A proteogenomic portrait of lung squamous cell carcinoma

Cell

2021 Aug 05

Satpathy, S;Krug, K;Jean Beltran, PM;Savage, SR;Petralia, F;Kumar-Sinha, C;Dou, Y;Reva, B;Kane, MH;Avanessian, SC;Vasaikar, SV;Krek, A;Lei, JT;Jaehnig, EJ;Omelchenko, T;Geffen, Y;Bergstrom, EJ;Stathias, V;Christianson, KE;Heiman, DI;Cieslik, MP;Cao, S;Song, X;Ji, J;Liu, W;Li, K;Wen, B;Li, Y;Gümüş, ZH;Selvan, ME;Soundararajan, R;Visal, TH;Raso, MG;Parra, ER;Babur, Ö;Vats, P;Anand, S;Schraink, T;Cornwell, M;Rodrigues, FM;Zhu, H;Mo, CK;Zhang, Y;da Veiga Leprevost, F;Huang, C;Chinnaiyan, AM;Wyczalkowski, MA;Omenn, GS;Newton, CJ;Schurer, S;Ruggles, KV;Fenyö, D;Jewell, SD;Thiagarajan, M;Mesri, M;Rodriguez, H;Mani, SA;Udeshi, ND;Getz, G;Suh, J;Li, QK;Hostetter, G;Paik, PK;Dhanasekaran, SM;Govindan, R;Ding, L;Robles, AI;Clauser, KR;Nesvizhskii, AI;Wang, P;Carr, SA;Zhang, B;Mani, DR;Gillette, MA;Clinical Proteomic Tumor Analysis Consortium, ;
PMID: 34358469 | DOI: 10.1016/j.cell.2021.07.016

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.

Epithelial STAT6 O-GlcNAcylation Drives Anti-Helminth Immunity via a Concerted Alarmin Response

SSRN Electronic Journal

2021 Sep 08

Zhao, M;Ren, K;Xiong, X;Xin, Y;Kim, A;Maynard, J;Zou, Y;Battist, A;Koneripalli, N;Huang, Z;Zhang, Z;Yu, J;Wang, H;Salgado, O;Hogquist, K;Revelo, X;Burlingame, A;Gao, X;Lin, Z;von Moltke, J;Ruan, H;
| DOI: 10.2139/ssrn.3917158

The epithelium is an integral component of mucosal barrier and host immunity. Following helminth parasite infection, the intestinal epithelial cells secrete "alarmin” cytokines, such as interleukin (IL)-25 and IL-33, to initiate the type 2 immune responses for helminth expulsion and tolerance. However, it is unknown how helminth infection and the resulting type 2 cytokine milieu drive epithelial remodeling and orchestrate alarmin secretion. Here we report that, intestinal epithelial O-linked N-Acetylglucosamine (O-GlcNAc) protein modification is induced upon helminth infections. By modifying and activating STAT6, O-GlcNAc transferase (OGT) promotes the transcription of lineage-defining transcription factor _Pou2f3_ in tuft cell differentiation and IL-25 production. Meanwhile, STAT6 O-GlcNAcylation activates the expression of _Gsdmc_ family genes. The resulting membrane pore formed by GSDMC facilitates the unconventional secretion of IL-33 from goblet cells. GSDMC-mediated IL-33 secretion is indispensable for the host to mount effective antihelminth immunity and support intestinal homeostasis. Protein O-GlcNAcylation can be harnessed for the future treatment of type 2 inflammation-associated human diseases.

Avances en citometría de masas y aplicabilidad en patología digital para estudios clínico-traslacionales en oncología

Advances in Laboratory Medicine / Avances en Medicina de Laboratorio

2021 Aug 25

Cereceda, K;Jorquera, R;Villarroel-Espíndola, F;
| DOI: 10.1515/almed-2021-0051

Resumen El desarrollo de la citometría de masas y posteriormente su adaptación para el análisis de secciones histológicas ha revolucionado la forma de caracterizar a nivel espacial múltiples componentes de manera simultánea, permitiendo la correlación genotípica y fenotípica de la célula y su entorno durante estudios clínicos-traslaciones. En este trabajo, hemos revisado los hitos más relevantes en el desarrollo, implementación y aplicabilidad del análisis de imágenes de componentes múltiples para el estudio de cáncer y otras dolencias, y enfocado nuestro interés que aquellos autores que utilizan imágenes obtenidas mediante citometría de masas o bien haz de iones. Esta revisión tiene como objetivo que el lector se familiarice con las estrategias técnicas de verificación de la herramienta y las múltiples posibilidades de uso abordadas por diferentes autores, y además, poder proyectar sus propias investigaciones hacia la utilización de imágenes obtenidas por citometría de masas (IMC), o imágenes por haz de iones multiplexados (MIBI) en cualquiera de los campos de investigación biomédica.

Prognostic value and cost benefit of HPV testing for oropharyngeal cancer patients

Oral diseases

2021 Jun 15

Lu, XJD;Liu, KYP;Prisman, E;Wu, J;Zhu, YS;Poh, C;
PMID: 34129700 | DOI: 10.1111/odi.13938

High-risk human papillomavirus (HR-HPV) can cause oropharyngeal squamous cell carcinoma (OpSCC). The revised 8th edition of the AJCC Staging Manual now stages OpSCC by incorporating p16 immunohistochemistry (IHC), the surrogate marker for HPV status. This study assessed the prognostic values of p16 and HPV markers.We identified 244 OpSCC patients diagnosed between 2000-2008 from the British Columbia Cancer Registry with enough tissue to conduct experiments. Formalin-fixed, paraffin-embedded tissue sections were stained for p16 IHC, RNA in situ hybridization (ISH) HPV 16 and 18, and DNA ISH HR-HPV. Electronic charts were reviewed to collect clinical and outcome data. Combined positive RNA and/or DNA ISH was used to denote HPV status.HPV was positive among 77.9% of samples. Using HPV as the benchmark, p16 IHC had high sensitivity (90.5%), but low specificity (68.5%). Distinct subgroups of patients were identified by sequential separation of p16 then HPV status. Among both p16-positive and p16-negative groups, HPV-positive patients were younger, more males, and had better clinical outcomes, especially 5-year overall survival. We further evaluated the technical costs associated with HPV testing.HPV is more prognostic than p16 for OpSCC. Clinical laboratories can adopt HPV RNA ISH for routine analysis.This article is protected by

Hypoxia-induced lncHILAR promotes renal cancer cell invasion and metastasis via ceRNA for the miR-613/206/1-1-3p/Jagged-1/Notch/CXCR4 signaling pathway

Molecular therapy : the journal of the American Society of Gene Therapy

2021 May 28

Hu, G;Ma, J;Zhang, J;Chen, Y;Liu, H;Huang, Y;Zheng, J;Xu, Y;Xue, W;Zhai, W;
PMID: 34058384 | DOI: 10.1016/j.ymthe.2021.05.020

Hypoxia has been identified as a common driving factor that contributes to tumor progression, including invasion and metastasis. However, the underlying mechanisms of enhanced invasion and metastasis under hypoxia remain unclear. A hypoxic microenvironment promoted invasion and metastasis of RCC by upregulating the expression of LOC100506178, which we named Hypoxia-Induced lncRNA Associated with Renal Cell Carcinoma (lncHILAR). Knockdown of lncHILAR inhibited cell invasion and migration while overexpression of lncHILAR conversely facilitated cell invasion and migration of RCC cells. Notably, hypoxic RCC cells secreted exosomes packaged with lncHILAR which were taken up by normoxic RCC cells and then drove normoxic cell invasion. Mechanistically, hypoxia-induced-lncHILAR elevated RCC invasion and metastasis by acting as a competing endogenous (ce)RNA for miR-613/206/1-1-3p, which led to the upregulation of Jagged-1 and C-X-C Motif Chemokine Receptor 4 (CXCR4). Activation of the of Jagged-1/Notch/CXCR4 axis induced RCC metastasis. Hypoxia-induced lncHILAR promotes RCC cell invasion and metastasis via ceRNA for the miR-613/206/1-1-3p/Jagged-1/Notch/CXCR4 axis. The novel lncHILAR may thus serve as a potential biomarker and therapeutic target in RCC.

Lateral ventral tegmental area GABAergic and glutamatergic modulation of conditioned learning

Cell reports

2021 Mar 16

Rizzi, G;Li, Z;Hogrefe, N;Tan, KR;
PMID: 33730568 | DOI: 10.1016/j.celrep.2021.108867

The firing activity of dorso-medial-striatal-cholinergic interneurons (dmCINs) is a neural correlate of classical conditioning. Tonically active, they pause in response to salient stimuli, mediating acquisition of predictive cues/outcome associations. Cortical and thalamic inputs are typical of the rather limited knowledge about underlying circuitry contributing to this function. Here, we dissect the midbrain GABA and glutamate-to-dmCIN pathways and evaluate how they influence conditioned behavior. We report that midbrain neurons discriminate auditory cues and encode the association of a predictive stimulus with a footshock. Furthermore, GABA and glutamate cells form selective monosynaptic contacts onto dmCINs and di-synaptic ones via the parafascicular thalamus. Pathway-specific inhibition of each sub-circuit produces differential impairments of fear-conditioned learning. Finally, Vglut2-expressing cells discriminate between CSs although Vgat-positive neurons associate the predictive cue with the outcome. Overall, these data suggest that each component of the network carries information pertinent to sub-domains of the behavioral strategy.

Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain

Nature communications

2021 Mar 08

Kupari, J;Usoskin, D;Parisien, M;Lou, D;Hu, Y;Fatt, M;Lönnerberg, P;Spångberg, M;Eriksson, B;Barkas, N;Kharchenko, PV;Loré, K;Khoury, S;Diatchenko, L;Ernfors, P;
PMID: 33686078 | DOI: 10.1038/s41467-021-21725-z

Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.

MAP3K2-regulated intestinal stromal cells define a distinct stem cell niche

Nature

2021 Mar 03

Wu, N;Sun, H;Zhao, X;Zhang, Y;Tan, J;Qi, Y;Wang, Q;Ng, M;Liu, Z;He, L;Niu, X;Chen, L;Liu, Z;Li, HB;Zeng, YA;Roulis, M;Liu, D;Cheng, J;Zhou, B;Ng, LG;Zou, D;Ye, Y;Flavell, RA;Ginhoux, F;Su, B;
PMID: 33658717 | DOI: 10.1038/s41586-021-03283-y

Intestinal stromal cells are known to modulate the propagation and differentiation of intestinal stem cells1,2. However, the precise cellular and molecular mechanisms by which this diverse stromal cell population maintains tissue homeostasis and repair are poorly understood. Here we describe a subset of intestinal stromal cells, named MAP3K2-regulated intestinal stromal cells (MRISCs), and show that they are the primary cellular source of the WNT agonist R-spondin 1 following intestinal injury in mice. MRISCs, which are epigenetically and transcriptomically distinct from subsets of intestinal stromal cells that have previously been reported3-6, are strategically localized at the bases of colon crypts, and function to maintain LGR5+ intestinal stem cells and protect against acute intestinal damage through enhanced R-spondin 1 production. Mechanistically, this MAP3K2 specific function is mediated by a previously unknown reactive oxygen species (ROS)-MAP3K2-ERK5-KLF2 axis to enhance production of R-spondin 1. Our results identify MRISCs as a key component of an intestinal stem cell niche that specifically depends on MAP3K2 to augment WNT signalling for the regeneration of damaged intestine.

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Science advances

2021 Feb 01

Kildisiute, G;Kholosy, WM;Young, MD;Roberts, K;Elmentaite, R;van Hooff, SR;Pacyna, CN;Khabirova, E;Piapi, A;Thevanesan, C;Bugallo-Blanco, E;Burke, C;Mamanova, L;Keller, KM;Langenberg-Ververgaert, KPS;Lijnzaad, P;Margaritis, T;Holstege, FCP;Tas, ML;Wijnen, MHWA;van Noesel, MM;Del Valle, I;Barone, G;van der Linden, R;Duncan, C;Anderson, J;Achermann, JC;Haniffa, M;Teichmann, SA;Rampling, D;Sebire, NJ;He, X;de Krijger, RR;Barker, RA;Meyer, KB;Bayraktar, O;Straathof, K;Molenaar, JJ;Behjati, S;
PMID: 33547074 | DOI: 10.1126/sciadv.abd3311

Neuroblastoma is a childhood cancer that resembles developmental stages of the neural crest. It is not established what developmental processes neuroblastoma cancer cells represent. Here, we sought to reveal the phenotype of neuroblastoma cancer cells by comparing cancer (n = 19,723) with normal fetal adrenal single-cell transcriptomes (n = 57,972). Our principal finding was that the neuroblastoma cancer cell resembled fetal sympathoblasts, but no other fetal adrenal cell type. The sympathoblastic state was a universal feature of neuroblastoma cells, transcending cell cluster diversity, individual patients, and clinical phenotypes. We substantiated our findings in 650 neuroblastoma bulk transcriptomes and by integrating canonical features of the neuroblastoma genome with transcriptional signals. Overall, our observations indicate that a pan-neuroblastoma cancer cell state exists, which may be attractive for novel immunotherapeutic and targeted avenues.

CRISPR Systems for COVID-19 Diagnosis

ACS sensors

2021 Jan 27

Rahimi, H;Salehiabar, M;Barsbay, M;Ghaffarlou, M;Kavetskyy, T;Sharafi, A;Davaran, S;Chauhan, SC;Danafar, H;Kaboli, S;Nosrati, H;Yallapu, MM;Conde, J;
PMID: 33502175 | DOI: 10.1021/acssensors.0c02312

The emergence of the new coronavirus 2019 (COVID-19) was first seen in December 2019, which has spread rapidly and become a global pandemic. The number of cases of COVID-19 and its associated mortality have raised serious concerns worldwide. Early diagnosis of viral infection undoubtedly allows rapid intervention, disease management, and substantial control of the rapid spread of the disease. Currently, the standard approach for COVID-19 diagnosis globally is the RT-qPCR test; however, the limited access to kits and associated reagents, the need for specialized lab equipment, and the need for highly skilled personnel has led to a detection slowdown. Recently, the development of clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic systems has reshaped molecular diagnosis. The benefits of the CRISPR system such as speed, precision, specificity, strength, efficiency, and versatility have inspired researchers to develop CRISPR-based diagnostic and therapeutic methods. With the global COVID-19 outbreak, different groups have begun to design and develop diagnostic and therapeutic programs based on the efficient CRISPR system. CRISPR-based COVID-19 diagnostic systems have advantages such as a high detection speed (i.e., 30 min from raw sample to reach a result), high sensitivity and precision, portability, and no need for specialized laboratory equipment. Here, we review contemporary studies on the detection of COVID-19 based on the CRISPR system.

Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesis

Nature communications

2021 Jan 13

Wu, CL;Dicks, A;Steward, N;Tang, R;Katz, DB;Choi, YR;Guilak, F;
PMID: 33441552 | DOI: 10.1038/s41467-020-20598-y

The therapeutic application of human induced pluripotent stem cells (hiPSCs) for cartilage regeneration is largely hindered by the low yield of chondrocytes accompanied by unpredictable and heterogeneous off-target differentiation of cells during chondrogenesis. Here, we combine bulk RNA sequencing, single cell RNA sequencing, and bioinformatic analyses, including weighted gene co-expression analysis (WGCNA), to investigate the gene regulatory networks regulating hiPSC differentiation under chondrogenic conditions. We identify specific WNTs and MITF as hub genes governing the generation of off-target differentiation into neural cells and melanocytes during hiPSC chondrogenesis. With heterocellular signaling models, we further show that WNT signaling produced by off-target cells is responsible for inducing chondrocyte hypertrophy. By targeting WNTs and MITF, we eliminate these cell lineages, significantly enhancing the yield and homogeneity of hiPSC-derived chondrocytes. Collectively, our findings identify the trajectories and molecular mechanisms governing cell fate decision in hiPSC chondrogenesis, as well as dynamic transcriptome profiles orchestrating chondrocyte proliferation and differentiation.

Clinicopathological and prognostic significance of immunophenotypic characterization of endocervical adenocarcinoma using CLDN18, CDH17, and PAX8 in association with HPV status

Virchows Archiv : an international journal of pathology

2021 Sep 28

Asaka, S;Nakajima, T;Ida, K;Asaka, R;Kobayashi, C;Ito, M;Miyamoto, T;Uehara, T;Ota, H;
PMID: 34581850 | DOI: 10.1007/s00428-021-03207-1

In 2020, the WHO published a new system for classifying invasive endocervical adenocarcinoma based on histological features and high-risk human papillomavirus (HPV) infection. However, immunophenotypes of each histological subtype require further investigation. We immunohistochemically analyzed 66 invasive endocervical adenocarcinomas using three cell-lineage-specific markers: claudin 18 (CLDN18) for gastric, cadherin 17 (CDH17) for intestinal, and PAX8 for Müllerian epithelial cells. We identified five immunophenotypes of endocervical adenocarcinoma: gastric (21%); intestinal (14%); gastrointestinal (11%); Müllerian (35%); and not otherwise specified (NOS) (20%). Adenocarcinomas with gastric immunophenotype, characterized by aging (p = 0.0050), infrequent HPV infection (p < 0.0001), concurrent lobular endocervical glandular hyperplasia (p = 0.0060), lymphovascular invasion (p = 0.0073), advanced clinical stage (p = 0.0001), and the poorest progression-free (p < 0.0001) and overall (p = 0.0023) survivals, were morphologically compatible with gastric-type adenocarcinoma of the WHO 2020 classification. Conversely, most adenocarcinomas with Müllerian (91%) and intestinal (89%) immunophenotypes were HPV associated and morphologically compatible with usual- or intestinal-type adenocarcinomas of the WHO 2020 classification. The morphology of adenocarcinomas with gastrointestinal immunophenotype was intermediate or mixed between those of gastric and intestinal immunophenotypes; 57% were HPV associated. Adenocarcinomas with NOS immunophenotype were mainly HPV associated (85%) and histologically poorly differentiated. Multivariate analysis revealed that gastric (p = 0.008), intestinal + gastrointestinal (p = 0.0103), and NOS (p = 0.009) immunophenotypes were independent predictors of progression-free survival. Immunophenotypes characterized by CLDN18, CDH17, and PAX8 exhibited clinicopathological relevance and may improve the diagnostic accuracy and prognostic value of conventional histological classification.

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	Description
sense Example: Hs-LAG3-sense	Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron# Example: Mm-Htt-intron2	Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)	A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp Example: Hs-PDGFB-No-XMm	Does not cross detect with the species (Sp)
XSp Example: Rn-Pde9a-XMm	designed to cross detect with the species (Sp)
O# Example: Mm-Islr-O1	Alternative design targeting different regions of the same transcript or isoforms
CDS Example: Hs-SLC31A-CDS	Probe targets the protein-coding sequence only
EnEm	Probe targets exons n and m
En-Em	Probe targets region from exon n to exon m
Retired Nomenclature
tvn Example: Hs-LEPR-tv1	Designed to target transcript variant n
ORF Example: Hs-ACVRL1-ORF	Probe targets open reading frame
UTR Example: Hs-HTT-UTR-C3	Probe targets the untranslated region (non-protein-coding region) only
5UTR Example: Hs-GNRHR-5UTR	Probe targets the 5' untranslated region only
3UTR Example: Rn-Npy1r-3UTR	Probe targets the 3' untranslated region only
Pan Example: Pool	A mixture of multiple probe sets targeting multiple genes or transcripts

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