar lung cancer risks for men and women. When HPV prevalence data were applied to age-standardized OPC incidence rates in the United States, Australia, the United Kingdom, and France, the M/F ratio for the HPV-positive OPC incidence rates was rather stable (around 4) in all countries. In contrast, the M/F ratio for the HPV-negative OPC incidence rates reached 10.2 in France versus <3 elsewhere. We showed that HPV prevalence in OPC differs by gender and country mainly as a consequence of the vast international variation in male smoking habits. Nevertheless, HPV-positive OPC may affect men more heavily than women in different populations for reasons that are unclear.
Orit Rozenblatt-Rosen, Rahul C Deo, Megha Padi, Guillaume Adelmant, Michael A Calderwood, Thomas Rolland, Miranda Grace, Amélie Dricot, Manor Askenazi, Maria Tavares, Samuel J Pevzner, Fieda Abderazzaq, Danielle Byrdsong, Anne-Ruxandra Carvunis, Alyce A Chen, Jingwei Cheng, Mick Correll, Melissa Duarte, Changyu Fan, Mariet C Feltkamp, Scott B Ficarro, Rachel Franchi, Brijesh K Garg, Natali Gulbahce, Tong Hao, Amy M Holthaus, Robert James, Anna Korkhin, Larisa Litovchick, Jessica C Mar, Theodore R Pak, Sabrina Rabello, Renee Rubio, Yun Shen, Saurav Singh, Jennifer M Spangle, Murat Tasan, Shelly Wanamaker, James T Webber, Jennifer Roecklein-Canfield, Eric Johannsen, Albert-László Barabási, Rameen Beroukhim, Elliott Kieff, Michael E Cusick, David E Hill, Karl Münger, Jarrod a Marto, John Quackenbush, Frederick P Roth, James A DeCaprio, and Marc Vidal. 2012. “Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.” Nature, 487, 7408, Pp. 491-5.Abstract
Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations. Genome sequencing efforts have identified numerous germline mutations, and large numbers of somatic genomic alterations, associated with a predisposition to cancer. However, it remains difficult to distinguish background, or 'passenger', cancer mutations from causal, or 'driver', mutations in these data sets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations. Here we test the hypothesis that genomic variations and tumour viruses may cause cancer through related mechanisms, by systematically examining host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways, such as Notch signalling and apoptosis, that go awry in cancer. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on a par with their identification through functional genomics and large-scale cataloguing of tumour mutations. Together, these complementary approaches increase the specificity of cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate the prioritization of cancer-causing driver genes to advance the understanding of the genetic basis of human cancer.
Natali Gulbahce, Han Yan, Amélie Dricot, Megha Padi, Danielle Byrdsong, Rachel Franchi, Deok-Sun Lee, Orit Rozenblatt-Rosen, Jessica C Mar, Michael A Calderwood, Amy Baldwin, Bo Zhao, Balaji Santhanam, Pascal Braun, Nicolas Simonis, Kyung-Won Huh, Karin Hellner, Miranda Grace, Alyce Chen, Renee Rubio, Jarrod a Marto, Nicholas A Christakis, Elliott Kieff, Frederick P Roth, Jennifer Roecklein-Canfield, James A DeCaprio, Michael E Cusick, John Quackenbush, David E Hill, Karl Münger, Marc Vidal, and Albert-László Barabási. 2012. “Viral perturbations of host networks reflect disease etiology.” PLoS Comput Biol, 8, 6, Pp. e1002531.Abstract
Many human diseases, arising from mutations of disease susceptibility genes (genetic diseases), are also associated with viral infections (virally implicated diseases), either in a directly causal manner or by indirect associations. Here we examine whether viral perturbations of host interactome may underlie such virally implicated disease relationships. Using as models two different human viruses, Epstein-Barr virus (EBV) and human papillomavirus (HPV), we find that host targets of viral proteins reside in network proximity to products of disease susceptibility genes. Expression changes in virally implicated disease tissues and comorbidity patterns cluster significantly in the network vicinity of viral targets. The topological proximity found between cellular targets of viral proteins and disease genes was exploited to uncover a novel pathway linking HPV to Fanconi anemia.
Alyce A Chen, Carmen J Marsit, Brock C Christensen, Andrés E Houseman, Michael D McClean, Judith F Smith, Janine T Bryan, Marshall R Posner, Heather H Nelson, and Karl T Kelsey. 2009. “Genetic variation in the vitamin C transporter, SLC23A2, modifies the risk of HPV16-associated head and neck cancer.” Carcinogenesis, 30, 6, Pp. 977-81.Abstract
Human papillomavirus (HPV) type 16 infection is an etiologic factor in a subset of head and neck squamous cell carcinomas (HNSCC). It is unknown if host genetic susceptibility modifies the HPV16-HNSCC association. DNA samples collected as part of a Boston area case-control study of HNSCC were genotyped for single-nucleotide polymorphisms (SNPs) from the National Cancer Institute's SNP500Cancer database. Analysis of demographic, phenotypic and genotypic data for 319 HNSCC cases and 495 frequency-matched controls was performed using unconditional logistic regression. All reported P-values are two sided. We identified a polymorphism in the sodium-dependent vitamin C transporter SLC23A2 that modifies the risk of HNSCC associated with HPV16 infection. Among those with a wild-type allele at SLC23A2, the risk of HNSCC associated with HPV16-positive serology was 5.0 (95% confidence interval (CI) = 3.2-7.8). However, among those with a homozygous variant genotype, the risk of HNSCC associated with HPV16 was attenuated [odds ratio (OR) = 2.8; 95% CI = 1.2-6.2]. Further, when we tested whether genotype modified the interaction between citrus exposure, HPV16, and HNSCC, we found a dramatically increased risk of HNSCC for those with a wild-type SLC23A2 allele, HPV16-positive serology and high citrus intake (OR = 7.4; 95% CI = 3.6-15.1). These results suggest that SLC23A2 genetic variation alters HPV16-associated HNSCC while also highlighting the important role of citrus exposure in this disease.